[English] 日本語
Yorodumi
- PDB-5e0u: Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e0u
TitleHuman PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
Components
  • Cyclin-dependent kinase inhibitor 1
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication / sliding clamp
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / mitotic telomere maintenance via semi-conservative replication ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / mitotic telomere maintenance via semi-conservative replication / : / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / regulation of cell cycle G1/S phase transition / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / tissue regeneration / Transcriptional regulation by RUNX2 / Processive synthesis on the lagging strand / PCNA complex / negative regulation of phosphorylation / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / cyclin-dependent protein serine/threonine kinase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / negative regulation of DNA biosynthetic process / Removal of the Flap Intermediate from the C-strand / response to arsenic-containing substance / replisome / positive regulation of programmed cell death / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / response to L-glutamate / stress-induced premature senescence / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / response to corticosterone / cellular response to UV-B / molecular function inhibitor activity / DNA polymerase processivity factor activity / G1/S-Specific Transcription / STAT5 activation downstream of FLT3 ITD mutants / leading strand elongation / protein kinase inhibitor activity / response to dexamethasone / replication fork processing / p53-Dependent G1 DNA Damage Response / nuclear replication fork / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / SUMOylation of DNA replication proteins / keratinocyte proliferation / response to X-ray / replicative senescence / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of protein kinase activity / response to hyperoxia / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / mismatch repair / translesion synthesis / Cyclin E associated events during G1/S transition / response to cadmium ion / DNA polymerase binding / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of B cell proliferation / keratinocyte differentiation / : / epithelial cell differentiation / protein sequestering activity / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of DNA repair / cellular response to amino acid starvation / Translesion synthesis by REV1 / intrinsic apoptotic signaling pathway / Translesion synthesis by POLK / cyclin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of protein phosphorylation
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. ...Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDuffy, C.M. / Hilbert, B.J. / Kelch, B.A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.
Authors: Duffy, C.M. / Hilbert, B.J. / Kelch, B.A.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1
E: Cyclin-dependent kinase inhibitor 1
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)95,1136
Polymers95,1136
Non-polymers00
Water12,629701
1
A: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-11 kcal/mol
Surface area13430 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
E: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area13310 Å2
MethodPISA
3
C: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-10 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.295, 143.295, 41.402
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein Proliferating cell nuclear antigen / PCNA / Cyclin


Mass: 28821.830 Da / Num. of mol.: 3 / Mutation: S228I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P12004
#2: Protein/peptide Cyclin-dependent kinase inhibitor 1 / CDK-interacting protein 1 / Melanoma differentiation-associated protein 6 / MDA-6 / p21


Mass: 2882.376 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P38936
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→34.44 Å / Num. obs: 71746 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/av σ(I): 14 / Net I/σ(I): 20.7
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.96 / % possible all: 98.65

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXC

1axc


Resolution: 1.93→34.439 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2211 2002 2.79 %
Rwork0.1623 --
obs0.1699 71743 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→34.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 0 701 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166471
X-RAY DIFFRACTIONf_angle_d1.5928728
X-RAY DIFFRACTIONf_dihedral_angle_d14.972431
X-RAY DIFFRACTIONf_chiral_restr0.0691024
X-RAY DIFFRACTIONf_plane_restr0.0081116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.97630.26131420.29025012X-RAY DIFFRACTION97
1.9763-2.02970.24421420.25124928X-RAY DIFFRACTION97
2.0297-2.08950.30711480.25334985X-RAY DIFFRACTION97
2.0895-2.15690.28011440.2374988X-RAY DIFFRACTION97
2.1569-2.23390.27721440.2324966X-RAY DIFFRACTION97
2.2339-2.32330.30411420.22974970X-RAY DIFFRACTION97
2.3233-2.4290.25741440.22725027X-RAY DIFFRACTION97
2.429-2.5570.22541480.21314928X-RAY DIFFRACTION97
2.557-2.71710.23181420.19974991X-RAY DIFFRACTION97
2.7171-2.92670.23571420.18775006X-RAY DIFFRACTION97
2.9267-3.22090.22471460.16674964X-RAY DIFFRACTION97
3.2209-3.68610.21241420.13714955X-RAY DIFFRACTION97
3.6861-4.64080.20531400.10854965X-RAY DIFFRACTION97
4.6408-28.47290.17611360.11974957X-RAY DIFFRACTION97

+
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://pdbjlvh1.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