9E2Z | pdb_00009e2z

Cryo-EM structure of human CMG helicase stalled at G4-containing DNA template


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation.

Batra, S.Allwein, B.Kumar, C.Devbhandari, S.Bruning, J.G.Bahng, S.Lee, C.M.Marians, K.J.Hite, R.K.Remus, D.

(2025) Science 387: eadt1978-eadt1978

  • DOI: https://doi.org/10.1126/science.adt1978
  • Primary Citation of Related Structures:  
    9E2W, 9E2X, 9E2Y, 9E2Z

  • PubMed Abstract: 

    DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork collisions with preformed G4s in the parental DNA using reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by arresting the CMG helicase. Cryo-electron microscopy structures of stalled yeast and human CMG complexes reveal that the folded G4 is lodged inside the central CMG channel, arresting translocation. The G4 stabilizes the CMG at distinct translocation intermediates, suggesting an unprecedented helical inchworm mechanism for DNA translocation. These findings illuminate the eukaryotic replication fork mechanism under normal and perturbed conditions.


  • Organizational Affiliation
    • Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]904Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
EC: 3.6.4.12
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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]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]883Homo sapiensMutation(s): 0 
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5D [auth 5]734Homo sapiensMutation(s): 0 
Gene Names: MCM5CDC46
EC: 3.6.4.12
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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]821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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PHAROS:  Q14566
GTEx:  ENSG00000076003 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]719Homo sapiensMutation(s): 0 
Gene Names: MCM7CDC47MCM2
EC: 3.6.4.12
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GTEx:  ENSG00000166508 
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UniProt GroupP33993
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth A]196Homo sapiensMutation(s): 0 
Gene Names: GINS1KIAA0186PSF1
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GTEx:  ENSG00000101003 
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UniProt GroupQ14691
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth B]222Homo sapiensMutation(s): 0 
Gene Names: GINS2PSF2CGI-122DC5HSPC037
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Find proteins for Q9Y248 (Homo sapiens)
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GTEx:  ENSG00000131153 
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UniProt GroupQ9Y248
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth C]216Homo sapiensMutation(s): 0 
Gene Names: GINS3PSF3
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Find proteins for Q9BRX5 (Homo sapiens)
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PHAROS:  Q9BRX5
GTEx:  ENSG00000181938 
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UniProt GroupQ9BRX5
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth D]223Homo sapiensMutation(s): 0 
Gene Names: GINS4SLD5
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Find proteins for Q9BRT9 (Homo sapiens)
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PHAROS:  Q9BRT9
GTEx:  ENSG00000147536 
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UniProt GroupQ9BRT9
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45 homologK [auth E]566Homo sapiensMutation(s): 0 
Gene Names: CDC45CDC45LCDC45L2UNQ374/PRO710
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PHAROS:  O75419
GTEx:  ENSG00000093009 
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UniProt GroupO75419
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Entity ID: 12
MoleculeChains LengthOrganismImage
Leading strand DNA templateL [auth F]40synthetic construct
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Entity ID: 13
MoleculeChains LengthOrganismImage
Lagging strand DNA templateM [auth G]13synthetic construct
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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AA [auth 7],
P [auth 3],
R [auth 4],
U [auth 5],
X [auth 6]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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N [auth 2]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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CA [auth 7],
T [auth 4],
W [auth 5],
Z [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
DA [auth F],
EA [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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BA [auth 7]
O [auth 2]
Q [auth 3]
S [auth 4]
V [auth 5]
BA [auth 7],
O [auth 2],
Q [auth 3],
S [auth 4],
V [auth 5],
Y [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.0
MODEL REFINEMENTPHENIX1.21-5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM152094
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM126907
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release