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- PDB-4yoo: p107 pocket domain in complex with LIN52 P29A peptide -

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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 / 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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