[English] 日本語
Yorodumi
- PDB-4yoo: p107 pocket domain in complex with LIN52 P29A peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yoo
Titlep107 pocket domain in complex with LIN52 P29A peptide
Components
  • LIN52 peptide
  • Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
KeywordsTRANSCRIPTION / Cyclin Box Pocket Protein Transcriptional Regulator Cell Cycle
Function / homology
Function and homology information


DRM complex / regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / Cyclin E associated events during G1/S transition ...DRM complex / regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cell cycle / Cyclin D associated events in G1 / chromatin organization / transcription regulator complex / cell differentiation / negative regulation of gene expression / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Protein LIN52 / Retinal tissue protein / 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 ...Protein LIN52 / Retinal tissue protein / 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-like protein 1 / Protein lin-52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuiley, K.Z. / Liban, T.J. / Felthousen, J.G. / Ramanan, P. / Tripathi, S. / Litovchick, L. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA132685 United States
CitationJournal: Genes Dev. / Year: 2015
Title: Structural mechanisms of DREAM complex assembly and regulation.
Authors: Guiley, K.Z. / Liban, T.J. / Felthousen, J.G. / Ramanan, P. / Litovchick, L. / Rubin, S.M.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
X: LIN52 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7816
Polymers45,3972
Non-polymers3844
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-60 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.815, 100.530, 142.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Retinoblastoma-like protein 1,Retinoblastoma-like protein 1 / 107 kDa retinoblastoma-associated protein / p107 / pRb1


Mass: 43037.766 Da / Num. of mol.: 1 / Fragment: unp residues 391-600,unp residues 781-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P28749
#2: Protein/peptide LIN52 peptide


Mass: 2359.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q52LA3*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density meas: 2.4 Mg/m3 / Density % sol: 58.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG 400 4%, 1.6M ammonium sulfate / PH range: 6.5 - 7

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.4→71.4 Å / Num. all: 21397 / Num. obs: 21369 / % possible obs: 99.3 % / Redundancy: 5.2 % / Net I/σ(I): 6.6

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
SCALAdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→71.395 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 2189 10.25 %
Rwork0.1954 --
obs0.2002 21350 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→71.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 20 128 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053011
X-RAY DIFFRACTIONf_angle_d1.0914074
X-RAY DIFFRACTIONf_dihedral_angle_d14.5641110
X-RAY DIFFRACTIONf_chiral_restr0.047461
X-RAY DIFFRACTIONf_plane_restr0.004507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3958-2.44790.34621230.26621126X-RAY DIFFRACTION95
2.4479-2.50490.31331480.25671212X-RAY DIFFRACTION100
2.5049-2.56750.28281410.24721158X-RAY DIFFRACTION100
2.5675-2.6370.3221500.24511170X-RAY DIFFRACTION100
2.637-2.71460.27591220.22851206X-RAY DIFFRACTION100
2.7146-2.80220.31881130.23921211X-RAY DIFFRACTION100
2.8022-2.90230.3131510.22161171X-RAY DIFFRACTION99
2.9023-3.01850.26361290.22611185X-RAY DIFFRACTION99
3.0185-3.15590.26951210.19971228X-RAY DIFFRACTION99
3.1559-3.32230.25351340.20531200X-RAY DIFFRACTION99
3.3223-3.53050.22811250.1881198X-RAY DIFFRACTION99
3.5305-3.8030.2321300.18011212X-RAY DIFFRACTION99
3.803-4.18570.1811520.16531199X-RAY DIFFRACTION99
4.1857-4.79130.18381500.15151176X-RAY DIFFRACTION98
4.7913-6.0360.25821530.17931214X-RAY DIFFRACTION99
6.036-71.42670.22051470.18741295X-RAY DIFFRACTION99
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)
15.3762-1.23271.43113.2583-0.1652.11990.1930.12830.3527-0.1141-0.1494-0.1616-0.0153-0.0656-0.03150.3024-0.07170.0520.22070.05440.274130.947122.055-5.973
21.8917-0.60790.15262.9589-1.08030.951-0.131-0.17330.14930.37760.1088-0.2157-0.16620.00350.02190.246-0.0116-0.00190.2168-0.04610.242626.255112.8786.466
33.42970.2103-0.77212.2828-0.4734.3854-0.0529-0.7813-0.00160.76950.10930.2998-0.2314-0.4218-0.02850.56940.06440.15970.4575-0.00820.27814.092105.72425.773
46.8859-2.77490.61562.0362-1.06012.83230.1735-0.13270.29780.57310.01450.8516-0.089-0.38180.08940.64550.12210.27361.22850.14850.7717-2.195105.48826.728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 389:485 )A389 - 485
2X-RAY DIFFRACTION2( CHAIN A AND RESID 486:593 )A486 - 593
3X-RAY DIFFRACTION3( CHAIN A AND RESID 784:965 )A784 - 965
4X-RAY DIFFRACTION4( CHAIN X AND RESID 1:14 )X1 - 14

+
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://pdbjlc1.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