7W1Y

Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The human pre-replication complex is an open complex.

Li, J.Dong, J.Wang, W.Yu, D.Fan, X.Hui, Y.C.Lee, C.S.K.Lam, W.H.Alary, N.Yang, Y.Zhang, Y.Zhao, Q.Chen, C.L.Tye, B.K.Dang, S.Zhai, Y.

(2023) Cell 186: 98-111.e21

  • DOI: https://doi.org/10.1016/j.cell.2022.12.008
  • Primary Citation of Related Structures:  
    7W1Y

  • PubMed Abstract: 

    In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this initial melting is unknown. Here, we report a 2.59-Å cryo-electron microscopy structure of the human MCM-DH (hMCM-DH), also known as the pre-replication complex. In this structure, the hMCM-DH with a constricted central channel untwists and stretches the DNA strands such that almost a half turn of the bound duplex DNA is distorted with 1 base pair completely separated, generating an initial open structure (IOS) at the hexamer junction. Disturbing the IOS inhibits DH formation and replication initiation. Mapping of hMCM-DH footprints indicates that IOSs are distributed across the genome in large clusters aligning well with initiation zones designed for stochastic origin firing. This work unravels an intrinsic mechanism that couples DH formation with initial DNA melting to license replication initiation in human cells.


  • Organizational Affiliation

    School of Biological Sciences, The University of Hong Kong, Hong Kong, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2],
G [auth A]
904Homo sapiensMutation(s): 0 
Gene Names: MCM2
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of DNA replication licensing factor MCM3B [auth 3],
H [auth B]
853Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4],
I [auth C]
863Homo sapiensMutation(s): 0 
Gene Names: MCM4
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5D [auth 5],
J [auth D]
734Homo sapiensMutation(s): 0 
Gene Names: MCM5
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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6],
K [auth E]
821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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PHAROS:  Q14566
GTEx:  ENSG00000076003 
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UniProt GroupQ14566
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7],
L [auth F]
719Homo sapiensMutation(s): 0 
Gene Names: MCM7CDC47MCM2
EC: 3.6.4.12
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GTEx:  ENSG00000166508 
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (49-MER)M [auth O]49Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (49-MER)N [auth S]49Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
EA [auth 7]
HA [auth A]
JA [auth B]
MA [auth C]
Q [auth 2]
EA [auth 7],
HA [auth A],
JA [auth B],
MA [auth C],
Q [auth 2],
S [auth 3],
V [auth 4],
VA [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth 6],
PA [auth D],
SA [auth E],
Y [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth 7]
FA [auth A]
KA [auth C]
NA [auth D]
O [auth 2]
CA [auth 7],
FA [auth A],
KA [auth C],
NA [auth D],
O [auth 2],
QA [auth E],
T [auth 4],
TA [auth F],
W [auth 5],
Z [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 6]
DA [auth 7]
GA [auth A]
IA [auth B]
LA [auth C]
AA [auth 6],
DA [auth 7],
GA [auth A],
IA [auth B],
LA [auth C],
OA [auth D],
P [auth 2],
R [auth 3],
RA [auth E],
U [auth 4],
UA [auth F],
X [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv3.0.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release