9RL4 | pdb_00009rl4

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6

PDB DOI: https://doi.org/10.2210/pdb9RL4/pdb
EM Map EMD-54030: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Aequorea victoria, synthetic construct
Expression System: Escherichia coli, Homo sapiens, Trichoplusia ni
Mutation(s): No

Deposited: 2025-06-16 Released: 2026-02-11
Deposition Author(s): Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H.
Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, European Molecular Biology Organization (EMBO), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6

Lastname, F.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,317.5 kDa
Atom Count: 38,125
Modeled Residue Count: 4,626
Deposited Residue Count: 11,126
Unique protein chains: 15
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	139	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD... HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04908
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	128	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2BJ, H2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899 Go to UniProtKB: P06899
PHAROS: P06899 GTEx: ENSG00000124635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06899
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription activator BRG1	I	1,647	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens) Explore P51532 Go to UniProtKB: P51532
PHAROS: P51532 GTEx: ENSG00000127616
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51532
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein 6A	J	429	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens) Explore O96019 Go to UniProtKB: O96019
PHAROS: O96019 GTEx: ENSG00000136518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96019
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, cytoplasmic 1, N-terminally processed	K	375	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens) Explore P60709 Go to UniProtKB: P60709
PHAROS: P60709 GTEx: ENSG00000075624
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
AT-rich interactive domain-containing protein 1A	L	2,285	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14497 (Homo sapiens) Explore O14497 Go to UniProtKB: O14497
PHAROS: O14497 GTEx: ENSG00000117713
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14497
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	M	385	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q12824 (Homo sapiens) Explore Q12824 Go to UniProtKB: Q12824
PHAROS: Q12824 GTEx: ENSG00000099956
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12824
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF complex subunit SMARCC2	N, O	1,214	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAQ2 (Homo sapiens) Explore Q8TAQ2 Go to UniProtKB: Q8TAQ2
PHAROS: Q8TAQ2 GTEx: ENSG00000139613
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TAQ2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1	P	515	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GM5 (Homo sapiens) Explore Q96GM5 Go to UniProtKB: Q96GM5
PHAROS: Q96GM5 GTEx: ENSG00000066117
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96GM5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1	Q	411	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q969G3 (Homo sapiens) Explore Q969G3 Go to UniProtKB: Q969G3
PHAROS: Q969G3 GTEx: ENSG00000073584
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q969G3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein ubi-d4	R	435	Homo sapiens	Mutation(s): 0 Gene Names: DPF2, BAF45D, REQ, UBID4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92785 (Homo sapiens) Explore Q92785 Go to UniProtKB: Q92785
PHAROS: Q92785 GTEx: ENSG00000133884
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92785
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,POU domain, class 5, transcription factor 1	S [auth V]	645	Aequorea victoria, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: GFP, POU5F1, OCT3, OCT4, OTF3
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for Q01860 (Homo sapiens) Explore Q01860 Go to UniProtKB: Q01860
PHAROS: Q01860 GTEx: ENSG00000204531
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212Q01860
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-2	T [auth W]	105	Homo sapiens	Mutation(s): 0 Gene Names: SOX2
UniProt & NIH Common Fund Data Resources
Find proteins for P48431 (Homo sapiens) Explore P48431 Go to UniProtKB: P48431
PHAROS: P48431 GTEx: ENSG00000181449
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48431
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 16
Molecule	Chains	Length	Organism	Image
DNA (148-MER)	U [auth X]	227	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 17
Molecule	Chains	Length	Organism	Image
DNA (148-MER)	V [auth Y]	227	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTD Query on PTD Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth I] SDF format, chain GA [auth L] SDF format, chain HA [auth M] SDF format, chain IA [auth N] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain LA [auth O] SDF format, chain MA [auth P] SDF format, chain W [auth A] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth N] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain LA [auth O] MOL2 format, chain MA [auth P] MOL2 format, chain W [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth L] mmCIF format, chain HA [auth M] mmCIF format, chain IA [auth N] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain LA [auth O] mmCIF format, chain MA [auth P] mmCIF format, chain W [auth A] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth E] CA [auth G] DA [auth H] EA [auth I] AA [auth E], BA [auth E], CA [auth G], DA [auth H], EA [auth I], GA [auth L], HA [auth M], IA [auth N], JA [auth N], KA [auth N], LA [auth O], MA [auth P], W [auth A], X [auth C], Y [auth D], Z [auth E]	PENTANEDIAL C₅ H₈ O₂ SXRSQZLOMIGNAQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain FA [auth L] MOL2 format, chain FA [auth L] mmCIF format, chain FA [auth L]	FA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain FA [auth L] Interactions & Density Focus chain FA [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--
Swiss National Science Foundation	Switzerland	--
European Molecular Biology Organization (EMBO)	European Union	--
Other private		--
Other private		--

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9RL4 | pdb_00009rl4

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 16

Sequence Annotations

Entity ID: 17

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9RL4 | pdb_00009rl4