9CAA | pdb_00009caa

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

PDB DOI: https://doi.org/10.2210/pdb9CAA/pdb
EM Map EMD-45384: EMDB EMDataResource
NAKB: 9CAA

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.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.04 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: 1,040.56 kDa
Atom Count: 40,983
Modeled Residue Count: 4,692
Deposited Residue Count: 8,451
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 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

Find similar proteins by:

| 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

Find similar proteins by:

| 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

Find similar proteins by:

| 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

Find similar proteins by:

| 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

Find similar proteins by:

| 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

Find similar proteins by:

| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

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

Find similar nucleic acids by:

(by identity cutoff)

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