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- PDB-3n5u: Crystal structure of an Rb C-terminal peptide bound to the cataly... -

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Basic information

Entry
Database: PDB / ID: 3n5u
TitleCrystal structure of an Rb C-terminal peptide bound to the catalytic subunit of PP1
Components
  • Retinoblastoma-associated protein
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / TRANSCRIPTION REGULATION / Retinoblastoma / pRb / Rb / protein phosphatase-1 / PP1 / phosphatase
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 centromere complex assembly / 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 / regulation of centromere complex assembly / 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 / regulation of glycogen catabolic process / sister chromatid biorientation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of mitotic metaphase/anaphase transition / positive regulation of macrophage differentiation / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / tissue homeostasis / glial cell apoptotic process / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / neuron maturation / digestive tract development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / aortic valve morphogenesis / regulation of canonical Wnt signaling pathway / SWI/SNF complex / myoblast differentiation / regulation of translational initiation / Replication of the SARS-CoV-1 genome / negative regulation of cold-induced thermogenesis / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / myosin phosphatase activity / protein serine/threonine phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / entrainment of circadian clock by photoperiod / Triglyceride catabolism / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / phosphatase activity / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / phosphoprotein phosphatase activity / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / DARPP-32 events / chromosome organization / glial cell proliferation / chondrocyte differentiation / heterochromatin formation / negative regulation of smoothened signaling pathway / ribonucleoprotein complex binding / Cyclin E associated events during G1/S transition / dephosphorylation / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / Condensation of Prophase Chromosomes / epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphoprotein binding / response to lead ion / adherens junction / lung development / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / circadian regulation of gene expression / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of circadian rhythm / Oncogene Induced Senescence / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body / spindle / kinase binding / negative regulation of inflammatory response / cellular response to insulin stimulus / transcription corepressor activity / Cyclin D associated events in G1 / neuron projection development / negative regulation of epithelial cell proliferation / disordered domain specific binding / Circadian Clock
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 / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Retinoblastoma-associated protein / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsHirschi, A.M. / Cecchini, M. / Steinhardt, R.C. / Dick, F.A. / Rubin, S.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein.
Authors: Hirschi, A. / Cecchini, M. / Steinhardt, R.C. / Schamber, M.R. / Dick, F.A. / Rubin, S.M.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Retinoblastoma-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5669
Polymers70,2763
Non-polymers2916
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Retinoblastoma-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0515
Polymers35,9052
Non-polymers1453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-44 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.946, 92.946, 192.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 7 - 300 / Label seq-ID: 7 - 300

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 7:300 )AA
2chain B and (resseq 7:300 )BB

NCS oper: (Code: given
Matrix: (-0.386983, 0.921948, -0.016028), (0.921479, 0.386038, -0.043035), (-0.033489, -0.031423, -0.998945)
Vector: 65.742104, -42.630001, 43.0872)

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Components

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34370.359 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1A, PPP1CA / Plasmid: pFLAG-CTS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide Retinoblastoma-associated protein / pRb / Rb / pp110 / p105-Rb


Mass: 1534.842 Da / Num. of mol.: 1 / Fragment: UNP residues 870-882 / Source method: obtained synthetically / Details: synthetic 13-mer peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P06400
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 100mM HEPES, 200mM MgCl2, 18% PEG 4000, pH 7.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2009
RadiationMonochromator: ASSYMETRIC CURVED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→83 Å / Num. obs: 13588

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→83 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.45 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1358 9.99 %
Rwork0.221 --
obs0.225 13588 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.556 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 156.86 Å2 / Biso mean: 53.969 Å2 / Biso min: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1-16.062 Å20 Å2-0 Å2
2--16.062 Å20 Å2
3----32.123 Å2
Refinement stepCycle: LAST / Resolution: 3.2→83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 6 0 4798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044900
X-RAY DIFFRACTIONf_angle_d0.7896616
X-RAY DIFFRACTIONf_chiral_restr0.058709
X-RAY DIFFRACTIONf_plane_restr0.003863
X-RAY DIFFRACTIONf_dihedral_angle_d14.9181809
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2364X-RAY DIFFRACTIONPOSITIONAL0.015
12B2364X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.3140.3121230.2751073119685
3.314-3.4470.2971320.2581153128590
3.447-3.6040.2741370.2441131126891
3.604-3.7940.2821280.2461210133893
3.794-4.0320.2831340.2231218135293
4.032-4.3430.2371570.1991207136495
4.343-4.780.2451360.1951251138796
4.78-5.4720.2491260.2131286141295
5.472-6.8930.2831450.2221288143396
6.893-83.7190.2041400.1941413155397

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