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Article ; Online: The MCM Helicase Motor of the Eukaryotic Replisome.

Abid Ali, Ferdos / Costa, Alessandro

2016 Volume 428, Issue 9 Pt B, Page(s) 1822–1832

Abstract: The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to ... ...

Abstract	The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate.
MeSH term(s)	Adenosine Triphosphate/metabolism ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Replication ; Eukaryota/enzymology ; Eukaryota/metabolism ; Hydrolysis ; Minichromosome Maintenance Proteins/metabolism ; Models, Biological ; Models, Molecular ; Protein Conformation
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; DNA Helicases (EC 3.6.4.-) ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2016-01-30
Publishing country	Netherlands
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.01.024
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Article: The MCM Helicase Motor of the Eukaryotic Replisome

Abid Ali, Ferdos / Costa, Alessandro

Journal of Molecular Biology. 2016 May 08, v. 428

2016

Abstract	The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate.
Keywords	DNA ; DNA replication ; adenosine triphosphate ; hydrolysis ; replication origin
Language	English
Dates of publication	2016-0508
Size	p. 1822-1832.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.01.024
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Article ; Online: The mechanism of eukaryotic CMG helicase activation.

Douglas, Max E / Ali, Ferdos Abid / Costa, Alessandro / Diffley, John F X

Nature

2018 Volume 555, Issue 7695, Page(s) 265–268

Abstract: The initiation of eukaryotic DNA replication occurs in two discrete stages: first, the minichromosome maintenance (MCM) complex assembles as a head-to-head double hexamer that encircles duplex replication origin DNA during G1 phase; then, 'firing factors' ...

Abstract	The initiation of eukaryotic DNA replication occurs in two discrete stages: first, the minichromosome maintenance (MCM) complex assembles as a head-to-head double hexamer that encircles duplex replication origin DNA during G1 phase; then, 'firing factors' convert each double hexamer into two active Cdc45-MCM-GINS helicases (CMG) during S phase. This second stage requires separation of the two origin DNA strands and remodelling of the double hexamer so that each MCM hexamer encircles a single DNA strand. Here we show that the MCM complex, which hydrolyses ATP during double-hexamer formation, remains stably bound to ADP in the double hexamer. Firing factors trigger ADP release, and subsequent ATP binding promotes stable CMG assembly. CMG assembly is accompanied by initial DNA untwisting and separation of the double hexamer into two discrete but inactive CMG helicases. Mcm10, together with ATP hydrolysis, then triggers further DNA untwisting and helicase activation. After activation, the two CMG helicases translocate in an 'N terminus-first' direction, and in doing so pass each other within the origin; this requires that each helicase is bound entirely to single-stranded DNA. Our experiments elucidate the mechanism of eukaryotic replicative helicase activation, which we propose provides a fail-safe mechanism for bidirectional replisome establishment.
MeSH term(s)	Adenosine Diphosphate/chemistry ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Cell Cycle Proteins/metabolism ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Replication ; DNA, Single-Stranded/biosynthesis ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; Enzyme Activation ; Enzyme Stability ; Minichromosome Maintenance Proteins/metabolism ; Nucleic Acid Conformation ; Replication Origin ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Cell Cycle Proteins ; DNA, Single-Stranded ; DNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Adenosine Diphosphate (61D2G4IYVH) ; Adenosine Triphosphate (8L70Q75FXE) ; DNA Helicases (EC 3.6.4.-) ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2018-02-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature25787
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Article ; Online: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome.

Eickhoff, Patrik / Kose, Hazal B / Martino, Fabrizio / Petojevic, Tatjana / Abid Ali, Ferdos / Locke, Julia / Tamberg, Nele / Nans, Andrea / Berger, James M / Botchan, Michael R / Yardimci, Hasan / Costa, Alessandro

Cell reports

2021 Volume 28, Issue 10, Page(s) 2673–2688.e8

Abstract: In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ... ...

Abstract	In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding.
MeSH term(s)	Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Cryoelectron Microscopy ; DNA/metabolism ; DNA/ultrastructure ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Helicases/ultrastructure ; DNA-Directed DNA Polymerase/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/enzymology ; Eukaryota/enzymology ; Hydrolysis ; Models, Molecular ; Multienzyme Complexes/metabolism ; Protein Domains ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Drosophila Proteins ; Multienzyme Complexes ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; DNA synthesome (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Adenosine Triphosphatases (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2021-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2019.07.104
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Article ; Online: Shulin packages axonemal outer dynein arms for ciliary targeting.

Mali, Girish R / Ali, Ferdos Abid / Lau, Clinton K / Begum, Farida / Boulanger, Jérôme / Howe, Jonathan D / Chen, Zhuo A / Rappsilber, Juri / Skehel, Mark / Carter, Andrew P

Science (New York, N.Y.)

2020 Volume 371, Issue 6532, Page(s) 910–916

Abstract: The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to cilia by an unknown mechanism. Here, we used the ... ...

Abstract	The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to cilia by an unknown mechanism. Here, we used the ciliate
MeSH term(s)	Axonemal Dyneins/chemistry ; Axonemal Dyneins/genetics ; Axonemal Dyneins/metabolism ; Cilia/metabolism ; Cryoelectron Microscopy ; Cytoplasm/metabolism ; Gene Knockdown Techniques ; Image Processing, Computer-Assisted ; Microtubules/physiology ; Models, Molecular ; Movement ; Protein Binding ; Protein Conformation ; Protein Domains ; Protozoan Proteins/chemistry ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Tetrahymena thermophila/genetics ; Tetrahymena thermophila/physiology
Chemical Substances	Protozoan Proteins ; Axonemal Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2020-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abe0526
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Article ; Online: Cryo-EM structure of a licensed DNA replication origin

Ferdos Abid Ali / Max E. Douglas / Julia Locke / Valerie E. Pye / Andrea Nans / John F. X. Diffley / Alessandro Costa

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 10

Abstract: Origins of replication are licensed by loading of MCM onto DNA, and origin firing depends on interaction with Cdc45 and GINS to form two CMG holo-helicases. Here, authors determine the cryo-EM structures of DNA-bound MCM and visualise a phospho-dependent ...

Abstract	Origins of replication are licensed by loading of MCM onto DNA, and origin firing depends on interaction with Cdc45 and GINS to form two CMG holo-helicases. Here, authors determine the cryo-EM structures of DNA-bound MCM and visualise a phospho-dependent MCM element important for Cdc45 recruitment.
Keywords	Science ; Q
Language	English
Publishing date	2017-12-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cryo-EM structure of a licensed DNA replication origin

Ferdos Abid Ali / Max E. Douglas / Julia Locke / Valerie E. Pye / Andrea Nans / John F. X. Diffley / Alessandro Costa

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 10

Abstract	Origins of replication are licensed by loading of MCM onto DNA, and origin firing depends on interaction with Cdc45 and GINS to form two CMG holo-helicases. Here, authors determine the cryo-EM structures of DNA-bound MCM and visualise a phospho-dependent MCM element important for Cdc45 recruitment.
Keywords	Science ; Q
Language	English
Publishing date	2017-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cryo-EM structure of a licensed DNA replication origin.

Abid Ali, Ferdos / Douglas, Max E / Locke, Julia / Pye, Valerie E / Nans, Andrea / Diffley, John F X / Costa, Alessandro

Nature communications

2017 Volume 8, Issue 1, Page(s) 2241

Abstract: Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM ...

Abstract	Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM engagement of Cdc45 and GINS to form the CMG holo-helicase. CMG assembly requires several steps including MCM phosphorylation by DDK. To understand origin activation, here we have determined the cryo-EM structures of DNA-bound MCM, either unmodified or phosphorylated, and visualize a phospho-dependent MCM element likely important for Cdc45 recruitment. MCM pore loops touch both the Watson and Crick strands, constraining duplex DNA in a bent configuration. By comparing our new MCM-DNA structure with the structure of CMG-DNA, we suggest how the conformational transition from the loaded, post-catalytic MCM to CMG might promote DNA untwisting and melting at the onset of replication.
MeSH term(s)	Cell Cycle Proteins/metabolism ; Cryoelectron Microscopy ; DNA/metabolism ; DNA/ultrastructure ; DNA Helicases ; DNA Replication ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/ultrastructure ; Holoenzymes ; Image Processing, Computer-Assisted ; Minichromosome Maintenance Proteins/metabolism ; Minichromosome Maintenance Proteins/ultrastructure ; Nuclear Proteins/metabolism ; Nuclear Proteins/ultrastructure ; Nucleic Acid Conformation ; Phosphorylation ; Protein Conformation ; Protein Serine-Threonine Kinases/metabolism ; Protein Structure, Quaternary ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/ultrastructure
Chemical Substances	CDC45 protein, S cerevisiae ; Cell Cycle Proteins ; DNA-Binding Proteins ; Holoenzymes ; Nuclear Proteins ; Saccharomyces cerevisiae Proteins ; DNA (9007-49-2) ; CDC7 protein, S cerevisiae (EC 2.7.1.-) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; DNA Helicases (EC 3.6.4.-) ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2017-12-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-017-02389-0
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Article ; Online: CMG-Pol epsilon dynamics suggests a mechanism for the establishment of leading-strand synthesis in the eukaryotic replisome.

Zhou, Jin Chuan / Janska, Agnieszka / Goswami, Panchali / Renault, Ludovic / Abid Ali, Ferdos / Kotecha, Abhay / Diffley, John F X / Costa, Alessandro

Proceedings of the National Academy of Sciences of the United States of America

2017 Volume 114, Issue 16, Page(s) 4141–4146

Abstract: The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting ...

Abstract	The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting to be elucidated, however the architecture and dynamics of the replication fork remain only partially understood, preventing a molecular understanding of chromosome replication. To address this issue, we conducted a systematic single-particle EM study on multiple permutations of the reconstituted CMG-Pol epsilon assembly. Pol epsilon contains two flexibly tethered lobes. The noncatalytic lobe is anchored to the motor of the helicase, whereas the polymerization domain extends toward the side of the helicase. We observe two alternate configurations of the DNA synthesis domain in the CMG-bound Pol epsilon. We propose that this conformational switch might control DNA template engagement and release, modulating replisome progression.
MeSH term(s)	DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Polymerase II/genetics ; DNA Polymerase II/metabolism ; DNA Replication ; Eukaryotic Cells/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; DNA Polymerase II (EC 2.7.7.7) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2017-04-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1700530114
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Article ; Online: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome

Patrik Eickhoff / Hazal B. Kose / Fabrizio Martino / Tatjana Petojevic / Ferdos Abid Ali / Julia Locke / Nele Tamberg / Andrea Nans / James M. Berger / Michael R. Botchan / Hasan Yardimci / Alessandro Costa

Cell Reports, Vol 28, Iss 10, Pp 2673-2688.e

2019 Volume 8

Abstract: Summary: In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not ... ...

Abstract	Summary: In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding. : Eickhoff et al. used cryo-EM to image DNA unwinding by the eukaryotic replicative helicase, Cdc45-MCM-GINS. As the hexameric MCM ring hydrolyses ATP, DNA is spooled asymmetrically around the ring pore. This asymmetry explains why selected ATPase sites are essential for DNA translocation. Understanding DNA unwinding informs on replication fork progression. Keywords: DNA replication, cryo-EM, AAA+ ATPase, helicase, molecular motor, DNA unwinding
Keywords	Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2019-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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