11RL | pdb_000011rl

CryoEM structure of the human origin recognition complex with DNA and CDC6 protein

PDB DOI: https://doi.org/10.2210/pdb11RL/pdb
EM Map EMD-75978: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Homo sapiens, DNA molecule
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-03-10 Released: 2026-09-30
Deposition Author(s): Chouhan, O.P., Joshua Tor, L.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Evolution of Origin Sequence and Recognition for Licensing of Eukaryotic DNA Replication

Bauer, J., Zali, N., Chouhan, O.P., El Demerdash, O., Loell, K., Kinney, J., Joshua-Tor, L., Stillman, B.

To be published.

Macromolecule Content

Total Structure Weight: 448.83 kDa
Atom Count: 21,274
Modeled Residue Count: 2,543
Deposited Residue Count: 3,703
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 2	A [auth B]	577	Homo sapiens	Mutation(s): 0 Gene Names: ORC2, ORC2L
UniProt & NIH Common Fund Data Resources
Find proteins for Q13416 (Homo sapiens) Explore Q13416 Go to UniProtKB: Q13416
PHAROS: Q13416 GTEx: ENSG00000115942
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13416
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 4	B [auth D]	436	Homo sapiens	Mutation(s): 0 Gene Names: ORC4, ORC4L
UniProt & NIH Common Fund Data Resources
Find proteins for O43929 (Homo sapiens) Explore O43929 Go to UniProtKB: O43929
PHAROS: O43929 GTEx: ENSG00000115947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43929
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 1	E [auth A]	862	Homo sapiens	Mutation(s): 0 Gene Names: ORC1, ORC1L, PARC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13415 (Homo sapiens) Explore Q13415 Go to UniProtKB: Q13415
PHAROS: Q13415 GTEx: ENSG00000085840
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13415
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 3	F [auth C]	712	Homo sapiens	Mutation(s): 0 Gene Names: ORC3, LATHEO, ORC3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBD5 (Homo sapiens) Explore Q9UBD5 Go to UniProtKB: Q9UBD5
PHAROS: Q9UBD5 GTEx: ENSG00000135336
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBD5
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 5	G [auth E]	435	Homo sapiens	Mutation(s): 0 Gene Names: ORC5, ORC5L
UniProt & NIH Common Fund Data Resources
Find proteins for O43913 (Homo sapiens) Explore O43913 Go to UniProtKB: O43913
PHAROS: O43913 GTEx: ENSG00000164815
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43913
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 6 homolog	H [auth G]	561	Homo sapiens	Mutation(s): 0 Gene Names: CDC6, CDC18L
UniProt & NIH Common Fund Data Resources
Find proteins for Q99741 (Homo sapiens) Explore Q99741 Go to UniProtKB: Q99741
PHAROS: Q99741 GTEx: ENSG00000094804
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99741
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (29-MER)	C [auth H]	60	DNA molecule
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (29-MER)	D [auth I]	60	DNA molecule
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain M [auth E] SDF format, chain K [auth A] SDF format, chain I [auth D] MOL2 format, chain O [auth G] MOL2 format, chain M [auth E] MOL2 format, chain K [auth A] MOL2 format, chain I [auth D] mmCIF format, chain O [auth G] mmCIF format, chain M [auth E] mmCIF format, chain K [auth A] mmCIF format, chain I [auth D]	I [auth D], K [auth A], M [auth E], O [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth D] Focus chain K [auth A] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth D] Focus chain K [auth A] Focus chain M [auth E] Focus chain O [auth G]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain N [auth E] SDF format, chain L [auth A] SDF format, chain J [auth D] MOL2 format, chain P [auth G] MOL2 format, chain N [auth E] MOL2 format, chain L [auth A] MOL2 format, chain J [auth D] mmCIF format, chain P [auth G] mmCIF format, chain N [auth E] mmCIF format, chain L [auth A] mmCIF format, chain J [auth D]	J [auth D], L [auth A], N [auth E], P [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain L [auth A] Focus chain N [auth E] Focus chain P [auth G] Interactions & Density Focus chain J [auth D] Focus chain L [auth A] Focus chain N [auth E] Focus chain P [auth G]