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- PDB-4elj: Crystal structure of the inactive retinoblastoma protein phosphor... -

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Basic information

Entry
Database: PDB / ID: 4elj
TitleCrystal structure of the inactive retinoblastoma protein phosphorylated at T373
ComponentsRetinoblastoma-associated protein
KeywordsCELL CYCLE / CYCLIN FOLD / TUMOR SUPPRESSOR PROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of macrophage differentiation / tissue homeostasis / glial cell apoptotic process / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / neuron maturation / digestive tract development / aortic valve morphogenesis / myoblast differentiation / Replication of the SARS-CoV-1 genome / SWI/SNF complex / negative regulation of cold-induced thermogenesis / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / hepatocyte apoptotic process / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / Nuclear events stimulated by ALK signaling in cancer / chondrocyte differentiation / heterochromatin formation / negative regulation of smoothened signaling pathway / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / negative regulation of cell growth / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / negative regulation of inflammatory response / spindle / cellular response to insulin stimulus / transcription corepressor activity / Cyclin D associated events in G1 / neuron projection development / negative regulation of epithelial cell proliferation / disordered domain specific binding / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / neuron apoptotic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / transcription by RNA polymerase II / molecular adaptor activity / cell differentiation / regulation of cell cycle / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
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 / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBurke, J.R. / Rubin, S.M.
CitationJournal: Genes Dev. / Year: 2012
Title: Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control.
Authors: Burke, J.R. / Hura, G.L. / Rubin, S.M.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)76,3671
Polymers76,3671
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 129.510, 135.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retinoblastoma-associated protein / p105-Rb / pRb / Rb / pp110


Mass: 76367.305 Da / Num. of mol.: 1 / Fragment: UNP residues 53-244, 268-582, 642-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06400
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM HEPES, 100mM Ammonium Fluoride, 16% PEG4K, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→58.39 Å / Num. all: 24399 / Num. obs: 23387 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / % possible all: 90

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→58.39 Å / SU ML: 0.45 / σ(F): 1.35 / σ(I): 2.3 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1984 8.5 %RANDOM
Rwork0.212 ---
obs0.2165 23354 91.06 %-
all-25338 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.663 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-33.6071 Å20 Å2-0 Å2
2---12.3261 Å20 Å2
3----21.281 Å2
Refinement stepCycle: LAST / Resolution: 2.7→58.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 0 57 4908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044940
X-RAY DIFFRACTIONf_angle_d0.876655
X-RAY DIFFRACTIONf_dihedral_angle_d15.7151867
X-RAY DIFFRACTIONf_chiral_restr0.065767
X-RAY DIFFRACTIONf_plane_restr0.003820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76760.45271300.36281460X-RAY DIFFRACTION89
2.7676-2.84240.42631380.32031468X-RAY DIFFRACTION89
2.8424-2.9260.36681340.31251481X-RAY DIFFRACTION90
2.926-3.02050.32481410.26991484X-RAY DIFFRACTION89
3.0205-3.12840.34321440.2411486X-RAY DIFFRACTION91
3.1284-3.25370.28451350.23611513X-RAY DIFFRACTION91
3.2537-3.40170.28621510.22621543X-RAY DIFFRACTION93
3.4017-3.5810.30161390.21641541X-RAY DIFFRACTION93
3.581-3.80540.27151490.21581556X-RAY DIFFRACTION93
3.8054-4.09910.24741420.19741557X-RAY DIFFRACTION93
4.0991-4.51150.21761410.16171572X-RAY DIFFRACTION93
4.5115-5.1640.19131460.1591571X-RAY DIFFRACTION91
5.164-6.50470.29031460.22971553X-RAY DIFFRACTION91
6.5047-58.390.18931480.17321585X-RAY DIFFRACTION87

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