9V5M: RBBP4-H3 complex

The crystal structure of RBBP4-H3 complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 3 Jun 2026.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,520
Mol. weight: 49.45 kDa
Ligands: BTN
Released: 3 Jun 2026

Explore 9V5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V5M contains 13 α-helices and 30 β-strands across 2 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 A: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	12-31	20
β-strand	32-39	8	1
β-strand	48-49	2	2
β-strand	54	1	2
β-strand	61-69	9	2
β-strand	77-87	11	2
α-helix	100-102	3
α-helix	104-106	3
β-strand	114-123	10	2
β-strand	129-133	5	3
β-strand	136-143	8	3
β-strand	149-153	5	3
α-helix	154-156	3
α-helix	161-162	2
β-strand	171-174	4	3
β-strand	183-185	3	4
β-strand	192-196	5	4
β-strand	202-206	5	4
α-helix	207-209	3
β-strand	216-218	3	3
β-strand	221-223	3	4
β-strand	230-235	6	5
β-strand	242-247	6	5
β-strand	251-256	6	5
β-strand	267-270	4	5
β-strand	276-281	6	6
β-strand	288-293	6	6
β-strand	297-302	6	6
α-helix	303-305	3
β-strand	311-314	4	6
β-strand	320-325	6	7
β-strand	332-337	6	7
β-strand	342-346	5	7
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	7
β-strand	377-382	6	1
β-strand	389-394	6	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-7	4
α-helix	9-10	2
α-helix	11-13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Histone H3.3C	D	protein	14	Homo sapiens	Q6NXT2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9V5M_1 Histone-binding protein RBBP4 (chains A)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDADQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 2 (D), FASTA

>9V5M_2 Histone H3.3C (chains D)
ARTKQTARKSTGGK

Ligands and cofactors

ID	Name	Formula	Copies
BTN	Biotin	C10 H16 N2 O3 S	1

Primary citation

The crystal structure of RBBP4-H3 complex. Zhang, M., Wang, X.X., He, X.Y. et al. To be published.

Other PDB entries of the same protein (UniProt Q09028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4R7A 1.85 Å, Crystal Structure of RBBP4 bound to PHF6 peptide
7M40 1.88 Å, Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)
2XU7 1.9 Å, Structural basis for RbAp48 binding to FOG-1
5XXQ 1.9 Å, Crystal structure of RBBP4: ZNF827 and its function in telomere
6BW4 2.0 Å, Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
5Y1U 2.14 Å, Crystal structure of RBBP4 bound to AEBP2 RRK motif
4PBZ 2.15 Å, Structure of the human RbAp48-MTA1(670-695) complex
6BW3 2.2 Å, Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
8TX8 2.2 Å, Crystal Structure of RBBP4 bound to ZNF512B peptide
3GFC 2.3 Å, Crystal Structure of Histone-binding protein RBBP4
5VTB 2.4 Å, Crystal structure of RBBP4 bound to BCL11a peptide
4PBY 2.5 Å, Structure of the human RbAp48-MTA1(656-686) complex

Browse structure collections

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