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- PDB-9dhc: The Retinoblastoma Protein with Mutation S751Y -

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Basic information

Entry
Database: PDB / ID: 9dhc
TitleThe Retinoblastoma Protein with Mutation S751Y
ComponentsRetinoblastoma-associated protein
KeywordsCELL CYCLE / Cancer Missense Mutation
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / importin-alpha family protein binding / positive regulation of transcription regulatory region 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 / regulation of centromere complex assembly / positive regulation of macrophage differentiation / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / negative regulation of hepatocyte apoptotic process / neuron maturation / myoblast differentiation / digestive tract development / aortic valve morphogenesis / Replication of the SARS-CoV-1 genome / SWI/SNF complex / negative regulation of cold-induced thermogenesis / 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 / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / skeletal muscle cell differentiation / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / chondrocyte differentiation / glial cell proliferation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / negative regulation of protein kinase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / phosphoprotein binding / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of cell growth / PML body / Oncogene Induced Senescence / spindle / negative regulation of inflammatory response / kinase binding / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / negative regulation of epithelial cell proliferation / neuron projection development / transcription corepressor activity / Cyclin D associated events in G1 / disordered domain specific binding / heterochromatin formation / cellular response to xenobiotic stimulus / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Replication of the SARS-CoV-2 genome / neuron apoptotic process / DNA-binding transcription factor binding / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / Ras protein signal transduction / cell differentiation / regulation of cell cycle / chromatin remodeling / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRuiz-Rivera, A. / Castro, A. / Burke, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5SC3GM135037 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional analysis of cancer-associated missense variants in the retinoblastoma protein pocket domain.
Authors: Castro, A. / Ruiz Rivera, A. / Moorman, C.C. / Wolf-Saxon, E.R. / Mims, H.N. / Vasquez Meza, V.I. / Rangel, M.A. / Loera, M.M. / Bond, I.C. / Buchanan, S.B. / Villarreal, E. / Tripathi, S. / ...Authors: Castro, A. / Ruiz Rivera, A. / Moorman, C.C. / Wolf-Saxon, E.R. / Mims, H.N. / Vasquez Meza, V.I. / Rangel, M.A. / Loera, M.M. / Bond, I.C. / Buchanan, S.B. / Villarreal, E. / Tripathi, S. / Rubin, S.M. / Burke, J.R.
History
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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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


Theoretical massNumber of molelcules
Total (without water)91,2302
Polymers91,2302
Non-polymers00
Water1,40578
1
A: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)255.036, 255.036, 35.358
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Retinoblastoma-associated protein / p105-Rb / p110-RB1 / pRb / Rb / pp110


Mass: 45614.844 Da / Num. of mol.: 2 / Mutation: S751Y, S608E, S612A, S780A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Plasmid: pGEX4T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06400
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 8K, 0.1M sodium citrate, 0.1M succinate pH5.5, 1M lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→48.2 Å / Num. obs: 37129 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 49.63 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 2.32→2.41 Å / Redundancy: 10 % / Num. unique obs: 3923 / CC1/2: 0.302 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→48.2 Å / SU ML: 0.4112 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.1616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 1994 5.37 %
Rwork0.2126 35110 -
obs0.2153 37104 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.89 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 0 78 5793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01525831
X-RAY DIFFRACTIONf_angle_d1.49527853
X-RAY DIFFRACTIONf_chiral_restr0.0705881
X-RAY DIFFRACTIONf_plane_restr0.0101977
X-RAY DIFFRACTIONf_dihedral_angle_d19.24662221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.40781440.36812538X-RAY DIFFRACTION99.89
2.38-2.440.37651410.35092477X-RAY DIFFRACTION99.85
2.44-2.510.36851440.31642559X-RAY DIFFRACTION99.89
2.51-2.60.33261380.30052464X-RAY DIFFRACTION99.96
2.6-2.690.27821470.28172523X-RAY DIFFRACTION99.93
2.69-2.80.28611400.26562476X-RAY DIFFRACTION100
2.8-2.920.3161420.24492525X-RAY DIFFRACTION99.89
2.92-3.080.291440.26092492X-RAY DIFFRACTION100
3.08-3.270.31811440.23982533X-RAY DIFFRACTION100
3.27-3.520.2951400.21362529X-RAY DIFFRACTION99.96
3.52-3.880.23951440.19922487X-RAY DIFFRACTION100
3.88-4.440.21311450.1792511X-RAY DIFFRACTION100
4.44-5.580.211430.16982473X-RAY DIFFRACTION100
5.59-48.20.24051380.16872523X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: 60.9295073086 Å / Origin y: -37.7346039262 Å / Origin z: 9.95360968338 Å
111213212223313233
T0.51348581457 Å2-0.065710536485 Å2-0.0275054895478 Å2-0.344426334878 Å20.0122878107534 Å2--0.431658358115 Å2
L1.1945780388 °2-0.098556600586 °20.084333650261 °2-0.233389833669 °20.0536491116994 °2--0.662207596333 °2
S-0.0532907063943 Å °-0.00243826737025 Å °0.365054465579 Å °0.0827936523934 Å °0.0341381585875 Å °-0.134786671224 Å °-0.299500912602 Å °0.186220255836 Å °0.0156692874034 Å °
Refinement TLS groupSelection details: all

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