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- PDB-1gux: RB POCKET BOUND TO E7 LXCXE MOTIF -

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Basic information

Entry
Database: PDB / ID: 1gux
TitleRB POCKET BOUND TO E7 LXCXE MOTIF
Components
  • (RETINOBLASTOMA PROTEIN) x 2
  • ONCOPROTEINOncogene
KeywordsCOMPLEX (TRANSCRIPTION REG/PEPTIDE) / COMPLEX (TRANSCRIPTION REGULATION-PEPTIDE) / TUMOR SUPPRESSOR PROTEIN / RETINOBLASTOMA / COMPLEX (TRANSCRIPTION REG-PEPTIDE) COMPLEX
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)
Human papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLee, J.O. / Russo, A.A. / Pavletich, N.P.
CitationJournal: Nature / Year: 1998
Title: Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7.
Authors: Lee, J.O. / Russo, A.A. / Pavletich, N.P.
History
DepositionNov 15, 1997Processing site: BNL
Revision 1.0Dec 2, 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINOBLASTOMA PROTEIN
B: RETINOBLASTOMA PROTEIN
E: ONCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)44,5273
Polymers44,5273
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-17 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.500, 76.800, 64.000
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RETINOBLASTOMA PROTEIN /


Mass: 25100.910 Da / Num. of mol.: 1 / Fragment: POCKET DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#2: Protein RETINOBLASTOMA PROTEIN /


Mass: 18265.477 Da / Num. of mol.: 1 / Fragment: POCKET DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#3: Protein/peptide ONCOPROTEIN / Oncogene


Mass: 1160.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE NINE RESIDUES OF PAPILLOMA VIRUS E7 PEPTIDE CONTAIN THE LXCXE MOTIF
Source: (natural) Human papillomavirus / Strain: E7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growpH: 7.5
Details: 3.5 M SODIUM FORMATE, 0.1M NA HEPES PH 7.5, 20 MIROMOLAR CDCL2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 Msodium formate1reservoir
20.02 M1reservoirCdCl2
30.1 MHEPES-Na1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jul 7, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. obs: 45533 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 2.98 % / Rsym value: 0.048 / Net I/σ(I): 25.1
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 1.98 % / Mean I/σ(I) obs: 5.93 / Rsym value: 0.211 / % possible all: 84.3
Reflection
*PLUS
Num. measured all: 135820 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.211

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.289 1945 4.6 %
Rwork0.218 --
obs0.218 39098 93 %
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 0 389 3102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.618
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.634
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.325 189 3.63 %
Rwork0.324 3666 -
obs--74.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.634
LS refinement shell
*PLUS
Rfactor obs: 0.324

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