9DHU: The Retinoblastoma Protein with Mutation E533K

The Retinoblastoma Protein with Mutation E533K. Determined by X-ray diffraction at 2.16 Å resolution. Released 19 Feb 2025.

Method: X-ray diffraction
Resolution: 2.16 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,753
Mol. weight: 91.14 kDa
Released: 19 Feb 2025

Explore 9DHU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DHU contains 47 α-helices and 4 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: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	384-390	7
α-helix	398-406	9
α-helix	412-434	23
α-helix	441-467	27
α-helix	470-477	8
α-helix	480-497	18
α-helix	516-521	6
α-helix	525-529	5
α-helix	532-538	7
α-helix	544-559	16
α-helix	561-563	3
α-helix	568-575	8
α-helix	602-606	5
α-helix	645-669	25
α-helix	676-690	15
α-helix	692-695	4
α-helix	700-714	15
α-helix	721-728	8
α-helix	737-740	4
β-strand	742-745	4	1
β-strand	748-750	3	1
α-helix	752-755	4
α-helix	756-760	5
α-helix	761-769	9
α-helix	770-772	3
α-helix	776-783	8

Chain B: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	385-391	7
α-helix	398-405	8
α-helix	412-434	23
α-helix	439-464	26
α-helix	470-478	9
α-helix	480-497	18
α-helix	516-520	5
α-helix	525-538	14
α-helix	544-559	16
α-helix	561-563	3
α-helix	568-578	11
α-helix	582-586	5
α-helix	602-607	6
α-helix	645-669	25
α-helix	676-690	15
α-helix	692-695	4
α-helix	700-714	15
α-helix	721-729	9
α-helix	737-740	4
β-strand	742-745	4	2
β-strand	748-750	3	2
α-helix	752-755	4
α-helix	756-760	5
α-helix	761-770	10
α-helix	776-785	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-associated protein	A, B	protein	390	Homo sapiens	P06400 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DHU_1 Retinoblastoma-associated protein (chains A, B)
GEFNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGQ
GCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMA
TYSRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIKSFIKAEGNLTREMIKHLERCEHR
IMESLAWLSDSPLFDLIKQSKDREGPTDHLESACPLNLPLQNNHTAADMYLEPVRAPKKK
STSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQI
MMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQR
LKTNILQYASTRPPTLAPIPHIPFMQRLKT

Primary citation

Structural and functional analysis of cancer-associated missense variants in the retinoblastoma protein pocket domain. Castro, A., Ruiz Rivera, A., Moorman, C.C. et al. J Biol Chem (2025) 301:108284-108284. DOI 10.1016/j.jbc.2025.108284 · PubMed

Other PDB entries of the same protein (UniProt P06400 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2R7G 1.67 Å, Structure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1…
1GUX 1.85 Å, Rb pocket bound to E7 lxcxe motif
4ELL 1.98 Å, Structure of the inactive retinoblastoma protein pocket domain
2QDJ 2.0 Å, Crystal structure of the Retinoblastoma protein N-domain provides insight into tumor…
1N4M 2.2 Å, Structure of Rb tumor suppressor bound to the transactivation domain of E2F-2
9DHF 2.26 Å, The Retinoblastoma Protein with Mutation E554K
1AD6 2.3 Å, Domain A of human retinoblastoma tumor suppressor
9DHC 2.32 Å, The Retinoblastoma Protein with Mutation S751Y
4CRI 2.35 Å, Crystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide
9DGK 2.38 Å, The Retinoblastoma Protein with Mutation M704V
1H25 2.5 Å, CDK2/Cyclin A in complex with an 11-residue recruitment peptide from…
1PJM 2.5 Å, Mouse Importin alpha-bipartite NLS from human retinoblastoma protein Complex

Browse structure collections

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