9CA8 | pdb_00009ca8

Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9CA8/pdb
NAKB: 9CA8
EM Map EMD-45382: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Xenopus laevis, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.92 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: 1,041.11 kDa
Atom Count: 42,947
Modeled Residue Count: 4,979
Deposited Residue Count: 8,451
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZRS2
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15906
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZN1
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43257
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y265
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Reference Sequence

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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
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UniProt Group	Q9Y230
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	K [auth Q], M [auth S]	128	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	L [auth R], N [auth T]	125	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
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UniProt Group	P02281
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	O [auth U], Q [auth W]	135	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
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UniProt Group	P84233
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	P [auth V], R [auth X]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
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UniProt Group	P62799
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Length	Organism	Image
DNA (285-MER)	S [auth Y]	285	synthetic construct
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Length	Organism	Image
DNA (285-MER)	T [auth Z]	285	synthetic construct
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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 U [auth A] SDF format, chain W [auth C] MOL2 format, chain U [auth A] MOL2 format, chain W [auth C] mmCIF format, chain U [auth A] mmCIF format, chain W [auth C]	U [auth A], W [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain U [auth A] Focus chain W [auth C] Interactions & Density Focus chain U [auth A] Focus chain W [auth C]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth J] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth J]	AA [auth E] CA [auth F] EA [auth G] FA [auth H] HA [auth I] AA [auth E], CA [auth F], EA [auth G], FA [auth H], HA [auth I], IA [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth J]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain Y [auth D] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain GA [auth H] SDF format, chain V [auth A] SDF format, chain X [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain V [auth A] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth H] mmCIF format, chain V [auth A] mmCIF format, chain X [auth C]	BA [auth E], DA [auth F], GA [auth H], V [auth A], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain DA [auth F] Focus chain GA [auth H] Focus chain V [auth A] Focus chain X [auth C] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth F] Focus chain GA [auth H] Focus chain V [auth A] Focus chain X [auth C]