6BW3: RBBP4

Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Dec 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,975
Mol. weight: 98.47 kDa
Released: 27 Dec 2017

Explore 6BW3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BW3 contains 11 α-helices and 60 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 A: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	10-31	22
β-strand	32-39	8	8
β-strand	47-49	3	9
β-strand	54	1	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
α-helix	161-162	2
β-strand	171-174	4	10
β-strand	183-185	3	11
β-strand	192-196	5	11
β-strand	202-206	5	11
β-strand	216-218	3	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
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

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4

Chain C: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	13-31	19
β-strand	32-39	8	1
β-strand	47-49	3	2
β-strand	54	1	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	183-185	3	4
β-strand	192-196	5	4
β-strand	202-206	5	4
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
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
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, C	protein	427	Homo sapiens	Q09028 (AlphaFold model)
MDS1 and EVI1 complex locus protein MDS1	B, D	protein	12	Homo sapiens	Q03112 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6BW3_1 Histone-binding protein RBBP4 (chains A, C)
GSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEG
KDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIE
IKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQK
EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLL
HESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTV
ALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPED
AEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSV
DPEGQGS

Sequence of entity 2 (B, D), FASTA

>6BW3_2 MDS1 and EVI1 complex locus protein MDS1 (chains B, D)
MRSKGRARKLAT

Primary citation

Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex. Ivanochko, D., Halabelian, L., Henderson, E. et al. Nucleic Acids Res (2019) 47:1225-1238. DOI 10.1093/nar/gky1192 · 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
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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