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- PDB-4ell: Structure of the inactive retinoblastoma protein pocket domain -

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Basic information

Entry
Database: PDB / ID: 4ell
TitleStructure of the inactive retinoblastoma protein pocket domain
ComponentsRetinoblastoma-associated protein
KeywordsCELL CYCLE / CYCLIN FOLD / TUMOR SUPPRESSOR
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 / negative regulation of cell growth / negative regulation of DNA-binding transcription factor activity / G1/S transition of mitotic cell cycle / 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 / 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: 1.98 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 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)95,3502
Polymers95,3502
Non-polymers00
Water6,395355
1
A: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)47,6751
Polymers47,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)47,6751
Polymers47,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)249.659, 249.659, 35.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 47674.980 Da / Num. of mol.: 2 / Fragment: POCKET DOMAIN, UNP residues 380-787 / Mutation: S608E, L561F
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.: 355 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM sodium citrate, 1mM LiCl, 18% PEG 8K., pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.0971 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0971 Å / Relative weight: 1
ReflectionResolution: 1.98→47.18 Å / Num. all: 57167 / Num. obs: 57109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.98→2.08 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→36.035 Å / SU ML: 0.24 / σ(F): 2.01 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 1993 3.49 %RANDOM
Rwork0.1928 ---
obs0.1943 57103 99.89 %-
all-57103 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.954 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3237 Å2-0 Å2-0 Å2
2--1.3237 Å20 Å2
3----2.6474 Å2
Refinement stepCycle: LAST / Resolution: 1.98→36.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 0 355 5961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085721
X-RAY DIFFRACTIONf_angle_d0.9967706
X-RAY DIFFRACTIONf_dihedral_angle_d15.0412172
X-RAY DIFFRACTIONf_chiral_restr0.065864
X-RAY DIFFRACTIONf_plane_restr0.004960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02540.3341430.26473924X-RAY DIFFRACTION100
2.0254-2.08020.27291440.23733960X-RAY DIFFRACTION100
2.0802-2.14140.26211400.20953905X-RAY DIFFRACTION100
2.1414-2.21050.26311470.2133977X-RAY DIFFRACTION100
2.2105-2.28950.36431420.27683937X-RAY DIFFRACTION100
2.2895-2.38110.24671440.20993950X-RAY DIFFRACTION100
2.3811-2.48950.24821350.19073954X-RAY DIFFRACTION100
2.4895-2.62070.24931410.19273888X-RAY DIFFRACTION100
2.6207-2.78480.24691450.19263958X-RAY DIFFRACTION100
2.7848-2.99980.23781450.1943938X-RAY DIFFRACTION100
2.9998-3.30140.24181420.19283930X-RAY DIFFRACTION100
3.3014-3.77870.20641450.17733950X-RAY DIFFRACTION100
3.7787-4.75910.19451400.15623928X-RAY DIFFRACTION100
4.7591-36.0350.22881400.18943911X-RAY DIFFRACTION99

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