6ZRC: 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 2.6 Å resolution. Released 28 Oct 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,335
Mol. weight: 99.24 kDa
Ligands: PXY
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

6ZRC contains 16 α-helices and 54 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, 27 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	1
β-strand	48-54	7	2
α-helix	55-56	2
β-strand	61-69	9	2
β-strand	78-87	10	2
β-strand	114-122	9	2
β-strand	129-133	5	3
β-strand	136-143	8	3
β-strand	149-153	5	3
α-helix	154-156	3
β-strand	183-185	3	4
β-strand	192-196	5	4
β-strand	202-206	5	4
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	309-314	6	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	356-359	4
β-strand	366-369	4	7
β-strand	377-382	6	1
β-strand	390-394	5	1
β-strand	398-404	7	1
α-helix	406-409	4

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	8
β-strand	48-54	7	9
α-helix	55-56	2
β-strand	61-69	9	9
β-strand	78-87	10	9
β-strand	115-122	8	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	183-185	3	11
β-strand	192-196	5	11
β-strand	202-206	5	11
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	309-314	6	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	366-369	4	14
β-strand	377-382	6	8
β-strand	390-394	5	8
β-strand	398-404	7	8
α-helix	406-409	4

Chains P and Q: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	13-14	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-binding protein RBBP4	A, B	protein	427	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

>6ZRC_1 Histone-binding protein RBBP4 (chains A, B)
GPMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEG
KDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIE
IKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQK
EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLL
HESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTV
ALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPED
AEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSV
DPEGQGS

Sequence of entity 2 (P, Q), FASTA

>6ZRC_2 macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1 (chains P, Q)
XCTKRAARRPYKPCAX

Ligands and cofactors

ID	Name	Formula	Copies
PXY	Para-xylene	C8 H10	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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