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- PDB-1ad6: DOMAIN A OF HUMAN RETINOBLASTOMA TUMOR SUPPRESSOR -

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Basic information

Entry
Database: PDB / ID: 1ad6
TitleDOMAIN A OF HUMAN RETINOBLASTOMA TUMOR SUPPRESSOR
ComponentsRETINOBLASTOMA TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION REGULATION / TUMOR SUPPRESSOR / DNA-BINDING
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 / negative regulation of myofibroblast differentiation / regulation of lipid kinase activity / 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 / negative regulation of myofibroblast differentiation / regulation of lipid kinase activity / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / positive regulation of extracellular matrix organization / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / 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 / neuron maturation / positive regulation of transcription regulatory region DNA binding / digestive tract development / aortic valve morphogenesis / SWI/SNF complex / myoblast differentiation / negative regulation of cold-induced thermogenesis / Replication of the SARS-CoV-1 genome / smoothened signaling pathway / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / 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 / negative regulation of smoothened signaling pathway / heterochromatin formation / 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 / negative regulation of DNA-binding transcription factor activity / Oncogene Induced Senescence / PML body / negative regulation of cell growth / spindle / negative regulation of inflammatory response / kinase binding / cellular response to insulin stimulus / neuron projection development / transcription corepressor activity / 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 / MIR / Resolution: 2.3 Å
AuthorsKim, H.Y. / Cho, Y.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structural similarity between the pocket region of retinoblastoma tumour suppressor and the cyclin-box.
Authors: Kim, H.Y. / Cho, Y.
History
DepositionFeb 21, 1997Processing site: BNL
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINOBLASTOMA TUMOR SUPPRESSOR


Theoretical massNumber of molelcules
Total (without water)21,3361
Polymers21,3361
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.600, 68.040, 80.830
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 TUMOR SUPPRESSOR


Mass: 21335.744 Da / Num. of mol.: 1 / Fragment: DOMAIN A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9925 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 9 / % possible all: 96.8

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Processing

Software
NameVersionClassification
MLPHAREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 2 / Stereochemistry target values: TNT PROTGEO / Details: INITIALLY X-PLOR, FINAL FEW CYCLES TNT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -10 %EVERY 10TH REFLECTION
Rwork0.201 ---
obs-8744 94 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 0 76 1567
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01215141
X-RAY DIFFRACTIONt_angle_deg1.7720301
X-RAY DIFFRACTIONt_dihedral_angle_d22.99290
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012421
X-RAY DIFFRACTIONt_gen_planes0.0112135
X-RAY DIFFRACTIONt_it2.612061
X-RAY DIFFRACTIONt_nbd0.068393

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