8TX8: RBBP4

Crystal Structure of RBBP4 bound to ZNF512B peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,600
Mol. weight: 104.1 kDa
Ligands: OXM
Released: 6 Nov 2024

Explore 8TX8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TX8 contains 11 α-helices and 58 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: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
β-strand	32-39	8	1
β-strand	48-54	7	2
β-strand	61-69	9	2
β-strand	77-87	11	2
β-strand	115-123	9	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	180-185	6	4
β-strand	192-197	6	4
β-strand	202-206	5	4
β-strand	215-218	4	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
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 B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
β-strand	32-39	8	8
β-strand	47-54	8	9
β-strand	61-69	9	9
β-strand	77-87	11	9
β-strand	115-123	9	9
β-strand	129-133	5	10
β-strand	136-143	8	10
β-strand	149-153	5	10
α-helix	154-156	3
β-strand	171-173	3	10
β-strand	182-185	4	11
β-strand	192-196	5	11
β-strand	202-206	5	11
β-strand	216-217	2	10
β-strand	221-223	3	11
β-strand	230-235	6	12
β-strand	242-247	6	12
β-strand	251-256	6	12
β-strand	267-270	4	12
β-strand	276-281	6	13
β-strand	288-293	6	13
β-strand	297-302	6	13
β-strand	311-314	4	13
β-strand	320-325	6	14
β-strand	332-337	6	14
β-strand	342-346	5	14
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	14
β-strand	377-382	6	8
β-strand	389-394	6	8
β-strand	398-404	7	8
α-helix	406-409	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	445	Homo sapiens	Q09028 (AlphaFold model)
Zinc finger protein 512B	C, D	protein	13	Homo sapiens	Q96KM6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8TX8_1 Histone-binding protein RBBP4 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHAL
EWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDS
EKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSK
PDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAK
TIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLS
FNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDR
RLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQ
VWQMAENIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (C, D), FASTA

>8TX8_2 Zinc finger protein 512B (chains C, D)
XKHRRKQKTPKKF

Ligands and cofactors

ID	Name	Formula	Copies
OXM	Oxamic acid	C2 H3 N O3	1

Water and common crystallization additives (ACT, EDO, FMT) are not listed.

Primary citation

ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner. Wunderlich, T.M., Deshpande, C., Paasche, L.W. et al. Nucleic Acids Res (2024) 52:12831-12849. DOI 10.1093/nar/gkae926 · PubMed

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
9V5M 2.1 Å, The crystal structure of RBBP4-H3 complex
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
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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