9NFY | pdb_00009nfy

Human SRCAP-CFDP1-prenucleosome complex in the pre-inserted state of the H2A.Z histone exchange reaction (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9NFY/pdb
EM Map EMD-49377: EMDB EMDataResource

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

Deposited: 2025-02-21 Released: 2026-08-12
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: 3.40 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 mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme.

Park, G., Wu, C., Louder, R.K.

(2026) Sci Adv 12: eaei7728-eaei7728

PubMed: 42536744 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aei7728
Primary Citation Related Structures:
9CA7, 9CA8, 9CA9, 9CAA, 9NFV, 9NFW, 9NFX, 9NFY, 9NFZ, 9NG0, 9PGC, 9PGD, 9Y3D, 9Y3E, 9Y3F, 9Y3G, 9Y3H, 9ZLA

PubMed Abstract:
The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that histone exchange by SRCAP requires the transient activator CFDP1 and resolve nine cryo-electron microscopy structures of the SRCAP-CFDP1 holoenzyme that define the stepwise exchange mechanism. CFDP1 recognizes the conformation of the fully engaged SRCAP-nucleosome complex through interactions with multiple subunits-including direct contact with the ATPase domain-and induces conformational transitions that drive extensive DNA unwrapping, eviction of the H2A-H2B dimer, and insertion of the H2A.Z-H2B dimer, all without necessarily requiring hydrolysis of bound ATP. Collectively, these findings provide unprecedented insight into the mechanism of activator- and nucleotide-driven histone exchange from nucleosomal H2A to H2A.Z.

Organizational Affiliation

Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Macromolecule Content

Total Structure Weight: 1,074.25 kDa
Atom Count: 42,380
Modeled Residue Count: 4,995
Deposited Residue Count: 8,749
Unique protein chains: 13
Unique nucleic acid chains: 2

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
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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y230
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Craniofacial development protein 1	K [auth P]	299	Homo sapiens	Mutation(s): 0 Gene Names: CFDP1, BCNT, CENP-29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UEE9 (Homo sapiens) Explore Q9UEE9 Go to UniProtKB: Q9UEE9
PHAROS: Q9UEE9 GTEx: ENSG00000153774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UEE9
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	L [auth Q]	127	Homo sapiens	Mutation(s): 0 Gene Names: H2AZ1, H2AFZ, H2AZ
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5 Go to UniProtKB: P0C0S5
PHAROS: P0C0S5 GTEx: ENSG00000164032
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UniProt Group	P0C0S5
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	M [auth R]	125	Homo sapiens	Mutation(s): 0 Gene Names: H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8... H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens) Explore P62807 Go to UniProtKB: P62807
PHAROS: P62807 GTEx: ENSG00000180596 ENSG00000277224 ENSG00000278588 ENSG00000273802 ENSG00000274290
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62807
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	N [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
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	O [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
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	P [auth U], R [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
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	Q [auth V], S [auth X]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
DNA(285-MER)	T [auth Y]	285	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA(285-MER)	U [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 V [auth A] SDF format, chain X [auth C] MOL2 format, chain V [auth A] MOL2 format, chain X [auth C] mmCIF format, chain V [auth A] mmCIF format, chain X [auth C]	V [auth A], X [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain V [auth A] Focus chain X [auth C] Interactions & Density Focus chain V [auth A] Focus chain X [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth J] SDF format, chain CA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain CA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain CA [auth F]	BA [auth E] CA [auth F] EA [auth G] FA [auth H] HA [auth I] BA [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 BA [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 BA [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 AA [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain Z [auth D]	AA [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain W [auth A] SDF format, chain Y [auth C] SDF format, chain JA [auth J] SDF format, chain DA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain JA [auth J] MOL2 format, chain DA [auth F] mmCIF format, chain GA [auth H] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain JA [auth J] mmCIF format, chain DA [auth F]	DA [auth F], GA [auth H], JA [auth J], W [auth A], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain GA [auth H] Focus chain JA [auth J] Focus chain W [auth A] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth F] Focus chain GA [auth H] Focus chain JA [auth J] Focus chain W [auth A] Focus chain Y [auth C]