5Y1U: RBBP4

Crystal structure of RBBP4 bound to AEBP2 RRK motif. Determined by X-ray diffraction at 2.14 Å resolution. Released 18 Apr 2018.

Method: X-ray diffraction
Resolution: 2.14 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,586
Mol. weight: 106.23 kDa
Released: 18 Apr 2018

Explore 5Y1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y1U contains 13 α-helices and 58 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: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	39-42	4
α-helix	46-62	17
β-strand	63-70	8	1
β-strand	78-85	8	2
β-strand	92-100	9	2
β-strand	108-118	11	2
β-strand	146-154	9	2
β-strand	160-164	5	3
β-strand	167-174	8	3
β-strand	180-184	5	3
α-helix	185-187	3
β-strand	202-205	4	3
β-strand	214-216	3	4
β-strand	223-227	5	4
β-strand	233-237	5	4
β-strand	247-249	3	3
β-strand	252-254	3	4
β-strand	261-266	6	5
β-strand	273-278	6	5
β-strand	282-287	6	5
β-strand	298-301	4	5
β-strand	307-312	6	6
β-strand	319-324	6	6
β-strand	329-333	5	6
α-helix	334-336	3
β-strand	342-344	3	6
β-strand	351-356	6	7
β-strand	363-368	6	7
β-strand	373-377	5	7
α-helix	378-380	3
α-helix	389-391	3
β-strand	397-401	5	7
β-strand	408-413	6	1
β-strand	420-425	6	1
β-strand	429-435	7	1
α-helix	439-441	3

Chain B: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	36-62	27
β-strand	63-70	8	8
β-strand	78-85	8	9
β-strand	92-100	9	9
β-strand	108-118	11	9
β-strand	146-154	9	9
β-strand	160-164	5	10
β-strand	167-174	8	10
β-strand	180-184	5	10
α-helix	185-187	3
α-helix	192-193	2
β-strand	202-205	4	10
β-strand	214-216	3	11
β-strand	223-227	5	11
β-strand	233-237	5	11
β-strand	246-249	4	10
β-strand	252-254	3	11
β-strand	261-266	6	12
β-strand	273-278	6	12
β-strand	282-287	6	12
β-strand	298-301	4	12
β-strand	307-312	6	13
β-strand	319-324	6	13
β-strand	329-333	5	13
β-strand	342-344	3	13
β-strand	351-356	6	14
β-strand	363-368	6	14
β-strand	373-377	5	14
α-helix	378-380	3
α-helix	387-390	4
β-strand	397-401	5	14
β-strand	408-413	6	8
β-strand	420-425	6	8
β-strand	429-435	7	8
α-helix	437-440	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	456	Homo sapiens	Q09028 (AlphaFold model)
Zinc finger protein AEBP2	C, D	protein	12	Homo sapiens	Q6ZN18 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5Y1U_1 Histone-binding protein RBBP4 (chains A, B)
MSYYHHHHHHDYDIPTTENLYFQGAMGSGIQMADKEAAFDDAVEERVINEEYKIWKKNTP
FLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPND
DAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDV
LVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
VPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSV
DAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHN
ETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWV
ICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

Sequence of entity 2 (C, D), FASTA

>5Y1U_2 Zinc finger protein AEBP2 (chains C, D)
KRRKLKNKRRRS

Primary citation

Structural and biochemical insights into human zinc finger protein AEBP2 reveals interactions with RBBP4. Sun, A., Li, F., Liu, Z. et al. Protein Cell (2017). DOI 10.1007/s13238-017-0483-6 · 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
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
4PBY 2.5 Å, Structure of the human RbAp48-MTA1(656-686) complex

Browse structure collections

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