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- PDB-1o9k: Crystal structure of the retinoblastoma tumour suppressor protein... -

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Basic information

Entry
Database: PDB / ID: 1o9k
TitleCrystal structure of the retinoblastoma tumour suppressor protein bound to E2F peptide
Components
  • (RETINOBLASTOMA-ASSOCIATED PROTEIN) x 2
  • TRANSCRIPTION FACTOR E2F1
KeywordsAPOPTOSIS / TUMOUR SUPPRESSOR / CELL CYCLE REGULATION / DNA-BINDING
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / negative regulation of fat cell proliferation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / lens fiber cell apoptotic process / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / chromatin lock complex ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / negative regulation of fat cell proliferation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / lens fiber cell apoptotic process / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / chromatin lock complex / cell morphogenesis involved in neuron differentiation / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / negative regulation of DNA binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of extracellular matrix organization / : / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / glial cell apoptotic process / positive regulation of macrophage differentiation / negative regulation of hepatocyte apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / neuron maturation / cellular response to fatty acid / mRNA stabilization / myoblast differentiation / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / anoikis / digestive tract development / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / Activation of PUMA and translocation to mitochondria / negative regulation of cold-induced thermogenesis / SWI/SNF complex / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / DNA-binding transcription activator activity / nuclear chromosome / hepatocyte apoptotic process / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of fat cell differentiation / G2 Phase / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / G1/S-Specific Transcription / RUNX2 regulates osteoblast differentiation / Transcriptional Regulation by E2F6 / forebrain development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / negative regulation of apoptotic signaling pathway / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / chondrocyte differentiation / chromosome organization / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of DNA-binding transcription factor activity / glial cell proliferation / Cyclin E associated events during G1/S transition / negative regulation of protein kinase activity / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / cis-regulatory region sequence-specific DNA binding / striated muscle cell differentiation / regulation of mitotic cell cycle / DNA damage checkpoint signaling / Condensation of Prophase Chromosomes / epithelial cell proliferation / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphoprotein binding / G1/S transition of mitotic cell cycle / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of cell growth / cellular response to nerve growth factor stimulus / PML body / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / negative regulation of inflammatory response / kinase binding / RNA polymerase II transcription regulator complex / spindle / cellular response to xenobiotic stimulus / cellular response to insulin stimulus / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / neuron projection development / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / disordered domain specific binding / Cyclin D associated events in G1 / transcription corepressor activity
Similarity search - Function
E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box ...E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein / Transcription factor E2F1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXiao, B. / Spencer, J. / Clements, A. / Ali-Khan, N. / Mittnacht, S. / Broceno, C. / Burghammer, M. / Perrakis, A. / Marmorstein, R. / Gamblin, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of the Retinoblastoma Tumor Suppressor Protein Bound to E2F and the Molecular Basis of its Regulation
Authors: Xiao, B. / Spencer, J. / Clements, A. / Ali-Khan, N. / Mittnacht, S. / Broceno, C. / Burghammer, M. / Perrakis, A. / Marmorstein, R. / Gamblin, S.J.
History
DepositionDec 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: RETINOBLASTOMA-ASSOCIATED PROTEIN
D: RETINOBLASTOMA-ASSOCIATED PROTEIN
E: RETINOBLASTOMA-ASSOCIATED PROTEIN
F: RETINOBLASTOMA-ASSOCIATED PROTEIN
G: RETINOBLASTOMA-ASSOCIATED PROTEIN
H: RETINOBLASTOMA-ASSOCIATED PROTEIN
P: TRANSCRIPTION FACTOR E2F1
Q: TRANSCRIPTION FACTOR E2F1
R: TRANSCRIPTION FACTOR E2F1
S: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)181,97512
Polymers181,97512
Non-polymers00
Water4,504250
1
A: RETINOBLASTOMA-ASSOCIATED PROTEIN
B: RETINOBLASTOMA-ASSOCIATED PROTEIN
P: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)45,4943
Polymers45,4943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-21.6 kcal/mol
Surface area17940 Å2
MethodPISA
2
C: RETINOBLASTOMA-ASSOCIATED PROTEIN
D: RETINOBLASTOMA-ASSOCIATED PROTEIN
Q: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)45,4943
Polymers45,4943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-20.2 kcal/mol
Surface area17770 Å2
MethodPISA
3
E: RETINOBLASTOMA-ASSOCIATED PROTEIN
F: RETINOBLASTOMA-ASSOCIATED PROTEIN
R: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)45,4943
Polymers45,4943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-21.6 kcal/mol
Surface area17500 Å2
MethodPISA
4
G: RETINOBLASTOMA-ASSOCIATED PROTEIN
H: RETINOBLASTOMA-ASSOCIATED PROTEIN
S: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)45,4943
Polymers45,4943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-21.3 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.996, 158.548, 110.617
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2014-

HOH

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Components

#1: Protein
RETINOBLASTOMA-ASSOCIATED PROTEIN / P105-RB / PRB


Mass: 25100.910 Da / Num. of mol.: 4 / Fragment: DOMAIN A, RESIDUES 372-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06400
#2: Protein
RETINOBLASTOMA-ASSOCIATED PROTEIN / P105-RB / PRB


Mass: 18265.477 Da / Num. of mol.: 4 / Fragment: DOMAIN B, RESIDUES 636-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06400
#3: Protein/peptide
TRANSCRIPTION FACTOR E2F1 / PBR3 / PRB-BINDING PROTEIN E2F-1 / RETINOBLASTOMA-ASSOCIATED PROTEIN 1


Mass: 2127.269 Da / Num. of mol.: 4 / Fragment: RESIDUES 409-426 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01094
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRETINOBLASTOMA-ASSOCIATED PROTEIN: REGULATOR OF OTHER GENES. ACTS AS A TUMOR SUPPRESSOR. INTERACTS ...RETINOBLASTOMA-ASSOCIATED PROTEIN: REGULATOR OF OTHER GENES. ACTS AS A TUMOR SUPPRESSOR. INTERACTS PREFERENTIALLY WITH TRANSCRIPTION FACTOR E2F1 TRANSCRIPTION FACTOR E2F1: TRANSCRIPTION ACTIVATOR THAT BINDS DNA COOPERATIVELY. FOUND IN THE PROMOTER REGION OF A NUMBER OF GENES WHOSE PRODUCTS ARE INVOLVED IN CELL CYCLE REGULATION OR IN DNA REPLICATION.
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growpH: 7.8 / Details: pH 7.80
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.14 Msodium citrate1reservoir
326 %PEG4001reservoir
44 %n-propanol1reservoir
50.1 MTris1reservoirpH7.8

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 53846 / % possible obs: 88.1 % / Redundancy: 8.8 % / Rsym value: 0.094 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.69 Å
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUX

1gux


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.823 / SU B: 13.486 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2386 5 %RANDOM
Rwork0.229 ---
obs0.232 44963 88.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20.47 Å2
2---0.56 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11724 0 0 250 11974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211956
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.96516096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.50231408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.414152391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.36227
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5609
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.3177
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6590.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.57092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.341211520
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1292.54864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.88834576
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 175
Rwork0.249 3219
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)
1-0.01380.00460.00320.2532-0.0086-0.00240.00020.00090.0195-0.00080.0070.0011-0.00080.0024-0.00730.0047-0.00010.00010.004700.004516.0485.64324.223
20.0435-0.066-0.01810.85970.01350.0217-0.00640.0062-0.0005-0.0036-0.0042-0.0065-0.0043-0.00830.01070.00430.00080.00080.0040.00020.005344.361-7.4214.97
30.1021-0.07750.10330.00960.0920.02940.0138-0.00790.030.01140.0016-0.01990.0042-0.0146-0.01530.005-0.000100.004700.004634.916117.8224.25
40.2437-0.01610.00160.2485-0.16330.1673-0.0035-0.00640.03050.00030.00120.0269-0.0181-0.03220.00220.00290.0011-0.00040.0049-0.00040.00556.626130.91714.949
50.16980.0026-0.0130.0523-0.01770.0046-0.01330.01520.02730.00050.00190.0098-0.01080.00650.01140.00480.00010.00010.004700.004522.237111.46594.235
60.42430.09610.09610.3858-0.28990.4705-0.00480.04080.0522-0.0448-0.01390.0203-0.04-0.00160.01860.00430.0004-0.00050.00280.0020.003527.31125.55364.979
70.17930.0610.13880.01790.0850.0047-0.00070.0156-0.0034-0.00770.0107-0.00970.01080.0046-0.010.00540.000100.004600.004465.48391.23594.168
80.41750.03060.02440.27320.10710.33830.02370.0688-0.0237-0.034-0.0043-0.03090.0489-0.0013-0.01930.00560.00050.0010.0076-0.00510.003860.42477.17364.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A379 - 578
2X-RAY DIFFRACTION2B644 - 787
3X-RAY DIFFRACTION2P409 - 426
4X-RAY DIFFRACTION3C379 - 578
5X-RAY DIFFRACTION4D644 - 787
6X-RAY DIFFRACTION4Q409 - 426
7X-RAY DIFFRACTION5E379 - 578
8X-RAY DIFFRACTION6F644 - 787
9X-RAY DIFFRACTION6R409 - 426
10X-RAY DIFFRACTION7G379 - 578
11X-RAY DIFFRACTION8H - G644 - 787
12X-RAY DIFFRACTION8S409 - 426
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.368

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