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- PDB-5mom: Crystal Structure of PCNA encoding the hypomorphic mutation S228I -

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Basic information

Entry
Database: PDB / ID: 5mom
TitleCrystal Structure of PCNA encoding the hypomorphic mutation S228I
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / PCNA
Function / homology
Function and homology information


positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / Polymerase switching / positive regulation of DNA-directed DNA polymerase activity / Processive synthesis on the lagging strand / MutLalpha complex binding ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / Polymerase switching / positive regulation of DNA-directed DNA polymerase activity / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Telomere C-strand (Lagging Strand) Synthesis / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / replisome / Processive synthesis on the C-strand of the telomere / response to L-glutamate / Removal of the Flap Intermediate from the C-strand / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / estrous cycle / mismatch repair / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / nuclear estrogen receptor binding / replication fork / Translesion synthesis by REV1 / positive regulation of DNA repair / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / male germ cell nucleus / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / cellular response to xenobiotic stimulus / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / chromatin binding / centrosome / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsBiasutto, A.J. / Mancini, E.J. / Green, C.M. / Wilson, R.H.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust099667/Z/12/Z United Kingdom
Medical Research Council (United Kingdom)MR/L006812/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: DNA Repair (Amst.) / Year: 2017
Title: PCNA dependent cellular activities tolerate dramatic perturbations in PCNA client interactions.
Authors: Wilson, R.H. / Biasutto, A.J. / Wang, L. / Fischer, R. / Baple, E.L. / Crosby, A.H. / Mancini, E.J. / Green, C.M.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)85,6463
Polymers85,6463
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.950, 162.950, 140.400
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
11(chain A and (resseq 2:23 or resseq 25:57 or (resid...
21(chain B and (resseq 2:23 or resseq 25:57 or (resid...
31(chain C and (resseq 2:23 or resseq 25:84 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEILEILE(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA2 - 232 - 23
12GLUGLUPHEPHE(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA25 - 5725 - 57
13ASPASPASPASP(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA5858
14METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA1 - 2581 - 258
15METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA1 - 2581 - 258
16METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA1 - 2581 - 258
17METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:57 or (resid...AA1 - 2581 - 258
21PHEPHEILEILE(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB2 - 232 - 23
22GLUGLUPHEPHE(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB25 - 5725 - 57
23ASPASPASPASP(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB5858
24METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB1 - 2561 - 256
25METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB1 - 2561 - 256
26METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB1 - 2561 - 256
27METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:57 or (resid...BB1 - 2561 - 256
31PHEPHEILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC2 - 232 - 23
32GLUGLUASNASN(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC25 - 8425 - 84
33GLUGLUGLUGLU(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC8585
34METMETILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC1 - 2551 - 255
35METMETILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC1 - 2551 - 255
36METMETILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC1 - 2551 - 255
37METMETILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC1 - 2551 - 255
38METMETILEILE(chain C and (resseq 2:23 or resseq 25:84 or (resid...CC1 - 2551 - 255

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Components

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


Mass: 28548.586 Da / Num. of mol.: 3 / Mutation: S228I
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) / Variant (production host): star / References: UniProt: P12004
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 5.44 Å3/Da / Density % sol: 77.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M NaAcO, 2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.27→89.07 Å / Num. obs: 87453 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 48.396 Å2 / Net I/σ(I): 17.7
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.564 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.7 Å89.07 Å
Translation8.7 Å89.07 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYM

1vym


Resolution: 2.27→89.069 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.14
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4470 5.12 %Random Selection
Rwork0.1987 ---
obs0.1996 87369 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.82 Å2 / Biso mean: 62.5271 Å2 / Biso min: 31.41 Å2
Refinement stepCycle: final / Resolution: 2.27→89.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 0 152 5731
Biso mean---58.74 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085654
X-RAY DIFFRACTIONf_angle_d1.1267656
X-RAY DIFFRACTIONf_chiral_restr0.065935
X-RAY DIFFRACTIONf_plane_restr0.007965
X-RAY DIFFRACTIONf_dihedral_angle_d16.0713460
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3043X-RAY DIFFRACTION9.706TORSIONAL
12B3043X-RAY DIFFRACTION9.706TORSIONAL
13C3043X-RAY DIFFRACTION9.706TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.27-2.29580.32491380.307227052843
2.2958-2.32280.34571440.300427382882
2.3228-2.35120.28031310.287427452876
2.3512-2.38090.30791510.272527152866
2.3809-2.41230.3241470.260627212868
2.4123-2.44530.27141500.255227322882
2.4453-2.48020.25371280.251427322860
2.4802-2.51730.31410.235427592900
2.5173-2.55660.27091620.231727172879
2.5566-2.59850.25011480.223727292877
2.5985-2.64330.24291620.222527202882
2.6433-2.69140.23871500.217127492899
2.6914-2.74320.2451470.218427222869
2.7432-2.79920.29461440.231727592903
2.7992-2.860.23931480.242427392887
2.86-2.92660.2771390.226827432882
2.9266-2.99980.27711540.225227532907
2.9998-3.08090.27431350.215827562891
3.0809-3.17150.23681820.218227272909
3.1715-3.27390.21931610.223227292890
3.2739-3.39090.22761390.218427872926
3.3909-3.52670.21351490.200527712920
3.5267-3.68720.22541590.197427572916
3.6872-3.88160.19911300.181727912921
3.8816-4.12480.2031370.172228052942
4.1248-4.44330.16971450.153428052950
4.4433-4.89040.15721770.138427842961
4.8904-5.59790.171330.167828502983
5.5979-7.05240.23851650.218128563021
7.0524-89.13730.18691740.200730033177
Refinement TLS params.Method: refined / Origin x: -8.2864 Å / Origin y: 30.6718 Å / Origin z: -29.7998 Å
111213212223313233
T0.3922 Å2-0.0446 Å2-0.0514 Å2-0.3256 Å2-0.0276 Å2--0.3293 Å2
L1.1978 °2-0.1641 °2-0.0627 °2-0.6863 °2-0.2678 °2--0.6166 °2
S0.028 Å °-0.0593 Å °-0.0289 Å °0.0425 Å °0.0172 Å °-0.0689 Å °0.0231 Å °0.0459 Å °-0.039 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 258
2X-RAY DIFFRACTION1allB1 - 256
3X-RAY DIFFRACTION1allC1 - 255
4X-RAY DIFFRACTION1allS1 - 152

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