9CA9 | pdb_00009ca9

Cryo-EM structure of the human SRCAP complex in the unbound state (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9CA9/pdb
EM Map EMD-45383: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-06-17 Released: 2025-06-18
Deposition Author(s): Louder, R.K., Park, G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.56 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

Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60

Park, G., Patel, A.B., Wu, C., Louder, R.K.

To be published.

Macromolecule Content

Total Structure Weight: 755.87 kDa
Atom Count: 28,589
Modeled Residue Count: 3,618
Deposited Residue Count: 6,901
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase SRCAP	A	3,230	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZRS2 (Homo sapiens) Explore Q6ZRS2 Go to UniProtKB: Q6ZRS2
PHAROS: Q6ZRS2 GTEx: ENSG00000080603
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZRS2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 72 homolog	B	364	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens) Explore Q15906 Go to UniProtKB: Q15906
PHAROS: Q15906 GTEx: ENSG00000163159
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15906
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 6	C	396	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZN1 (Homo sapiens) Explore Q9GZN1 Go to UniProtKB: Q9GZN1
PHAROS: Q9GZN1 GTEx: ENSG00000075089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GZN1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger HIT domain-containing protein 1	D	154	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43257 (Homo sapiens) Explore O43257 Go to UniProtKB: O43257
PHAROS: O43257 GTEx: ENSG00000106400
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43257
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	E, G, I	456	Homo sapiens	Mutation(s): 0 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens) Explore Q9Y265 Go to UniProtKB: Q9Y265
PHAROS: Q9Y265 GTEx: ENSG00000175792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y265
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2	F, H, J	463	Homo sapiens	Mutation(s): 0 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens) Explore Q9Y230 Go to UniProtKB: Q9Y230
PHAROS: Q9Y230 GTEx: ENSG00000183207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y230
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain P [auth F]	O [auth E] P [auth F] R [auth G] S [auth H] U [auth I] O [auth E], P [auth F], R [auth G], S [auth H], U [auth I], V [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain V [auth J] Interactions & Density Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain V [auth J]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain Q [auth F] SDF format, chain T [auth H] SDF format, chain W [auth J] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth F] MOL2 format, chain T [auth H] MOL2 format, chain W [auth J] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth F] mmCIF format, chain T [auth H] mmCIF format, chain W [auth J]	L [auth C], Q [auth F], T [auth H], W [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain Q [auth F] Focus chain T [auth H] Focus chain W [auth J] Interactions & Density Focus chain L [auth C] Focus chain Q [auth F] Focus chain T [auth H] Focus chain W [auth J]