[English] 日本語
Yorodumi
- PDB-1gh6: RETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gh6
TitleRETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN
Components
  • Large T antigenLarge tumor 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 / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of centromere complex assembly / negative regulation of myofibroblast differentiation / regulation of lipid kinase activity / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of centromere complex assembly / negative regulation of myofibroblast differentiation / regulation of lipid kinase activity / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / positive regulation of extracellular matrix organization / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of mitotic metaphase/anaphase transition / positive regulation of macrophage differentiation / tissue homeostasis / glial cell apoptotic process / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / bidirectional double-stranded viral DNA replication / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / neuron maturation / positive regulation of transcription regulatory region DNA binding / viral DNA genome replication / digestive tract development / aortic valve morphogenesis / SWI/SNF complex / myoblast differentiation / negative regulation of cold-induced thermogenesis / Replication of the SARS-CoV-1 genome / smoothened signaling pathway / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / DNA unwinding involved in DNA replication / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / DNA replication origin binding / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / chondrocyte differentiation / negative regulation of smoothened signaling pathway / heterochromatin formation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / helicase activity / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of DNA-binding transcription factor activity / Oncogene Induced Senescence / PML body / negative regulation of cell growth / spindle / negative regulation of inflammatory response / kinase binding / cellular response to insulin stimulus / neuron projection development / transcription corepressor activity / Cyclin D associated events in G1 / disordered domain specific binding / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / single-stranded DNA binding / Replication of the SARS-CoV-2 genome / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / spermatogenesis / neuron apoptotic process / DNA-binding transcription factor binding / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / molecular adaptor activity / regulation of cell cycle / hydrolase activity / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus
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 / 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 / DnaJ domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,4632
Polymers52,4632
Non-polymers00
Water0
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

-
Components

#1: Protein Large T antigen / Large tumor 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: PolyomavirusPolyomaviridae / 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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more