5XWR: RBBP4-peptide complex

Crystal Structure of RBBP4-peptide complex. Determined by X-ray diffraction at 2.69 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,176
Mol. weight: 102.92 kDa
Released: 11 Jul 2018

Explore 5XWR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XWR contains 10 α-helices and 60 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: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	16-27	12
α-helix	28-30	3
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	130-132	3	3
β-strand	139-143	5	3
β-strand	149-153	5	3
α-helix	154-156	3
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	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

Chain B: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	16-27	12
α-helix	28-30	3
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	129-132	4	10
β-strand	139-143	5	10
β-strand	149-153	5	10
α-helix	154-156	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	443	Homo sapiens	Q09028 (AlphaFold model)
Met-ser-arg-arg-lys-gln-ala-lys-pro-gln-his-ile	C, D	protein	12	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5XWR_1 Histone-binding protein RBBP4 (chains A, B)
HHHHHHHHHHLEVLFQGPMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEW
PSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEK
GEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPD
PSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTI
FTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFN
PYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRL
NVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVW
QMAENIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (C, D), FASTA

>5XWR_2 MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE (chains C, D)
MSRRKQAKPQHI

Primary citation

Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide. Liu, B.H., Jobichen, C., Chia, C.S.B. et al. Proc Natl Acad Sci U S A (2018) 115:E7119-E7128. DOI 10.1073/pnas.1801253115 · 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
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

Browse structure collections

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