6ZRD: HUMAN RBAP48

STRUCTURE OF THE HUMAN RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Dec 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,623
Mol. weight: 99.02 kDa
Ligands: SEZ
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

6ZRD contains 14 α-helices and 60 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, 31 β-strands

Element	Residues	Length	Sheet
α-helix	2-31	30
β-strand	32-39	8	1
β-strand	47-54	8	2
β-strand	61-69	9	2
β-strand	78-87	10	2
β-strand	102	1	3
β-strand	108	1	3
α-helix	111-113	3
β-strand	115-122	8	2
β-strand	130-133	4	4
β-strand	136-143	8	4
β-strand	149-153	5	4
α-helix	154-156	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	4
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	311-314	4	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

Chain B: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	2-31	30
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	115-123	9	10
β-strand	130-132	3	11
β-strand	139-143	5	11
β-strand	149-153	5	11
α-helix	154-156	3
α-helix	161-162	2
β-strand	171-174	4	11
β-strand	183-185	3	12
β-strand	192-196	5	12
β-strand	202-206	5	12
β-strand	216-218	3	11
β-strand	221-223	3	12
β-strand	230-235	6	13
β-strand	242-247	6	13
β-strand	251-256	6	13
β-strand	267-270	4	13
β-strand	276-281	6	14
β-strand	288-293	6	14
β-strand	297-302	6	14
β-strand	311-314	4	14
β-strand	320-325	6	15
β-strand	332-337	6	15
β-strand	342-346	5	15
α-helix	347-349	3
α-helix	356-361	6
β-strand	366-370	5	15
β-strand	377-382	6	9
β-strand	389-394	6	9
β-strand	398-404	7	9
α-helix	406-409	4

Chains P and Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	425	Homo sapiens	Q09028 (AlphaFold model)
macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1	P, Q	protein	16	Homo sapiens	Q13330 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ZRD_1 Histone-binding protein RBBP4 (chains A, B)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 2 (P, Q), FASTA

>6ZRD_2 macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1 (chains P, Q)
XCTKRCARRPYKPCAX

Ligands and cofactors

ID	Name	Formula	Copies
SEZ	1,3,5-trimethylbenzene	C9 H12	2

Primary citation

Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48. Hart, P.'., Hommen, P., Noisier, A. et al. Angew Chem Int Ed Engl (2021) 60:1813-1820. DOI 10.1002/anie.202009749 · 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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