4PBY: Human RbAp48-MTA1(656-686) complex

Structure of the human RbAp48-MTA1(656-686) complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Jun 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,763
Mol. weight: 102.96 kDa
Ligands: IPA
Released: 11 Jun 2014

Explore 4PBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PBY contains 17 α-helices and 58 β-strands across 4 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, 29 β-strands

Element	Residues	Length	Sheet
α-helix	5-31	27
β-strand	32-39	8	1
β-strand	47-54	8	2
β-strand	61-69	9	2
β-strand	77-87	11	2
β-strand	115-123	9	2
β-strand	129-133	5	3
β-strand	136-143	8	3
α-helix	148	1
β-strand	149-153	5	3
α-helix	154-156	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	267-270	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	389-394	6	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain B: 9 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	32-39	8	8
β-strand	47-54	8	9
β-strand	61-69	9	9
β-strand	77-87	11	9
α-helix	92-93	2
α-helix	95-98	4
α-helix	111-114	4
β-strand	115-123	9	9
β-strand	129-133	5	10
β-strand	136-143	8	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
α-helix	303-305	3
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	356-359	4
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	406-408	3

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	677-681	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	675-681	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Metastasis-associated protein MTA1	C, D	protein	31	Homo sapiens	Q13330 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PBY_1 Histone-binding protein RBBP4 (chains A, B)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 2 (C, D), FASTA

>4PBY_2 Metastasis-associated protein MTA1 (chains C, D)
DVFYMATEETRKIRKLLSSSETKRAARRPYK

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1

Primary citation

Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 sub-complex. Alqarni, S.S., Murthy, A., Zhang, W. et al. J Biol Chem (2014) 289:21844. DOI 10.1074/jbc.M114.558940 · 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

About this viewer

MolViewer shows 4PBY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.