[English] 日本語
Yorodumi
- PDB-1ad6: DOMAIN A OF HUMAN RETINOBLASTOMA TUMOR SUPPRESSOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ad6
TitleDOMAIN A OF HUMAN RETINOBLASTOMA TUMOR SUPPRESSOR
ComponentsRETINOBLASTOMA TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION REGULATION / TUMOR SUPPRESSOR / DNA-BINDING
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / cell morphogenesis involved in neuron differentiation / Positive Regulation of CDH1 Gene Transcription / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding ...Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / cell morphogenesis involved in neuron differentiation / Positive Regulation of CDH1 Gene Transcription / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / positive regulation of extracellular matrix organization / Aberrant regulation of mitotic exit in cancer due to RB1 defects / negative regulation of hepatocyte apoptotic process / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / protein localization to chromosome, centromeric region / importin-alpha family protein binding / myoblast differentiation / positive regulation of mitotic metaphase/anaphase transition / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / SWI/SNF complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of G1/S transition of mitotic cell cycle / 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) / negative regulation of cell cycle / chondrocyte differentiation / negative regulation of apoptotic signaling pathway / chromosome organization / Cyclin E associated events during G1/S transition / negative regulation of protein kinase activity / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphoprotein binding / negative regulation of cell growth / negative regulation of inflammatory response / PML body / Oncogene Induced Senescence / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / spindle / kinase binding / neuron projection development / cellular response to insulin stimulus / disordered domain specific binding / Cyclin D associated events in G1 / transcription corepressor activity / heterochromatin formation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Replication of the SARS-CoV-2 genome / DNA-binding transcription factor binding / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / cell differentiation / regulation of cell cycle / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / Cyclin-like / Cyclin A; domain 1 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsKim, H.Y. / Cho, Y.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structural similarity between the pocket region of retinoblastoma tumour suppressor and the cyclin-box.
Authors: Kim, H.Y. / Cho, Y.
History
DepositionFeb 21, 1997Processing site: BNL
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RETINOBLASTOMA TUMOR SUPPRESSOR


Theoretical massNumber of molelcules
Total (without water)21,3361
Polymers21,3361
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.600, 68.040, 80.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RETINOBLASTOMA TUMOR SUPPRESSOR


Mass: 21335.744 Da / Num. of mol.: 1 / Fragment: DOMAIN A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 6 / Details: pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9925 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 9 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
MLPHAREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 2 / Stereochemistry target values: TNT PROTGEO / Details: INITIALLY X-PLOR, FINAL FEW CYCLES TNT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -10 %EVERY 10TH REFLECTION
Rwork0.201 ---
obs-8744 94 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 0 76 1567
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01215141
X-RAY DIFFRACTIONt_angle_deg1.7720301
X-RAY DIFFRACTIONt_dihedral_angle_d22.99290
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012421
X-RAY DIFFRACTIONt_gen_planes0.0112135
X-RAY DIFFRACTIONt_it2.612061
X-RAY DIFFRACTIONt_nbd0.068393

+
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