1GH6: Retinoblastoma pocket

Retinoblastoma pocket complexed with SV40 large T antigen. Determined by X-ray diffraction at 3.2 Å resolution. Released 15 Nov 2001.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Simian virus 40, Homo sapiens
Chains: 2
Atoms: 3,627
Mol. weight: 52.46 kDa
Released: 15 Nov 2001

Explore 1GH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1GH6 contains 27 α-helices and 2 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-16	11
α-helix	27-36	10
α-helix	53-67	15
α-helix	91-102	12

Chain B: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	382-390	9
α-helix	398-404	7
α-helix	412-431	20
α-helix	440-465	26
α-helix	474-477	4
α-helix	480-497	18
α-helix	498-500	3
α-helix	515-520	6
α-helix	525-537	13
α-helix	544-559	16
α-helix	561-563	3
α-helix	568-575	8
α-helix	647-669	23
α-helix	674-676	3
α-helix	677-690	14
α-helix	692-695	4
α-helix	700-714	15
α-helix	721-728	8
α-helix	737-740	4
β-strand	742-743	2	1
β-strand	749-750	2	1
α-helix	752-755	4
α-helix	756-760	5
α-helix	761-763	3
α-helix	765-769	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large T antigen	A	protein	114	Simian virus 40	P03070 (AlphaFold model)
Retinoblastoma-associated protein	B	protein	333	Homo sapiens	P06400 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1GH6_1 Large T antigen (chains A)
SHMREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPDKGGDEEKMKKMNTLYKKME
DGVKYAHQPDFGGFWDATEIPTYGTDEWEQWWNAFNEENLFCSEEMPSSDDEAT

Sequence of entity 2 (B), FASTA

>1GH6_2 Retinoblastoma-associated protein (chains B)
MNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESILKRVKDIGYIFKEKFAKAVGAGC
VAIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATY
SRSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIM
ESLAWLSDSPLFDLIKQSKLVPRGSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHI
IWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETF
KRVLIKEEEYDSIIVFYNSVFMQRLKTNILQYA

Primary citation

Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen. Kim, H.Y., Ahn, B.Y., Cho, Y. EMBO J (2001) 20:295-304. DOI 10.1093/emboj/20.1.295 · PubMed

Other PDB entries of the same protein (UniProt P03070 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FUF 1.45 Å, Crystal structure of the SV40 large T antigen origin-binding domain
2IPR 1.5 Å, Origin binding domain of the SV40 large T antigen (residues 131-259). P21 crystal form
3QK2 1.64 Å, Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin…
2ITL 1.65 Å, The origin binding domain of the SV40 large T antigen bound to the functional pen…
3QN2 1.66 Å, Structure-based design of a disulfide-linked oligomeric form of the Simian Virus 40…
5D9I 1.7 Å, SV40 Large T antigen origin binding domain bound to artificial DNA fork
4RXH 1.76 Å, Crystal Structure of Importin-alpha from Neurospora crassa complexed with SV40NLS
1SVM 1.94 Å, Co-crystal structure of SV40 large T antigen helicase domain and ATP
1SVL 1.95 Å, Co-crystal structure of SV40 large T antigen helicase domain and ADP
1Q1S 2.3 Å, Mouse Importin alpha- phosphorylated SV40 CN peptide complex
2NL8 2.3 Å, The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp…
2NTC 2.4 Å, Crystal Structure of sv40 large T antigen origin binding domain with DNA

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