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- PDB-1n4m: Structure of Rb tumor suppressor bound to the transactivation dom... -

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Basic information

Entry
Database: PDB / ID: 1n4m
TitleStructure of Rb tumor suppressor bound to the transactivation domain of E2F-2
Components
  • Retinoblastoma Pocket
  • Transcription factor E2F2
KeywordsCELL CYCLE / PROTEIN-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 / lens fiber cell apoptotic process / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / 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 / lens fiber cell apoptotic process / 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 / CDC6 association with the ORC:origin complex / negative regulation of sprouting angiogenesis / sister chromatid biorientation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / chromatin => GO:0000785 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of macrophage differentiation / glial cell apoptotic process / tissue homeostasis / 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 / Replication of the SARS-CoV-1 genome / myoblast differentiation / 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 / 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 / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / chromosome organization / glial cell proliferation / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / Nuclear events stimulated by ALK signaling in cancer / heterochromatin formation / Cyclin E associated events during G1/S transition / negative regulation of smoothened signaling pathway / 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 / transcription initiation at RNA polymerase II promoter / 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 DNA-binding transcription factor activity / negative regulation of cell growth / PML body / kinase binding / negative regulation of inflammatory response / spindle / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / transcription corepressor activity / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / neuron projection development / sequence-specific double-stranded DNA binding / disordered domain specific binding / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / Ras protein signal transduction / molecular adaptor activity / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / chromatin remodeling / cell cycle
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 E2F2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, C. / Chang, J.H. / Lee, H.S. / Cho, Y.
CitationJournal: GENES DEV. / Year: 2002
Title: Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor
Authors: Lee, C. / Chang, J.H. / Lee, H.S. / Cho, Y.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: Retinoblastoma Pocket
B: Retinoblastoma Pocket
C: Transcription factor E2F2
D: Transcription factor E2F2
E: Transcription factor E2F2


Theoretical massNumber of molelcules
Total (without water)86,7355
Polymers86,7355
Non-polymers00
Water4,702261
1
A: Retinoblastoma Pocket
C: Transcription factor E2F2


Theoretical massNumber of molelcules
Total (without water)42,3602
Polymers42,3602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-10 kcal/mol
Surface area16870 Å2
MethodPISA
2
B: Retinoblastoma Pocket
D: Transcription factor E2F2
E: Transcription factor E2F2


Theoretical massNumber of molelcules
Total (without water)44,3753
Polymers44,3753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-18 kcal/mol
Surface area17560 Å2
MethodPISA
3
E: Transcription factor E2F2

A: Retinoblastoma Pocket
C: Transcription factor E2F2


Theoretical massNumber of molelcules
Total (without water)44,3753
Polymers44,3753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_644x+1,y-1,z-11
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-17 kcal/mol
Surface area17500 Å2
MethodPISA
4
B: Retinoblastoma Pocket
D: Transcription factor E2F2


Theoretical massNumber of molelcules
Total (without water)42,3602
Polymers42,3602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.369, 65.164, 69.339
Angle α, β, γ (deg.)85.55, 79.48, 67.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Retinoblastoma Pocket


Mass: 40344.926 Da / Num. of mol.: 2 / Fragment: Residues 380-785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P06400*PLUS
#2: Protein/peptide Transcription factor E2F2 / E2F-2


Mass: 2015.094 Da / Num. of mol.: 3 / Fragment: Residues 410-427 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo Sapiens (human).
References: UniProt: Q14209
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMTris-HCl1droppH7.5
3200 mM1dropNaCl
45 mMdithiothreitol1drop
51.5 Mammonium sulfate1reservoir
6100 mMsodium citrate1reservoirpH5.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37599 / Observed criterion σ(I): 1 / Biso Wilson estimate: 4.8 Å2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 86.3 % / Num. measured all: 93798 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 70.3 % / Rmerge(I) obs: 0.237

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 369771.74 / Data cutoff high rms absF: 369771.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1867 5 %RANDOM
Rwork0.222 ---
all0.222 ---
obs0.222 37466 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9332 Å2 / ksol: 0.390844 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.31 Å2-1.02 Å23.57 Å2
2---0.86 Å20.77 Å2
3----3.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 0 261 6249
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 262 5.2 %
Rwork0.288 4759 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.328 / Rfactor Rwork: 0.287

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