8S0D | pdb_00008s0d

H. sapiens MCM bound to double stranded DNA and ORC1-6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

MCM double hexamer loading visualized with human proteins.

Weissmann, F.Greiwe, J.F.Puhringer, T.Eastwood, E.L.Couves, E.C.Miller, T.C.R.Diffley, J.F.X.Costa, A.

(2024) Nature 636: 499-508

  • DOI: https://doi.org/10.1038/s41586-024-08263-6
  • Primary Citation of Related Structures:  
    8S09, 8S0A, 8S0B, 8S0C, 8S0D, 8S0E, 8S0F

  • PubMed Abstract: 

    Eukaryotic DNA replication begins with the loading of the MCM replicative DNA helicase as a head-to-head double hexamer at origins of DNA replication 1-3 . Our current understanding of how the double hexamer is assembled by the origin recognition complex (ORC), CDC6 and CDT1 comes mostly from budding yeast. Here we characterize human double hexamer (hDH) loading using biochemical reconstitution and cryo-electron microscopy with purified proteins. We show that the human double hexamer engages DNA differently from the yeast double hexamer (yDH), and generates approximately five base pairs of underwound DNA at the interface between hexamers, as seen in hDH isolated from cells 4 . We identify several differences from the yeast double hexamer in the order of factor recruitment and dependencies during hDH assembly. Unlike in yeast 5-8 , the ORC6 subunit of the ORC is not essential for initial MCM recruitment or hDH loading, but contributes to an alternative hDH assembly pathway that requires an intrinsically disordered region in ORC1, which may work through a MCM-ORC intermediate. Our work presents a detailed view of how double hexamers are assembled in an organism that uses sequence-independent replication origins, provides further evidence for diversity in eukaryotic double hexamer assembly mechanisms 9 , and represents a first step towards reconstitution of DNA replication initiation with purified human proteins.


  • Organizational Affiliation

    Chromosome Replication Laboratory, The Francis Crick Institute, London, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6A [auth F]251Homo sapiensMutation(s): 0 
Gene Names: ORC6ORC6L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N6 (Homo sapiens)
Explore Q9Y5N6 
Go to UniProtKB:  Q9Y5N6
PHAROS:  Q9Y5N6
GTEx:  ENSG00000091651 
Entity Groups  
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UniProt GroupQ9Y5N6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2B [auth 2]902Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens)
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PHAROS:  P49736
GTEx:  ENSG00000073111 
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UniProt GroupP49736
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3C [auth 3]810Homo sapiensMutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
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Find proteins for P25205 (Homo sapiens)
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PHAROS:  P25205
GTEx:  ENSG00000112118 
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UniProt GroupP25205
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4D [auth 4]863Homo sapiensMutation(s): 1 
Gene Names: MCM4CDC21
EC: 3.6.4.12
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Find proteins for P33991 (Homo sapiens)
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PHAROS:  P33991
GTEx:  ENSG00000104738 
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UniProt GroupP33991
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5E [auth 5]734Homo sapiensMutation(s): 0 
Gene Names: MCM5CDC46
EC: 3.6.4.12
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Find proteins for P33992 (Homo sapiens)
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PHAROS:  P33992
GTEx:  ENSG00000100297 
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UniProt GroupP33992
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6F [auth 6]821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14566 (Homo sapiens)
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PHAROS:  Q14566
GTEx:  ENSG00000076003 
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UniProt GroupQ14566
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7G [auth 7]719Homo sapiensMutation(s): 0 
Gene Names: MCM7CDC47MCM2
EC: 3.6.4.12
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Find proteins for P33993 (Homo sapiens)
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GTEx:  ENSG00000166508 
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UniProt GroupP33993
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1J [auth A]861Homo sapiensMutation(s): 0 
Gene Names: ORC1ORC1LPARC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13415 (Homo sapiens)
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PHAROS:  Q13415
GTEx:  ENSG00000085840 
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UniProt GroupQ13415
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2K [auth B]577Homo sapiensMutation(s): 0 
Gene Names: ORC2ORC2L
UniProt & NIH Common Fund Data Resources
Find proteins for Q13416 (Homo sapiens)
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PHAROS:  Q13416
GTEx:  ENSG00000115942 
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UniProt GroupQ13416
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Origin recognition complex subunit 3L [auth C]712Homo sapiensMutation(s): 0 
Gene Names: ORC3LATHEOORC3L
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Find proteins for Q9UBD5 (Homo sapiens)
Explore Q9UBD5 
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PHAROS:  Q9UBD5
GTEx:  ENSG00000135336 
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UniProt GroupQ9UBD5
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4M [auth D]436Homo sapiensMutation(s): 0 
Gene Names: ORC4ORC4L
UniProt & NIH Common Fund Data Resources
Find proteins for O43929 (Homo sapiens)
Explore O43929 
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PHAROS:  O43929
GTEx:  ENSG00000115947 
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UniProt GroupO43929
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5N [auth E]435Homo sapiensMutation(s): 0 
Gene Names: ORC5ORC5L
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Find proteins for O43913 (Homo sapiens)
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PHAROS:  O43913
GTEx:  ENSG00000164815 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
CA [auth 7],
FA [auth D],
HA [auth E],
O [auth 2],
Y [auth 6]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
R [auth 3],
U [auth 4],
V [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth 6],
EA [auth 7],
Q [auth 2],
T [auth 4],
X [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth 7]
DA [auth 7]
GA [auth D]
IA [auth E]
P [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.21_5207
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomCC2002, CC2009
European Research Council (ERC)European Union820102
Wellcome TrustUnited Kingdom219527/Z/19/Z
European Research Council (ERC)European Union101020432-MeChroRep

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-12-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-12-25
    Changes: Data collection, Database references