5WAK: Suz12-Rbbp4 Binary Complex

Crystal Structure of a Suz12-Rbbp4 Binary Complex. Determined by X-ray diffraction at 3.2 Å resolution. Released 14 Mar 2018.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,766
Mol. weight: 105.12 kDa
Ligands: ZN
Released: 14 Mar 2018

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

Secondary structure: helices and β-sheets

5WAK contains 12 α-helices and 38 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	9-27	19
α-helix	28-30	3
β-strand	32-39	8	1
β-strand	49-54	6	2
β-strand	61-69	9	2
β-strand	77-87	11	2
β-strand	115-123	9	2
β-strand	129-132	4	3
β-strand	139-143	5	3
β-strand	149-153	5	3
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	267-269	3	5
β-strand	276-281	6	6
β-strand	288-293	6	6
β-strand	297-302	6	6
β-strand	305	1	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	406-408	3

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	86-88	3
α-helix	92-106	15
α-helix	112-114	3
α-helix	116-121	6
α-helix	127-129	3
α-helix	136-146	11
β-strand	191-193	3	8
β-strand	198-199	2	8
β-strand	246-247	2	8
β-strand	429-433	5	9
β-strand	439-443	5	9
α-helix	460-470	11
β-strand	474-479	6	9
β-strand	486-491	6	9
β-strand	526-531	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A	protein	439	Homo sapiens	Q09028 (AlphaFold model)
Polycomb protein SUZ12	B	protein	478	Homo sapiens	Q15022 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5WAK_1 Histone-binding protein RBBP4 (chains A)
MSHHHHHHLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLT
AQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFG
GFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGE
CNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGH
TAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSE
FILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWD
LSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAE
NIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (B), FASTA

>5WAK_2 Polycomb protein SUZ12 (chains B)
MEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVD
DMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKK
RKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVT
RPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEY
EVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAK
PLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYN
NNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECY
DGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLEWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Unique Structural Platforms of Suz12 Dictate Distinct Classes of PRC2 for Chromatin Binding. Chen, S., Jiao, L., Shubbar, M. et al. Mol Cell (2018) 69:840-852.e5. DOI 10.1016/j.molcel.2018.01.039 · 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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