6NQ3: Histone-binding protein RBBP4

Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex. Determined by X-ray diffraction at 2.89 Å resolution. Released 29 Jan 2020.

Method: X-ray diffraction
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,928
Mol. weight: 232.94 kDa
Ligands: ZN
Released: 29 Jan 2020

Explore 6NQ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NQ3 contains 39 α-helices and 104 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, 30 β-strands

Element	Residues	Length	Sheet
α-helix	10-31	22
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	130-132	3	3
β-strand	139-143	5	3
β-strand	149-153	5	3
α-helix	154-156	3
α-helix	161-162	2
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	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	406-409	4

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	80-82	3
α-helix	83-106	24
α-helix	112-114	3
α-helix	116-121	6
α-helix	128-131	4
α-helix	136-142	7
β-strand	157-160	4	8
β-strand	185-193	9	9
β-strand	198-200	3	9
α-helix	201-203	3
β-strand	204-205	2	9
α-helix	206-207	2
β-strand	229-232	4	8
α-helix	234-236	3
α-helix	238-240	3
β-strand	245-253	9	9
β-strand	296-297	2	9
β-strand	302	1	9
β-strand	308	1	9
β-strand	313-316	4	8
β-strand	320	1	9
β-strand	354-358	5	8
β-strand	427-434	8	10
β-strand	437-441	5	10
β-strand	443	1	11
α-helix	460-470	11
β-strand	474-481	8	10
β-strand	484-491	8	10
α-helix	506-508	3
β-strand	525-531	7	1

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	531-543	13
α-helix	545-551	7
β-strand	555-563	9	12
β-strand	567-574	8	12

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	153	1	11
α-helix	154-163	10

Chain E: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	10-27	18
α-helix	28-30	3
β-strand	32-39	8	13
β-strand	49-54	6	14
β-strand	61-69	9	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	161-162	2
β-strand	171-174	4	15
β-strand	182-185	4	16
β-strand	192-196	5	16
β-strand	202-206	5	16
β-strand	216-218	3	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	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: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	82-106	25
α-helix	112-114	3
α-helix	116-121	6
α-helix	128-131	4
α-helix	136-145	10
β-strand	157	1	20
β-strand	158-161	4	21
β-strand	186-193	8	22
β-strand	198-200	3	22
β-strand	204-205	2	22
β-strand	232	1	20
α-helix	234-236	3
β-strand	241	1	23
β-strand	244	1	23
β-strand	245-253	9	22
β-strand	296-300	5	22
β-strand	302	1	24
β-strand	308	1	24
β-strand	313-316	4	21
β-strand	320	1	22
β-strand	354-358	5	21
β-strand	428-433	6	25
β-strand	438-441	4	25
β-strand	443	1	26
α-helix	460-470	11
β-strand	474-481	8	25
β-strand	484-491	8	25
α-helix	493-495	3
β-strand	525-531	7	13

Chain G: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	531-543	13
α-helix	546-551	6
β-strand	557-562	6	27
β-strand	568-572	5	27

Chain H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	150-152	3
β-strand	153	1	26
α-helix	154-163	10

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)
PHD finger protein 19	C, G	protein	84	Homo sapiens	Q5T6S3 (AlphaFold model)
Protein Jumonji	D, H	protein	19	Homo sapiens	Q92833 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6NQ3_1 Histone-binding protein RBBP4 (chains A, E)
MSHHHHHHLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLT
AQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFG
GFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGE
CNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGH
TAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSE
FILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWD
LSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAE
NIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (B, F), FASTA

>6NQ3_2 Polycomb protein SUZ12 (chains B, F)
MEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVD
DMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKK
RKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVT
RPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEY
EVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAK
PLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYN
NNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECY
DGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLEWSHPQFEK

Sequence of entity 3 (C, G), FASTA

>6NQ3_3 PHD finger protein 19 (chains C, G)
SNASDSSAEGASVPERPDEGIDSHTFESISEDDSSLSHLKSSITNYFGAAGRLACGEKYQ
VLARRVTPEGKVQYLVEWEGTTPY

Sequence of entity 4 (D, H), FASTA

>6NQ3_4 Protein Jumonji (chains D, H)
LSKRKPKTEDFLTFLCLRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

A Dimeric Structural Scaffold for PRC2-PCL Targeting to CpG Island Chromatin. Chen, S., Jiao, L., Liu, X. et al. Mol Cell (2020) 77:1265. DOI 10.1016/j.molcel.2019.12.019 · 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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