9O34 | pdb_00009o34

Replisome (map E)

PDB DOI: https://doi.org/10.2210/pdb9O34/pdb
EM Map EMD-70068: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Homo sapiens, Homo sapiens environmental sample, synthetic construct
Expression System: Trichoplusia ni, Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-04-04 Released: 2026-10-14
Deposition Author(s): Steinruecke, F., Markert, J., Farnung, L.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of human replisome progression into a nucleosome

Steinruecke, F., Markert, J., Farnung, L.

To be published.

Macromolecule Content

Total Structure Weight: 1,537.25 kDa
Atom Count: 58,632
Modeled Residue Count: 7,233
Deposited Residue Count: 12,914
Unique protein chains: 15
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	A [auth 2]	904	Homo sapiens	Mutation(s): 0 Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens) Explore P49736 Go to UniProtKB: P49736
PHAROS: P49736 GTEx: ENSG00000073111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49736
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM3	B [auth 3]	808	Homo sapiens	Mutation(s): 0 Gene Names: MCM3 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P25205 (Homo sapiens) Explore P25205 Go to UniProtKB: P25205
PHAROS: P25205 GTEx: ENSG00000112118
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25205
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	C [auth 4]	863	Homo sapiens environmental sample	Mutation(s): 0 Gene Names: MCM4, CDC21 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33991 (Homo sapiens) Explore P33991 Go to UniProtKB: P33991
PHAROS: P33991 GTEx: ENSG00000104738
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33991
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM5	D [auth 5]	734	Homo sapiens	Mutation(s): 0 Gene Names: MCM5, CDC46 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33992 (Homo sapiens) Explore P33992 Go to UniProtKB: P33992
PHAROS: P33992 GTEx: ENSG00000100297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33992
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	E [auth 6]	821	Homo sapiens	Mutation(s): 0 Gene Names: MCM6 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14566 (Homo sapiens) Explore Q14566 Go to UniProtKB: Q14566
PHAROS: Q14566 GTEx: ENSG00000076003
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14566
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	F [auth 7]	719	Homo sapiens	Mutation(s): 0 Gene Names: MCM7, CDC47, MCM2 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33993 (Homo sapiens) Explore P33993 Go to UniProtKB: P33993
PHAROS: P33993 GTEx: ENSG00000166508
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33993
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 45 homolog	G [auth C]	569	Homo sapiens	Mutation(s): 0 Gene Names: CDC45, CDC45L, CDC45L2, UNQ374/PRO710
UniProt & NIH Common Fund Data Resources
Find proteins for O75419 (Homo sapiens) Explore O75419 Go to UniProtKB: O75419
PHAROS: O75419 GTEx: ENSG00000093009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75419
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication complex GINS protein PSF1	H [auth D]	196	Homo sapiens	Mutation(s): 0 Gene Names: GINS1, KIAA0186, PSF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14691 (Homo sapiens) Explore Q14691 Go to UniProtKB: Q14691
PHAROS: Q14691 GTEx: ENSG00000101003
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14691
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication complex GINS protein PSF2	I [auth E]	185	Homo sapiens	Mutation(s): 0 Gene Names: GINS2, PSF2, CGI-122, DC5, HSPC037
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y248 (Homo sapiens) Explore Q9Y248 Go to UniProtKB: Q9Y248
PHAROS: Q9Y248 GTEx: ENSG00000131153
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y248
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication complex GINS protein PSF3	J [auth F]	216	Homo sapiens	Mutation(s): 0 Gene Names: GINS3, PSF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRX5 (Homo sapiens) Explore Q9BRX5 Go to UniProtKB: Q9BRX5
PHAROS: Q9BRX5 GTEx: ENSG00000181938
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BRX5
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication complex GINS protein SLD5	K [auth G]	264	Homo sapiens	Mutation(s): 0 Gene Names: GINS4, SLD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRT9 (Homo sapiens) Explore Q9BRT9 Go to UniProtKB: Q9BRT9
PHAROS: Q9BRT9 GTEx: ENSG00000147536
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BRT9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat and HMG-box DNA-binding protein 1	L [auth H], M [auth I], N [auth J]	1,132	Homo sapiens	Mutation(s): 0 Gene Names: WDHD1, AND1
UniProt & NIH Common Fund Data Resources
Find proteins for O75717 (Homo sapiens) Explore O75717 Go to UniProtKB: O75717
PHAROS: O75717 GTEx: ENSG00000198554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75717
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein timeless homolog	O [auth K]	1,211	Homo sapiens	Mutation(s): 0 Gene Names: TIMELESS, TIM, TIM1, TIMELESS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNS1 (Homo sapiens) Explore Q9UNS1 Go to UniProtKB: Q9UNS1
PHAROS: Q9UNS1 GTEx: ENSG00000111602
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UNS1
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
TIMELESS-interacting protein	P [auth L]	301	Homo sapiens	Mutation(s): 0 Gene Names: TIPIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVW5 (Homo sapiens) Explore Q9BVW5 Go to UniProtKB: Q9BVW5
PHAROS: Q9BVW5 GTEx: ENSG00000075131
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BVW5
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Claspin	S [auth Q]	1,345	Homo sapiens	Mutation(s): 0 Gene Names: CLSPN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAW4 (Homo sapiens) Explore Q9HAW4 Go to UniProtKB: Q9HAW4
PHAROS: Q9HAW4 GTEx: ENSG00000092853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HAW4
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
Leading Strand DNA	Q [auth M]	200	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
Lagging strand DNA	R [auth N]	182	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain Y [auth 5] SDF format, chain V [auth 3] SDF format, chain U [auth 2] SDF format, chain DA [auth 6] MOL2 format, chain Y [auth 5] MOL2 format, chain V [auth 3] MOL2 format, chain U [auth 2] MOL2 format, chain DA [auth 6] mmCIF format, chain Y [auth 5] mmCIF format, chain V [auth 3] mmCIF format, chain U [auth 2] mmCIF format, chain DA [auth 6]	DA [auth 6], U [auth 2], V [auth 3], Y [auth 5]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain DA [auth 6] Focus chain U [auth 2] Focus chain V [auth 3] Focus chain Y [auth 5] Interactions & Density Focus chain DA [auth 6] Focus chain U [auth 2] Focus chain V [auth 3] Focus chain Y [auth 5]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain EA [auth 7] SDF format, chain Z [auth 5] SDF format, chain X [auth 4] SDF format, chain BA [auth 6] MOL2 format, chain EA [auth 7] MOL2 format, chain Z [auth 5] MOL2 format, chain X [auth 4] MOL2 format, chain BA [auth 6] mmCIF format, chain EA [auth 7] mmCIF format, chain Z [auth 5] mmCIF format, chain X [auth 4] mmCIF format, chain BA [auth 6]	BA [auth 6], EA [auth 7], X [auth 4], Z [auth 5]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth 6] Focus chain EA [auth 7] Focus chain X [auth 4] Focus chain Z [auth 5] Interactions & Density Focus chain BA [auth 6] Focus chain EA [auth 7] Focus chain X [auth 4] Focus chain Z [auth 5]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth 2] SDF format, chain W [auth 3] SDF format, chain CA [auth 6] SDF format, chain AA [auth 5] MOL2 format, chain T [auth 2] MOL2 format, chain W [auth 3] MOL2 format, chain CA [auth 6] MOL2 format, chain AA [auth 5] mmCIF format, chain T [auth 2] mmCIF format, chain W [auth 3] mmCIF format, chain CA [auth 6] mmCIF format, chain AA [auth 5]	AA [auth 5], CA [auth 6], T [auth 2], W [auth 3]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth 5] Focus chain CA [auth 6] Focus chain T [auth 2] Focus chain W [auth 3] Interactions & Density Focus chain AA [auth 5] Focus chain CA [auth 6] Focus chain T [auth 2] Focus chain W [auth 3]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Steinruecke, F.

Markert, J.

Farnung, L.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE 2140743
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	DP2-ES036404

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release

9O34 | pdb_00009o34

Replisome (map E)

Literature

Structural basis of human replisome progression into a nucleosome

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

Sequence Annotations

Entity ID: 16

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)