9PGD: Actin-related protein 6

ARP6-ZNHIT1 module from fully-engaged state of SRCAP-nucleosome complex, with H3-bound ARP6 (focused refinement, filtered by local resolution). Determined by electron microscopy at 3.2 Å resolution. Released 22 Jul 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 3
Atoms: 4,251
Mol. weight: 79.41 kDa
Ligands: ZN, MG, AGS
Released: 22 Jul 2026

Explore 9PGD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PGD contains 29 α-helices and 27 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	12-17	6	1
β-strand	23-26	4	1
β-strand	29-31	3	2
β-strand	40-41	2	2
α-helix	42-46	5
β-strand	55-57	3	2
β-strand	60-61	2	3
β-strand	64-65	2	3
α-helix	68-79	12
α-helix	88-90	3
β-strand	91-97	7	1
α-helix	103-111	9
α-helix	112-116	5
β-strand	121-126	6	1
α-helix	127-138	12
β-strand	144-150	7	4
β-strand	155-161	7	4
β-strand	165	1	4
β-strand	171-173	3	4
α-helix	177-191	15
β-strand	193	1	5
α-helix	199-209	11
α-helix	216-224	9
β-strand	234-237	4	6
β-strand	248-249	2	6
α-helix	250-251	2
α-helix	252-254	3
β-strand	267-270	4	6
α-helix	273-276	4
α-helix	279-282	4
α-helix	284-286	3
α-helix	294-304	11
α-helix	310-314	5
β-strand	317-320	4	4
α-helix	322-325	4
α-helix	329-340	12
β-strand	349-350	2	4
α-helix	358-368	11
α-helix	372-375	4
β-strand	377-378	2	1
α-helix	379-381	3
α-helix	382-386	5
α-helix	387-393	7

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	21-34	14
α-helix	84-91	8
β-strand	105	1	4
α-helix	112-115	4
β-strand	116	1	7
β-strand	123	1	7
β-strand	126-127	2	8
β-strand	134-135	2	8
α-helix	138-147	10

Chain U: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-42	2
β-strand	43	1	5
α-helix	45-53	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 6	C	protein	396	Homo sapiens	Q9GZN1 (AlphaFold model)
Zinc finger HIT domain-containing protein 1	D	protein	154	Homo sapiens	O43257 (AlphaFold model)
Histone H3.2	U	protein	135	Xenopus laevis	P84233 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9PGD_1 Actin-related protein 6 (chains C)
MTTLVLDNGAYNAKIGYSHENVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF
QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ
AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL
TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEENTVMIDYVLPD
FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY
SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYAW
EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI

Sequence of entity 2 (D), FASTA

>9PGD_2 Zinc finger HIT domain-containing protein 1 (chains D)
MVEKKTSVRSQDPGQRRVLDRAARQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDD
DADTGKKKKKTRGDHFKLRFRKNFQALLEEQNLSVAEGPNYLTACAGPPSRPQRPFCAVC
GFPSPYTCVSCGARYCTVRCLGTHQETRCLKWTV

Sequence of entity 3 (U), FASTA

>9PGD_3 Histone H3.2 (chains U)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	1
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	1

Primary citation

Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme. Park, G., Wu, C., Louder, R.K. Sci Adv (2026) 12:eaei7728-eaei7728. DOI 10.1126/sciadv.aei7728 · PubMed

Other PDB entries of the same protein (UniProt Q9GZN1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8X15 3.2 Å, Structure of nucleosome-bound SRCAP-C in the apo state
8X19 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
8X1C 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-bound state
9NFX 3.3 Å, Human SRCAP-CFDP1-hexasome complex in the evicted state of the H2A.Z histone exchange…
9CA7 3.35 Å, Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state…
9NFY 3.4 Å, Human SRCAP-CFDP1-prenucleosome complex in the pre-inserted state of the H2A.Z histone…
9CA9 3.56 Å, Cryo-EM structure of the human SRCAP complex in the unbound state (composite structure)
9NFV 3.8 Å, Human SRCAP-CFDP1-nucleosome complex in the poised state of the H2A.Z histone exchange…
9NFW 3.8 Å, Human SRCAP-CFDP1-nucleosome complex in the activated state of the H2A.Z histone…
9NFZ 3.8 Å, Human SRCAP-nucleosome complex in the fully inserted state of the H2A.Z histone exchange…
9NG0 3.9 Å, Human SRCAP-nucleosome complex in the pre-dissociation state of the H2A.Z histone…
9CA8 3.92 Å, Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state…

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