[English] 日本語
Yorodumi
- PDB-3n5u: Crystal structure of an Rb C-terminal peptide bound to the cataly... -

+
Open data


ID or keywords:

Loading...

-
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 / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / chromatin lock complex / regulation of glycogen catabolic process / Positive Regulation of CDH1 Gene Transcription ...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 / maintenance of mitotic sister chromatid cohesion / negative regulation of myofibroblast differentiation / chromatin lock complex / regulation of glycogen catabolic process / Positive Regulation of CDH1 Gene Transcription / cell morphogenesis involved in neuron differentiation / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / positive regulation of extracellular matrix organization / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cadherin binding involved in cell-cell adhesion / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / glial cell apoptotic process / regulation of translational initiation in response to stress / protein phosphatase 1 binding / positive regulation of macrophage differentiation / negative regulation of hepatocyte apoptotic process / protein localization to chromosome, centromeric region / tissue homeostasis / importin-alpha family protein binding / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / myoblast differentiation / positive regulation of mitotic metaphase/anaphase transition / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / digestive tract development / regulation of canonical Wnt signaling pathway / negative regulation of cold-induced thermogenesis / protein dephosphorylation / negative regulation of glial cell proliferation / SWI/SNF complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / smoothened signaling pathway / glycogen metabolic process / branching morphogenesis of an epithelial tube / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / Triglyceride catabolism / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / entrainment of circadian clock by photoperiod / hepatocyte apoptotic process / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / protein serine/threonine phosphatase activity / telomere maintenance in response to DNA damage / phosphatase activity / Maturation of hRSV A proteins / negative regulation of cell cycle / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / negative regulation of apoptotic signaling pathway / skeletal muscle cell differentiation / DARPP-32 events / positive regulation of glycogen biosynthetic process / chromosome organization / chondrocyte differentiation / ribonucleoprotein complex binding / negative regulation of protein kinase activity / Cyclin E associated events during G1/S transition / glial cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / Nuclear events stimulated by ALK signaling in cancer / phosphoprotein phosphatase activity / lung development / epithelial cell proliferation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / Downregulation of TGF-beta receptor signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / adherens junction / positive regulation of transcription elongation by RNA polymerase II / centriole / sperm end piece / phosphoprotein binding / G1/S transition of mitotic cell cycle / negative regulation of cell growth / regulation of circadian rhythm / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / PML body / Oncogene Induced Senescence / response to lead ion / negative regulation of inflammatory response / cellular response to xenobiotic stimulus / spindle
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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 (eV)
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)

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more