6G16: Histone-binding protein RBBP4

Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange. Determined by X-ray diffraction at 2.8 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,642
Mol. weight: 229.93 kDa
Released: 13 Jun 2018

Explore 6G16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G16 contains 46 α-helices and 125 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	11-31	21
β-strand	32-39	8	1
β-strand	48-54	7	2
β-strand	61-69	9	2
β-strand	77-87	11	2
β-strand	108-109	2	1
β-strand	115-123	9	2
β-strand	129-132	4	3
β-strand	139-143	5	3
β-strand	149-153	5	3
α-helix	154-156	3
α-helix	161-163	3
β-strand	171-173	3	4
β-strand	183-185	3	5
β-strand	192-196	5	5
β-strand	202-206	5	5
β-strand	216-217	2	3
β-strand	221-223	3	5
β-strand	230-235	6	6
β-strand	242-247	6	6
β-strand	251-256	6	6
β-strand	267-270	4	6
β-strand	276-281	6	7
β-strand	288-293	6	7
β-strand	297-302	6	7
β-strand	309-314	6	7
β-strand	320-325	6	8
β-strand	332-337	6	8
β-strand	342-346	5	8
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	8
β-strand	377-382	6	1
β-strand	389-394	6	1
β-strand	398-404	7	1
α-helix	406-409	4

Chains B, D and F: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	472-474	3	1
α-helix	477-485	9
α-helix	487-490	4
α-helix	492-495	4
α-helix	502-503	2
α-helix	505-514	10
α-helix	534-542	9

Chain C: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	9
β-strand	47-54	8	10
β-strand	61-69	9	10
β-strand	77-87	11	10
β-strand	108-109	2	9
β-strand	115-123	9	10
β-strand	129-132	4	4
β-strand	139-143	5	4
β-strand	149-153	5	4
α-helix	154-156	3
α-helix	161-163	3
β-strand	171-173	3	3
β-strand	183-185	3	11
β-strand	192-196	5	11
β-strand	202-206	5	11
β-strand	216-217	2	4
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
α-helix	356-361	6
β-strand	366-370	5	14
β-strand	377-382	6	9
β-strand	389-394	6	9
β-strand	398-404	7	9
α-helix	406-409	4

Chain E: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	12-31	20
β-strand	32-39	8	15
β-strand	47-54	8	16
β-strand	61-68	8	16
β-strand	77-87	11	16
β-strand	108-109	2	15
β-strand	115-123	9	16
β-strand	129-132	4	17
β-strand	139-143	5	17
β-strand	149-153	5	17
α-helix	154-156	3
β-strand	171-173	3	18
β-strand	183-185	3	19
β-strand	192-196	5	19
β-strand	202-206	5	19
β-strand	216-217	2	17
β-strand	221-223	3	19
β-strand	230-235	6	20
β-strand	242-247	6	20
β-strand	251-256	6	20
β-strand	267-270	4	20
β-strand	276-281	6	21
β-strand	288-293	6	21
β-strand	298-302	5	21
β-strand	311-313	3	21
β-strand	320-325	6	22
β-strand	332-337	6	22
β-strand	342-346	5	22
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	22
β-strand	377-382	6	15
β-strand	389-394	6	15
β-strand	398-404	7	15
α-helix	406-409	4

Chain G: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	23
β-strand	47-49	3	24
β-strand	54	1	24
β-strand	61-69	9	24
β-strand	77-87	11	24
β-strand	108-109	2	23
β-strand	115-123	9	24
β-strand	129-132	4	18
β-strand	139-143	5	18
β-strand	149-153	5	18
α-helix	154-156	3
β-strand	171-173	3	17
β-strand	183-185	3	25
β-strand	192-196	5	25
β-strand	202-206	5	25
β-strand	216-217	2	18
β-strand	221-223	3	25
β-strand	230-235	6	26
β-strand	242-247	6	26
β-strand	251-256	6	26
β-strand	267-270	4	26
β-strand	276-281	6	27
β-strand	288-293	6	27
β-strand	297-302	6	27
β-strand	311-314	4	27
β-strand	320-325	6	28
β-strand	332-337	6	28
β-strand	342-346	5	28
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	28
β-strand	377-382	6	23
β-strand	389-394	6	23
β-strand	398-404	7	23
α-helix	406-409	4

Chain H: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	472-474	3	23
α-helix	477-485	9
α-helix	487-490	4
α-helix	492-495	4
α-helix	502-503	2
α-helix	505-515	11
α-helix	534-542	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, C, E, G	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Metastasis-associated protein MTA1	B, D, F, H	protein	85	Homo sapiens	Q13330 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6G16_1 Histone-binding protein RBBP4 (chains A, C, E, G)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 2 (B, D, F, H), FASTA

>6G16_2 Metastasis-associated protein MTA1 (chains B, D, F, H)
GAAMKTRQAFYLHTTKLTRIARRLCREILRPWHAARHPYLPINSAAIKAECTARLPEASQ
SPLVLKQAVRKPLEAVLRYLETHPR

Primary citation

The structure of the core NuRD repression complex provides insights into its interaction with chromatin. Millard, C.J., Varma, N., Saleh, A. et al. Elife (2016) 5:e13941-e13941. DOI 10.7554/eLife.13941 · 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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