[English] 日本語
Yorodumi
- PDB-6cbi: PCNA in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cbi
TitlePCNA in complex with inhibitor
Components
  • GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
  • Proliferating cell nuclear antigen
KeywordsCELL CYCLE / PCNA / sliding clamp / proliferating cell nuclear antigen
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of phosphorylation / intestinal epithelial cell maturation / tissue regeneration / positive regulation of deoxyribonuclease activity ...cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of phosphorylation / intestinal epithelial cell maturation / tissue regeneration / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / regulation of cell cycle G1/S phase transition / import into nucleus / Transcriptional regulation by RUNX2 / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / negative regulation of DNA biosynthetic process / Processive synthesis on the lagging strand / cyclin-dependent protein serine/threonine kinase inhibitor activity / PCNA complex / response to arsenic-containing substance / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / positive regulation of programmed cell death / Transcriptional activation of cell cycle inhibitor p21 / oncogene-induced cell senescence / replisome / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / : / stress-induced premature senescence / response to corticosterone / molecular function inhibitor activity / response to L-glutamate / cellular response to UV-B / regulation of cyclin-dependent protein serine/threonine kinase activity / response to aldosterone / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / STAT5 activation downstream of FLT3 ITD mutants / p53-Dependent G1 DNA Damage Response / DNA polymerase processivity factor activity / protein kinase inhibitor activity / G1/S-Specific Transcription / leading strand elongation / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / mitotic G2 DNA damage checkpoint signaling / replication fork processing / response to dexamethasone / regulation of G1/S transition of mitotic cell cycle / negative regulation of vascular associated smooth muscle cell proliferation / nuclear replication fork / SUMOylation of DNA replication proteins / keratinocyte proliferation / replicative senescence / positive regulation of protein kinase activity / response to X-ray / PCNA-Dependent Long Patch Base Excision Repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to hyperoxia / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / animal organ regeneration / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / mismatch repair / translesion synthesis / Cyclin E associated events during G1/S transition / negative regulation of protein phosphorylation / : / response to cadmium ion / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein serine/threonine kinase binding / estrous cycle / DNA polymerase binding / keratinocyte differentiation / base-excision repair, gap-filling / regulation of G2/M transition of mitotic cell cycle / positive regulation of B cell proliferation / epithelial cell differentiation / Signaling by FLT3 fusion proteins / protein sequestering activity / cyclin binding / positive regulation of DNA repair / intrinsic apoptotic signaling pathway / cellular response to amino acid starvation / negative regulation of protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1
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: 2.75 Å
AuthorsBruning, J.B. / Wegener, K.L.
CitationJournal: Chemistry / Year: 2018
Title: Rational Design of a 310-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp.
Authors: Wegener, K.L. / McGrath, A.E. / Dixon, N.E. / Oakley, A.J. / Scanlon, D.B. / Abell, A.D. / Bruning, J.B.
History
DepositionFeb 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
H: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
I: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
J: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
K: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,17112
Polymers179,97910
Non-polymers1922
Water3,819212
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
H: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
I: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
K: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS


Theoretical massNumber of molelcules
Total (without water)91,7906
Polymers91,7906
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-45 kcal/mol
Surface area33880 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
J: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3806
Polymers88,1884
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-56 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.260, 144.820, 174.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 28795.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12004
#2: Protein/peptide
GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS


Mass: 1801.061 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: peptide mimetic with covalent lactam bridge between DAB and Glu side chains
Source: (synth.) Homo sapiens (human) / References: UniProt: P38936*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 2M ammonium sulfate 0.1M Tris pH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 8, 2015 / Details: mirror
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→46.68 Å / Num. obs: 47028 / % possible obs: 91 % / Redundancy: 3.6 % / Biso Wilson estimate: 57.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.108 / Rrim(I) all: 0.225 / Net I/σ(I): 4.8 / Num. measured all: 171431 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.843.51.89938910.2061.0762.281.9
11-46.684.30.0487880.9940.0250.05590.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementResolution: 2.75→41.086 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2328 4.96 %
Rwork0.2082 --
obs0.2104 46931 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→41.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11682 0 10 212 11904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611893
X-RAY DIFFRACTIONf_angle_d1.01116059
X-RAY DIFFRACTIONf_dihedral_angle_d13.797331
X-RAY DIFFRACTIONf_chiral_restr0.0521909
X-RAY DIFFRACTIONf_plane_restr0.0092038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80620.35771120.34212322X-RAY DIFFRACTION80
2.8062-2.86720.39751280.32672338X-RAY DIFFRACTION81
2.8672-2.93380.38071320.32522353X-RAY DIFFRACTION82
2.9338-3.00720.34451210.31212369X-RAY DIFFRACTION82
3.0072-3.08850.38251440.2992419X-RAY DIFFRACTION85
3.0885-3.17930.33981350.29222494X-RAY DIFFRACTION87
3.1793-3.28190.33441540.2672565X-RAY DIFFRACTION89
3.2819-3.39910.32671220.24072667X-RAY DIFFRACTION91
3.3991-3.53520.28631380.22282673X-RAY DIFFRACTION92
3.5352-3.6960.2411470.21232705X-RAY DIFFRACTION94
3.696-3.89070.22931470.19842763X-RAY DIFFRACTION94
3.8907-4.13420.23241280.18442799X-RAY DIFFRACTION95
4.1342-4.45310.19921400.16362797X-RAY DIFFRACTION95
4.4531-4.90060.19681400.13932831X-RAY DIFFRACTION96
4.9006-5.60820.19151490.15732826X-RAY DIFFRACTION96
5.6082-7.05990.22431400.21472845X-RAY DIFFRACTION95
7.0599-41.09040.21991510.19662837X-RAY DIFFRACTION91

+
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