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- PDB-2r7g: Structure of the retinoblastoma protein pocket domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 2r7g
TitleStructure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1 domain
Components
  • Early E1A 32 kDa protein
  • Retinoblastoma-associated protein
KeywordsTRANSCRIPTION REPRESSOR / CELL CYCLE / Retinoblastoma protein / E1A / E2F displacement
Function / homology
Function and homology information


regulation by virus of viral protein levels in host cell / 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 ...regulation by virus of viral protein levels in host cell / 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 macrophage differentiation / positive regulation of mitotic metaphase/anaphase transition / molecular sequestering activity / positive regulation of protein sumoylation / 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 / regulation of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / 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 / negative regulation of cell growth / PML body / 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 / regulation of protein localization / disordered domain specific binding / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 / symbiont-mediated suppression of host gene expression / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ubiquitin protein ligase binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription
Similarity search - Function
Adenovirus early E1A protein / Early E1A protein / 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 ...Adenovirus early E1A protein / Early E1A protein / 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
Early E1A protein / Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.671 Å
AuthorsLiu, X. / Marmorstein, R.
CitationJournal: Genes Dev. / Year: 2007
Title: Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a tumor suppressor
Authors: Liu, X. / Marmorstein, R.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoblastoma-associated protein
B: Early E1A 32 kDa protein
C: Retinoblastoma-associated protein
D: Early E1A 32 kDa protein
E: Early E1A 32 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2447
Polymers85,0525
Non-polymers1922
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.713, 57.706, 92.268
Angle α, β, γ (deg.)94.340, 92.690, 105.790
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Retinoblastoma-associated protein / PP110 / P105-RB / RB


Mass: 40728.309 Da / Num. of mol.: 2 / Fragment: Pocket domain, deletion of residues 582-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Plasmid: pGex4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06400
#2: Protein/peptide Early E1A 32 kDa protein


Mass: 1198.344 Da / Num. of mol.: 3 / Fragment: CR1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / Strain: type 5 / Plasmid: pGex4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03255
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 15mM magnesium acetate tetrahydrate, 50mM sodium cacodylate trihydrate, pH 6.0 and 1.7M ammonium sulfate, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.671→50 Å / Num. all: 121240 / Num. obs: 121240 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.035 / Χ2: 1.078 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.671-1.731.70.39274851.025156.7
1.73-1.82.10.335113531.052185.8
1.8-1.882.50.262124921.081195.2
1.88-1.982.60.176127381.099196.5
1.98-2.12.60.105127281.096196.9
2.1-2.272.60.072127641.095197.2
2.27-2.492.70.05129401.08197.5
2.49-2.862.70.038128211.095197.8
2.86-3.62.70.027129631.085198.2
3.6-502.60.021129561.02198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.99 Å40.84 Å
Translation1.99 Å40.84 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.671→40.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.237 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21823 11573 10 %RANDOM
Rwork0.19532 ---
all0.19759 115475 --
obs0.19759 115475 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.01 Å20.09 Å2
2--0.32 Å20.37 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.671→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 10 482 6267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225955
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9738025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6315699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80823.858269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.904151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1951536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024326
X-RAY DIFFRACTIONr_nbd_refined0.2120.23281
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2552
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.28
X-RAY DIFFRACTIONr_mcbond_it0.861.53646
X-RAY DIFFRACTIONr_mcangle_it1.40525766
X-RAY DIFFRACTIONr_scbond_it2.20632594
X-RAY DIFFRACTIONr_scangle_it3.3324.52259
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 403 -
Rwork0.271 3627 -
all-4030 -
obs--81.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.853-0.0569-0.09790.67260.04031.22050.03880.16430.0659-0.2048-0.02120.09060.0317-0.1991-0.0176-0.0437-0.0009-0.0189-0.04480.0263-0.03990.10550.25930.6307
27.8664-3.2532-0.48443.4987-1.24129.66750.2488-0.08470.0306-0.30150.0190.19530.4032-0.4823-0.2678-0.0571-0.0373-0.0242-0.06120.0015-0.0494-6.631-5.242714.1492
30.9331-0.0566-0.09790.8510.00491.1186-0.0003-0.29-0.10180.15230.0133-0.0890.16750.0427-0.0131-0.0549-0.0015-0.0258-0.02910.0283-0.041417.9239-13.643632.4229
45.7954-4.43470.88946.03180.591210.40350.0633-0.4209-0.12320.0020.1471-0.04270.5732-0.1259-0.2103-0.0344-0.0408-0.0084-0.06860.0379-0.055914.7209-21.460718.9919
511.74155.5691-3.006213.8033-0.242828.1912-0.02110.58920.07460.55350.2573-0.41850.95770.0877-0.23620.00030.0001-0.00030.00020.000202.1919-13.0292-30.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA380 - 7851 - 345
2X-RAY DIFFRACTION2BB40 - 491 - 10
3X-RAY DIFFRACTION3CC380 - 7851 - 345
4X-RAY DIFFRACTION4DD40 - 491 - 10
5X-RAY DIFFRACTION5EE40 - 481 - 9

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