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- PDB-2aze: Structure of the Rb C-terminal domain bound to an E2F1-DP1 heterodimer -

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Basic information

Entry
Database: PDB / ID: 2aze
TitleStructure of the Rb C-terminal domain bound to an E2F1-DP1 heterodimer
Components
  • Retinoblastoma-associated protein
  • Transcription factor Dp-1
  • Transcription factor E2F1
KeywordsCELL CYCLE / TRANSCRIPTION / coiled coil / beta sandwich
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / cell morphogenesis involved in neuron differentiation / positive regulation of collagen fibril organization / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / Positive Regulation of CDH1 Gene Transcription / negative regulation of DNA binding / negative regulation of fat cell proliferation ...Defective translocation of RB1 mutants to the nucleus / Rb-E2F complex / regulation of lipid kinase activity / cell morphogenesis involved in neuron differentiation / positive regulation of collagen fibril organization / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / Positive Regulation of CDH1 Gene Transcription / negative regulation of DNA binding / negative regulation of fat cell proliferation / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / positive regulation of extracellular matrix organization / negative regulation of hepatocyte apoptotic process / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / myoblast differentiation / protein localization to chromosome, centromeric region / importin-alpha family protein binding / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of glial cell proliferation / positive regulation of mitotic metaphase/anaphase transition / cellular response to fatty acid / chondrocyte differentiation / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / SWI/SNF complex / Activation of PUMA and translocation to mitochondria / negative regulation of cold-induced thermogenesis / negative regulation of fat cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / mRNA stabilization / chromosome organization / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of cell cycle / DNA-binding transcription activator activity / G2 Phase / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / G1/S-Specific Transcription / RUNX2 regulates osteoblast differentiation / nuclear chromosome / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / Transcriptional Regulation by E2F6 / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / cis-regulatory region sequence-specific DNA binding / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / DNA damage checkpoint signaling / regulation of G1/S transition of mitotic cell cycle / Nuclear events stimulated by ALK signaling in cancer / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of fibroblast proliferation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / intrinsic apoptotic signaling pathway in response to DNA damage / RNA polymerase II transcription regulator complex / phosphoprotein binding / cellular response to nerve growth factor stimulus / negative regulation of inflammatory response / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of cell growth / PML body / Oncogene Induced Senescence / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / transcription by RNA polymerase II / Pre-NOTCH Transcription and Translation / spindle / kinase binding / neuron projection development / Transcriptional regulation of granulopoiesis / disordered domain specific binding / sequence-specific double-stranded DNA binding / Cyclin D associated events in G1 / cellular response to insulin stimulus / transcription corepressor activity / response to lipopolysaccharide / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Replication of the SARS-CoV-2 genome / DNA-binding transcription activator activity, RNA polymerase II-specific / heterochromatin formation / spermatogenesis / cellular response to hypoxia / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ras protein signal transduction / regulation of cell cycle / cell differentiation / protein dimerization activity / positive regulation of apoptotic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #540 / Transcription factor DP / Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #540 / Transcription factor DP / Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Helix non-globular / Special / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein / Transcription factor E2F1 / Transcription factor Dp-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsRubin, S.M. / Gall, A.L. / Zheng, N. / Pavletich, N.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structure of the Rb C-terminal domain bound to E2F1-DP1: a mechanism for phosphorylation-induced E2F release.
Authors: Rubin, S.M. / Gall, A.L. / Zheng, N. / Pavletich, N.P.
History
DepositionSep 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor Dp-1
B: Transcription factor E2F1
C: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)34,6163
Polymers34,6163
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-66 kcal/mol
Surface area16800 Å2
MethodPISA
2
A: Transcription factor Dp-1
B: Transcription factor E2F1
C: Retinoblastoma-associated protein

A: Transcription factor Dp-1
B: Transcription factor E2F1
C: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)69,2336
Polymers69,2336
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area20820 Å2
ΔGint-145 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.8, 168.6, 48.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcription factor Dp-1 / E2F dimerization partner 1 / DRTF1-polypeptide-1 / DRTF1


Mass: 17603.086 Da / Num. of mol.: 1
Fragment: coiled coil and marked box domains (residues 199-350)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFDP1, DP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14186
#2: Protein Transcription factor E2F1 / E2F-1 / Retinoblastoma binding protein 3 / RBBP-3 / PRB-binding protein E2F-1 / PBR3 / ...E2F-1 / Retinoblastoma binding protein 3 / RBBP-3 / PRB-binding protein E2F-1 / PBR3 / Retinoblastoma-associated protein 1 / RBAP-1


Mass: 11898.352 Da / Num. of mol.: 1
Fragment: coiled coil and marked box domains (residues 200-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2F1, RBBP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01094
#3: Protein/peptide Retinoblastoma-associated protein / PP110 / P105-RB / RB


Mass: 5114.920 Da / Num. of mol.: 1 / Fragment: C-terminal core domain (residues 829-874)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06400
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium Citrate, Ammonium Sulfate, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9498
SYNCHROTRONNSLS X4A20.97916, 0.97241, 0.97929
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 20, 2005
ADSC QUANTUM 42CCDJan 23, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Insertion DeviceSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.94981
20.979161
30.972411
40.979291
ReflectionResolution: 2.55→20 Å / Num. obs: 19350 / % possible obs: 97.8 % / Rsym value: 0.053
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.55→15 Å / σ(F): 0 / Details: REFMAC was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 872 5.1 %Random
Rwork0.221 ---
obs-17600 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 0 131 2456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.157
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_mcbond_it1.47
X-RAY DIFFRACTIONc_scbond_it2.58
LS refinement shellResolution: 2.55→2.62 Å
RfactorNum. reflection% reflection
Rfree0.284 --
Rwork0.273 1104 -
obs--82.9 %

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