[English] 日本語
Yorodumi
- PDB-2r7g: Structure of the retinoblastoma protein pocket domain in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r7g
TitleStructure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1 domain
Components
  • Early E1A 32 kDa protein
  • Retinoblastoma-associated protein
KeywordsTRANSCRIPTION REPRESSOR / CELL CYCLE / Retinoblastoma protein / E1A / E2F displacement
Function / homology
Function and homology information


regulation by virus of viral protein levels in host cell / Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / cell morphogenesis involved in neuron differentiation / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / chromatin lock complex / Positive Regulation of CDH1 Gene Transcription / maintenance of mitotic sister chromatid cohesion ...regulation by virus of viral protein levels in host cell / Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / cell morphogenesis involved in neuron differentiation / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / chromatin lock complex / Positive Regulation of CDH1 Gene Transcription / maintenance of mitotic sister chromatid cohesion / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / positive regulation of extracellular matrix organization / negative regulation of hepatocyte apoptotic process / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / myoblast differentiation / positive regulation of protein sumoylation / protein localization to chromosome, centromeric region / importin-alpha family protein binding / positive regulation of mitotic metaphase/anaphase transition / chondrocyte differentiation / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / SWI/SNF complex / negative regulation of cold-induced thermogenesis / negative regulation of G1/S transition of mitotic cell cycle / chromosome organization / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of cell cycle / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RUNX2 regulates osteoblast differentiation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / molecular sequestering activity / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of protein kinase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 inflammatory response / negative regulation of cell growth / 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 / neuron projection development / kinase binding / disordered domain specific binding / Cyclin D associated events in G1 / transcription corepressor activity / cellular response to insulin stimulus / regulation of protein localization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / heterochromatin formation / Replication of the SARS-CoV-2 genome / spermatogenesis / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / regulation of cell cycle / Ras protein signal transduction / symbiont-mediated suppression of host innate immune response / chromatin remodeling / apoptotic process / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / host cell nucleus / chromatin / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenovirus early E1A protein / Early E1A protein / 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 / Rb C-terminal domain ...Adenovirus early E1A protein / Early E1A protein / 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 / Rb C-terminal 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
Early E1A protein / Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.671 Å
AuthorsLiu, X. / Marmorstein, R.
CitationJournal: Genes Dev. / Year: 2007
Title: Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a tumor suppressor
Authors: Liu, X. / Marmorstein, R.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoblastoma-associated protein
B: Early E1A 32 kDa protein
C: Retinoblastoma-associated protein
D: Early E1A 32 kDa protein
E: Early E1A 32 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2447
Polymers85,0525
Non-polymers1922
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.713, 57.706, 92.268
Angle α, β, γ (deg.)94.340, 92.690, 105.790
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Retinoblastoma-associated protein / PP110 / P105-RB / RB


Mass: 40728.309 Da / Num. of mol.: 2 / Fragment: Pocket domain, deletion of residues 582-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Plasmid: pGex4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#2: Protein/peptide Early E1A 32 kDa protein


Mass: 1198.344 Da / Num. of mol.: 3 / Fragment: CR1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / Strain: type 5 / Plasmid: pGex4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03255
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 15mM magnesium acetate tetrahydrate, 50mM sodium cacodylate trihydrate, pH 6.0 and 1.7M ammonium sulfate, VAPOR DIFFUSION, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.671→50 Å / Num. all: 121240 / Num. obs: 121240 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.035 / Χ2: 1.078 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.671-1.731.70.39274851.025156.7
1.73-1.82.10.335113531.052185.8
1.8-1.882.50.262124921.081195.2
1.88-1.982.60.176127381.099196.5
1.98-2.12.60.105127281.096196.9
2.1-2.272.60.072127641.095197.2
2.27-2.492.70.05129401.08197.5
2.49-2.862.70.038128211.095197.8
2.86-3.62.70.027129631.085198.2
3.6-502.60.021129561.02198.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.99 Å40.84 Å
Translation1.99 Å40.84 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.671→40.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.237 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21823 11573 10 %RANDOM
Rwork0.19532 ---
all0.19759 115475 --
obs0.19759 115475 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.01 Å20.09 Å2
2--0.32 Å20.37 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.671→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 10 482 6267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225955
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9738025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6315699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80823.858269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.904151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1951536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024326
X-RAY DIFFRACTIONr_nbd_refined0.2120.23281
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2552
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.28
X-RAY DIFFRACTIONr_mcbond_it0.861.53646
X-RAY DIFFRACTIONr_mcangle_it1.40525766
X-RAY DIFFRACTIONr_scbond_it2.20632594
X-RAY DIFFRACTIONr_scangle_it3.3324.52259
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 403 -
Rwork0.271 3627 -
all-4030 -
obs--81.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.853-0.0569-0.09790.67260.04031.22050.03880.16430.0659-0.2048-0.02120.09060.0317-0.1991-0.0176-0.0437-0.0009-0.0189-0.04480.0263-0.03990.10550.25930.6307
27.8664-3.2532-0.48443.4987-1.24129.66750.2488-0.08470.0306-0.30150.0190.19530.4032-0.4823-0.2678-0.0571-0.0373-0.0242-0.06120.0015-0.0494-6.631-5.242714.1492
30.9331-0.0566-0.09790.8510.00491.1186-0.0003-0.29-0.10180.15230.0133-0.0890.16750.0427-0.0131-0.0549-0.0015-0.0258-0.02910.0283-0.041417.9239-13.643632.4229
45.7954-4.43470.88946.03180.591210.40350.0633-0.4209-0.12320.0020.1471-0.04270.5732-0.1259-0.2103-0.0344-0.0408-0.0084-0.06860.0379-0.055914.7209-21.460718.9919
511.74155.5691-3.006213.8033-0.242828.1912-0.02110.58920.07460.55350.2573-0.41850.95770.0877-0.23620.00030.0001-0.00030.00020.000202.1919-13.0292-30.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA380 - 7851 - 345
2X-RAY DIFFRACTION2BB40 - 491 - 10
3X-RAY DIFFRACTION3CC380 - 7851 - 345
4X-RAY DIFFRACTION4DD40 - 491 - 10
5X-RAY DIFFRACTION5EE40 - 481 - 9

+
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