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- PDB-3pom: Crystal Structure of the Unliganded Retinoblastoma Protein Pocket... -

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Basic information

Entry
Database: PDB / ID: 3pom
TitleCrystal Structure of the Unliganded Retinoblastoma Protein Pocket Domain
ComponentsRetinoblastoma-associated protein
KeywordsCELL CYCLE / Cyclin Fold / Tumor Suppressor Protein
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 centromere complex assembly / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation ...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 centromere complex assembly / 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 / positive regulation of mitotic metaphase/anaphase transition / 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 / 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 / SWI/SNF complex / myoblast differentiation / negative regulation of cold-induced thermogenesis / Replication of the SARS-CoV-1 genome / 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 / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / 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 / 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 / G1/S transition of mitotic cell cycle / 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 / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body / spindle / kinase binding / negative regulation of inflammatory response / cellular response to insulin stimulus / transcription corepressor activity / neuron projection development / Cyclin D associated events in G1 / disordered domain specific binding / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / neuron apoptotic process / DNA-binding transcription factor binding / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / molecular adaptor activity / 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 / 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-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBalog, E.R.M. / Burke, J.R. / Rubin, S.M.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of the unliganded retinoblastoma protein pocket domain.
Authors: Balog, E.R. / Burke, J.R. / Hura, G.L. / Rubin, S.M.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 999Domain A (residues 380-577) and Domain B (residues 643-787) linked by six residues linker (LEU VAL ...Domain A (residues 380-577) and Domain B (residues 643-787) linked by six residues linker (LEU VAL PRO ARG GLY SER).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoblastoma-associated protein
B: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)82,4282
Polymers82,4282
Non-polymers00
Water3,243180
1
A: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)41,2141
Polymers41,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)41,2141
Polymers41,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.282, 111.164, 138.930
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: 41213.926 Da / Num. of mol.: 2
Fragment: Pocket Domain, Domain A, UNP residues 380-577, Domain B, UNP residues 643-787
Source method: isolated from a genetically manipulated source
Details: Fusion protein of domain A linked to domain B via the linker residues (LVPRGS).
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.: 180 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.6
Details: 100 mM CAPS, 10% PEG 3350, pH 10.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2009
RadiationMonochromator: side scattering I-beam bent Si(111) single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
ReflectionResolution: 2.5→60.3 Å / Num. all: 33106 / Num. obs: 33106 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.5 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7827 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 3152 RANDOM
Rwork0.213 28321 -
all0.213 31473 -
obs0.213 31473 -
Solvent computationBsol: 15.002 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 98.53 Å2 / Biso mean: 16.2997 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-38.785 Å20 Å20 Å2
2--43.557 Å2-0 Å2
3---20.415 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5551 0 0 180 5731
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.4663
X-RAY DIFFRACTIONf_bond_d0.0023
X-RAY DIFFRACTIONf_chiral_restr0.0413
X-RAY DIFFRACTIONf_dihedral_angle_d11.5823
X-RAY DIFFRACTIONf_plane_restr0.0023
X-RAY DIFFRACTIONf_nbd_refined4.063

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