5WAI: Histone-binding protein RBBP4

Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 14 Mar 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Neovison vison
Chains: 8
Atoms: 12,890
Mol. weight: 237.94 kDa
Ligands: ZN
Released: 14 Mar 2018

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

Secondary structure: helices and β-sheets

5WAI contains 47 α-helices and 107 β-strands across 8 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, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-27	24
α-helix	28-30	3
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
β-strand	108-111	4	1
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
β-strand	171-173	3	3
β-strand	183-185	3	4
β-strand	192-196	5	4
β-strand	202-206	5	4
β-strand	216-217	2	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	390-394	5	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	80-106	27
α-helix	112-114	3
α-helix	116-121	6
α-helix	128-131	4
α-helix	134-136	3
α-helix	137-146	10
β-strand	156-165	10	8
β-strand	183	1	9
β-strand	186-192	7	10
α-helix	193-195	3
β-strand	203-207	5	10
β-strand	212	1	9
β-strand	215	1	8
α-helix	217-218	2
β-strand	229-233	5	8
α-helix	241-243	3
β-strand	245-252	8	10
β-strand	296	1	11
β-strand	297-302	6	10
β-strand	308	1	10
β-strand	313-318	6	8
β-strand	320	1	11
β-strand	354-362	9	8
β-strand	427-434	8	12
β-strand	437-443	7	12
α-helix	460-470	11
β-strand	474-481	8	12
β-strand	484-491	8	12
β-strand	525-531	7	1
α-helix	541-543	3
β-strand	545	1	2

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	415-420	6
β-strand	427-440	14	8
β-strand	445-452	8	8
α-helix	458-459	2
β-strand	460-463	4	8
α-helix	464-467	4
β-strand	472-476	5	8
α-helix	477-479	3
α-helix	482-485	4
α-helix	486-488	3

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	151-152	2
β-strand	153	1	12
α-helix	154-162	9

Chain E: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
α-helix	28-30	3
β-strand	32-39	8	13
β-strand	47-49	3	14
β-strand	54	1	14
β-strand	61-68	8	14
β-strand	77-87	11	14
β-strand	115-123	9	14
β-strand	129-133	5	15
β-strand	136-143	8	15
α-helix	148	1
β-strand	149-153	5	15
α-helix	154-156	3
β-strand	171-173	3	15
β-strand	183-185	3	16
β-strand	192-196	5	16
β-strand	202-206	5	16
β-strand	217	1	15
β-strand	221-223	3	16
β-strand	230-235	6	17
β-strand	242-247	6	17
β-strand	251-256	6	17
β-strand	267-270	4	17
β-strand	276-281	6	18
β-strand	288-293	6	18
β-strand	297-302	6	18
β-strand	311-314	4	18
β-strand	320-325	6	19
β-strand	332-337	6	19
β-strand	342-346	5	19
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	19
β-strand	377-382	6	13
β-strand	389-394	6	13
β-strand	398-404	7	13
α-helix	406-409	4

Chain F: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	80-106	27
α-helix	112-114	3
α-helix	116-121	6
α-helix	127-130	4
α-helix	134-136	3
α-helix	137-146	10
β-strand	156-165	10	20
β-strand	183-192	10	21
α-helix	193-194	2
β-strand	203-212	10	21
α-helix	213-214	2
β-strand	215	1	20
β-strand	229-234	6	20
α-helix	239-241	3
β-strand	245-254	10	21
β-strand	295-302	8	21
β-strand	308	1	21
β-strand	313-318	6	20
β-strand	320-321	2	21
β-strand	354-362	9	20
β-strand	427-433	7	22
β-strand	438-443	6	22
α-helix	460-470	11
β-strand	474-479	6	22
β-strand	484-491	8	22
β-strand	526-531	6	13

Chain G: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	427-440	14	20
β-strand	445-452	8	20
α-helix	458-459	2
β-strand	460-463	4	20
β-strand	472-476	5	20
α-helix	477-479	3
α-helix	482-485	4
α-helix	486-488	3

Chain H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	153	1	22
α-helix	154-162	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, E	protein	439	Homo sapiens	Q09028 (AlphaFold model)
Polycomb protein SUZ12	B, F	protein	478	Homo sapiens	Q15022 (AlphaFold model)
Zinc finger protein AEBP2	C, G	protein	100	Homo sapiens	Q6ZN18 (AlphaFold model)
Jumonji, AT-rich interactive domain 2	D, H	protein	19	Neovison vison	Q92833 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5WAI_1 Histone-binding protein RBBP4 (chains A, E)
MSHHHHHHLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLT
AQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFG
GFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGE
CNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGH
TAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSE
FILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWD
LSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAE
NIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (B, F), FASTA

>5WAI_2 Polycomb protein SUZ12 (chains B, F)
MEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVD
DMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKK
RKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVT
RPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEY
EVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAK
PLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYN
NNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECY
DGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLEWSHPQFEK

Sequence of entity 3 (C, G), FASTA

>5WAI_3 Zinc finger protein AEBP2 (chains C, G)
SNARHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLLHWMPEDILPDVWVN
ESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR

Sequence of entity 4 (D, H), FASTA

>5WAI_4 Jumonji, AT-rich interactive domain 2 (chains D, H)
LSKRKPKTEDFLTFLCLRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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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