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- PDB-4yos: p107 pocket domain complexed with LIN52 peptide -

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Basic information

Entry
Database: PDB / ID: 4yos
Titlep107 pocket domain complexed with LIN52 peptide
Components
  • Protein lin-52 homolog
  • Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
KeywordsTRANSCRIPTION / Cyclin Box Pocket Transcriptional Regulator DREAM
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 / G0 and Early G1 / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / regulation of cell division / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest ...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 / G0 and Early G1 / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / regulation of cell division / negative regulation of cellular senescence / 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 / regulation of cell cycle / negative regulation of gene expression / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Retinoblastoma-like protein 1 / 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-like protein 1 / 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 / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-like protein 1 / Retinoblastoma-like protein 1 / Protein lin-52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Myotis davidii (bat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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
E: Protein lin-52 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8648
Polymers45,4232
Non-polymers4406
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-28 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.430, 101.060, 140.685
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 781-969,unp residues 391-600,unp residues 781-969
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Myotis davidii (bat)
Gene: RBL1, MDA_GLEAN10022721 / Production host: Escherichia coli (E. coli) / References: UniProt: P28749, UniProt: L5LUA8
#2: Protein/peptide Protein lin-52 homolog


Mass: 2385.518 Da / Num. of mol.: 1 / Fragment: unp residues 15-34 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: Q5ZJQ3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
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: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→60.5 Å / Num. all: 24252 / Num. obs: 24232 / % possible obs: 99.5 % / Redundancy: 6.6 % / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
SCALAdata scaling
Aimlessdata scaling
RefinementResolution: 2.3→60.449 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 2469 10.19 %
Rwork0.1989 --
obs0.2033 24229 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→60.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 26 95 2970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052927
X-RAY DIFFRACTIONf_angle_d0.923954
X-RAY DIFFRACTIONf_dihedral_angle_d13.8131076
X-RAY DIFFRACTIONf_chiral_restr0.037450
X-RAY DIFFRACTIONf_plane_restr0.004494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2959-2.34010.3011250.27611146X-RAY DIFFRACTION95
2.3401-2.38790.29391320.26741167X-RAY DIFFRACTION99
2.3879-2.43980.29421190.25171217X-RAY DIFFRACTION99
2.4398-2.49660.29961400.23971182X-RAY DIFFRACTION100
2.4966-2.5590.31881550.23821183X-RAY DIFFRACTION100
2.559-2.62820.27491240.22161213X-RAY DIFFRACTION99
2.6282-2.70550.26831350.22051199X-RAY DIFFRACTION99
2.7055-2.79280.27961480.21221176X-RAY DIFFRACTION100
2.7928-2.89270.28781240.21481220X-RAY DIFFRACTION100
2.8927-3.00850.27291320.21011217X-RAY DIFFRACTION99
3.0085-3.14540.2741400.2071206X-RAY DIFFRACTION100
3.1454-3.31120.25411400.21121197X-RAY DIFFRACTION100
3.3112-3.51860.26681530.20971208X-RAY DIFFRACTION100
3.5186-3.79030.25051420.18061210X-RAY DIFFRACTION100
3.7903-4.17160.2161400.16731230X-RAY DIFFRACTION100
4.1716-4.77510.16381470.15551222X-RAY DIFFRACTION100
4.7751-6.01520.22171160.18331272X-RAY DIFFRACTION100
6.0152-60.46960.22051570.19661295X-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)
14.9572-0.44810.37773.0114-0.43071.5477-0.00160.17060.1483-0.09320.0672-0.076-0.0398-0.0283-0.07460.2886-0.04730.02850.23930.00520.300732.5187121.285-4.8547
22.0065-1.22780.62244.1211-0.77571.7676-0.3297-0.6168-0.03971.23910.45830.3195-0.1688-0.2162-0.04970.55720.1130.14190.44330.00630.249420.8617110.205417.7878
34.76640.46010.31884.8097-1.40062.587-0.1869-0.6513-0.24831.05940.65651.1589-0.4231-0.8372-0.48680.71180.22390.37290.77890.26750.81169.9836103.588522.9645
41.03650.42771.14040.23770.33811.27750.1411-1.2241-0.0582-0.24090.07290.38120.1019-0.52030.12350.85240.1380.32351.34010.24821.3916-2.6619107.297324.4199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 389:512 )A389 - 512
2X-RAY DIFFRACTION2( CHAIN A AND RESID 513:869 )A513 - 869
3X-RAY DIFFRACTION3( CHAIN A AND RESID 870:950 )A870 - 950
4X-RAY DIFFRACTION4( CHAIN E AND RESID 1:13 )E1 - 13

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