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- PDB-1gh6: RETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1gh6
TitleRETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN
Components
  • Large T antigen
  • Retinoblastoma-associated protein
KeywordsANTITUMOR PROTEIN / TUMOR SUPPRESSOR / ONCOPROTEIN
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / importin-alpha family protein binding / positive regulation of transcription regulatory region DNA binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of extracellular matrix organization / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of centromere complex assembly / positive regulation of macrophage differentiation / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / negative regulation of hepatocyte apoptotic process / neuron maturation / bidirectional double-stranded viral DNA replication / myoblast differentiation / digestive tract development / aortic valve morphogenesis / viral DNA genome replication / Replication of the SARS-CoV-1 genome / SWI/SNF complex / negative regulation of cold-induced thermogenesis / negative regulation of glial cell proliferation / DNA 3'-5' helicase / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / skeletal muscle cell differentiation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / DNA replication origin binding / chromosome organization / chondrocyte differentiation / glial cell proliferation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / negative regulation of protein kinase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / isomerase activity / helicase activity / negative regulation of DNA-binding transcription factor activity / phosphoprotein binding / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of cell growth / PML body / Oncogene Induced Senescence / spindle / negative regulation of inflammatory response / kinase binding / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / negative regulation of epithelial cell proliferation / neuron projection development / transcription corepressor activity / Cyclin D associated events in G1 / disordered domain specific binding / heterochromatin formation / cellular response to xenobiotic stimulus / single-stranded DNA binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Replication of the SARS-CoV-2 genome / double-stranded DNA binding / neuron apoptotic process / DNA-binding transcription factor binding / spermatogenesis / symbiont-mediated perturbation of host ubiquitin-like protein modification / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / Ras protein signal transduction / cell differentiation / DNA replication / regulation of cell cycle / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / DnaJ domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Cyclin-like / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Cyclin A; domain 1 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large T antigen / Retinoblastoma-associated protein
Similarity search - Component
Biological speciesSimian virus 40
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKim, H.Y. / Cho, Y.
CitationJournal: EMBO J. / Year: 2001
Title: Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen.
Authors: Kim, H.Y. / Ahn, B.Y. / Cho, Y.
History
DepositionNov 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity.src_method / _struct_ref_seq.ref_id
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large T antigen
B: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)52,4632
Polymers52,4632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.130, 127.130, 96.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Large T antigen / LT-AG


Mass: 13436.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Plasmid: PET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P03070, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Retinoblastoma-associated protein / p105-Rb / pRb / Rb / pp110


Mass: 39026.504 Da / Num. of mol.: 1 / Fragment: UNP residues 379-577 and 645-772
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P06400

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.79 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlRb pocket1drop
230 mg/mlT antigen1drop
325 mMTris-HCl1drop
4150 mM1dropNaCl
55 mMdithiothreitol1droppH7.5
64-6 %PEG60001reservoir
770 mMpotassium phosphate1reservoir
810 mMdithiothreitol1reservoirpH7.2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→99 Å / Num. obs: 12666 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.106 / Net I/σ(I): 15.9
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.369 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 50139
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUX

1gux


Resolution: 3.2→19.92 Å / Rfactor Rfree error: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.314 630 5 %RANDOM
Rwork0.248 ---
obs0.248 12171 96 %-
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 0 0 3627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.445 104 5.5 %
Rwork0.377 1778 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.2 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.44
LS refinement shell
*PLUS
Rfactor Rfree: 0.445 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.377

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