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- PDB-2qdj: Crystal structure of the Retinoblastoma protein N-domain provides... -

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Basic information

Entry
Database: PDB / ID: 2qdj
TitleCrystal structure of the Retinoblastoma protein N-domain provides insight into tumor suppression, ligand interaction and holoprotein architecture
ComponentsRetinoblastoma-associated protein
KeywordsANTITUMOR PROTEIN / cyclin fold / cyclin wedge
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 / 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 ...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 lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of extracellular matrix organization / positive regulation of transcription regulatory region DNA binding / 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 protein serine/threonine kinase activity / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / neuron maturation / digestive tract development / aortic valve morphogenesis / Replication of the SARS-CoV-1 genome / myoblast differentiation / SWI/SNF complex / negative regulation of cold-induced thermogenesis / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of G1/S transition of mitotic cell cycle / smoothened signaling pathway / 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 / negative regulation of cell cycle / chromosome organization / glial cell proliferation / chondrocyte differentiation / Cyclin E associated events during G1/S transition / Nuclear events stimulated by ALK signaling in cancer / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of smoothened signaling pathway / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphoprotein 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 / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / Oncogene Induced Senescence / PML body / heterochromatin formation / kinase binding / negative regulation of inflammatory response / spindle / cellular response to insulin stimulus / G1/S transition of mitotic cell cycle / negative regulation of epithelial cell proliferation / transcription corepressor activity / Cyclin D associated events in G1 / disordered domain specific binding / neuron projection development / cellular response to xenobiotic stimulus / Replication of the SARS-CoV-2 genome / spermatogenesis / DNA-binding transcription factor binding / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / transcription by RNA polymerase II / molecular adaptor activity / 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
Cyclin A; domain 1 - #140 / Helix Hairpins - #1380 / 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 ...Cyclin A; domain 1 - #140 / Helix Hairpins - #1380 / 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 A; domain 1 / Helix Hairpins / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHassler, M. / Mittnacht, S. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2007
Title: Crystal structure of the retinoblastoma protein N domain provides insight into tumor suppression, ligand interaction, and holoprotein architecture.
Authors: Hassler, M. / Singh, S. / Yue, W.W. / Luczynski, M. / Lakbir, R. / Sanchez-Sanchez, F. / Bader, T. / Pearl, L.H. / Mittnacht, S.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoblastoma-associated protein


Theoretical massNumber of molelcules
Total (without water)35,4281
Polymers35,4281
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.296, 106.649, 98.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-477-

HOH

31A-496-

HOH

41A-589-

HOH

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Components

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


Mass: 35427.969 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 plysS / References: UniProt: P06400
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Na acetate, 25% (w/v) PEG 4000, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→51.1 Å / Num. obs: 25840 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.9 / % possible all: 99.4

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
12.78825.14223.472SE31.22.49
23.81622.5810.711SE46.63.05
329.2335.2437.183SE45.22.52
421.97512.2737.666SE54.42.27
547.64825.07522.441SE602.06
Phasing dmFOM : 0.67 / FOM acentric: 0.68 / FOM centric: 0.59 / Reflection: 9666 / Reflection acentric: 8435 / Reflection centric: 1231
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-14.9860.860.90.77391275116
5-80.740.780.613361098238
4-50.830.850.7416361405231
3.5-40.760.780.6116451456189
3-3.50.620.630.5128772587290
2.8-30.410.420.3317811614167

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Processing

Software
NameVersionClassificationNB
SOLVE2.08phasing
RESOLVE2.08phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→51.1 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27609 1288 5 %RANDOM
Rwork0.22834 ---
obs0.23064 24550 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2→51.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 234 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9772901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7925253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5122594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8915416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.965158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.21170
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21531
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4791.51295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.42122108
X-RAY DIFFRACTIONr_scbond_it3.8663857
X-RAY DIFFRACTIONr_scangle_it5.034.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 97 -
Rwork0.26 1778 -
obs--99 %

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