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- PDB-6fcn: Crystal structure of human PCNA soaked with p47phox(106-127) peptide -

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Basic information

Entry
Database: PDB / ID: 6fcn
TitleCrystal structure of human PCNA soaked with p47phox(106-127) peptide
ComponentsProliferating cell nuclear antigen
KeywordsNUCLEAR PROTEIN / Proliferating cell nuclear antigen
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 / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...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 / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / 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 / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / replication fork processing / response to dexamethasone / leading strand elongation / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / nuclear estrogen receptor binding / liver regeneration / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / Resolution: 3.22 Å
AuthorsHousset, D. / Frachet, P.
CitationJournal: J.Exp.Med. / Year: 2019
Title: Cytosolic PCNA interacts with p47phox and controls NADPH oxidase NOX2 activation in neutrophils.
Authors: Ohayon, D. / De Chiara, A. / Dang, P.M. / Thieblemont, N. / Chatfield, S. / Marzaioli, V. / Burgener, S.S. / Mocek, J. / Candalh, C. / Pintard, C. / Tacnet-Delorme, P. / Renault, G. / ...Authors: Ohayon, D. / De Chiara, A. / Dang, P.M. / Thieblemont, N. / Chatfield, S. / Marzaioli, V. / Burgener, S.S. / Mocek, J. / Candalh, C. / Pintard, C. / Tacnet-Delorme, P. / Renault, G. / Lagoutte, I. / Favier, M. / Walker, F. / Hurtado-Nedelec, M. / Desplancq, D. / Weiss, E. / Benarafa, C. / Housset, D. / Marie, J.C. / Frachet, P. / El-Benna, J. / Witko-Sarsat, V.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)93,2953
Polymers93,2953
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.880, 140.670, 171.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12A
22C
32E
13A
23C
33E
14A
24C
34E
15A
25C
35E

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA3 - 9224 - 113
21GLUGLUALAALACB3 - 9224 - 113
31GLUGLUALAALAEC3 - 9224 - 113
12ALAALAALAALAAA96 - 105117 - 126
22ALAALAALAALACB96 - 105117 - 126
32ALAALAALAALAEC96 - 105117 - 126
13LYSLYSLEULEUAA110 - 121131 - 142
23LYSLYSLEULEUCB110 - 121131 - 142
33LYSLYSLEULEUEC110 - 121131 - 142
14GLUGLUTHRTHRAA132 - 185153 - 206
24GLUGLUTHRTHRCB132 - 185153 - 206
34GLUGLUTHRTHREC132 - 185153 - 206
15GLUGLUILEILEAA192 - 255213 - 276
25GLUGLUILEILECB192 - 255213 - 276
35GLUGLUILEILEEC192 - 255213 - 276

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.982072, 0.140338, 0.12586), (-0.043213, -0.482282, 0.87495), (0.183488, -0.864702, -0.467571)2.52553, 18.48782, -32.57957
3given(0.984523, -0.054899, 0.166436), (0.11589, -0.508471, -0.853245), (0.13147, 0.859327, -0.494239)3.80108, -19.64861, -32.58945
4given(1), (1), (1)
5given(0.973509, 0.16468, 0.158623), (-0.091943, -0.353235, 0.931005), (0.209349, -0.920926, -0.328736)2.45214, 15.85979, -28.70097
6given(0.984806, 0.029343, 0.171162), (0.169473, -0.377484, -0.910376), (0.037897, 0.925551, -0.376721)5.20913, -17.24378, -31.61068
7given(1), (1), (1)
8given(0.979602, 0.158824, 0.123108), (-0.037067, -0.459304, 0.887506), (0.197501, -0.873965, -0.444048)1.993, 17.90472, -32.09895
9given(0.977287, -0.076373, 0.197679), (0.125668, -0.542239, -0.830773), (0.170638, 0.836746, -0.520326)3.27276, -20.35778, -33.49889
10given(1), (1), (1)
11given(0.983994, 0.132479, 0.119184), (-0.036206, -0.506241, 0.861632), (0.174484, -0.852156, -0.493341)2.49889, 18.33656, -33.63534
12given(0.985538, -0.051808, 0.161338), (0.115021, -0.494647, -0.861449), (0.124435, 0.867548, -0.481535)3.79609, -19.62603, -32.69951
13given(1), (1), (1)
14given(0.985609, 0.123935, 0.114954), (-0.038048, -0.499943, 0.865222), (0.164702, -0.857145, -0.488033)2.38291, 18.54349, -33.3517
15given(0.986657, -0.051145, 0.154572), (0.108611, -0.500514, -0.858889), (0.121293, 0.864216, -0.488281)3.74096, -19.47413, -32.62668

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Components

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


Mass: 31098.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19 to 23% PEG 3350, 0.2 to 0.3 M NaCl, 0.1 M Tris-HCl pH 8.5 12h prior to crystal freezing, 100 uM of p47phox(106-127) peptide was added to the crystallization drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.22→41 Å / Num. obs: 16369 / % possible obs: 99.4 % / Redundancy: 5.71 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.106 / Net I/σ(I): 14.3
Reflection shellResolution: 3.22→3.3 Å / Redundancy: 5.61 % / Rmerge(I) obs: 1.71 / Num. unique obs: 1175 / CC1/2: 0.59 / Rrim(I) all: 1.88 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION May 1, 2016 BUILT=20160617data reduction
XSCALEVERSION May 1, 2016 BUILT=20160617data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXC

1axc


Resolution: 3.22→41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.719 / SU ML: 0.48 / Cross valid method: THROUGHOUT / ESU R Free: 0.581 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27178 733 4.9 %RANDOM
Rwork0.2089 ---
obs0.21206 14362 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 118.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.22→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 0 7 5784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195852
X-RAY DIFFRACTIONr_bond_other_d0.0020.025546
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9827903
X-RAY DIFFRACTIONr_angle_other_deg0.855312903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.81425.607239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.483151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8561524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026436
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.92611.8733014
X-RAY DIFFRACTIONr_mcbond_other5.92111.8723013
X-RAY DIFFRACTIONr_mcangle_it9.53717.8073757
X-RAY DIFFRACTIONr_mcangle_other9.53617.8083758
X-RAY DIFFRACTIONr_scbond_it5.72912.3782838
X-RAY DIFFRACTIONr_scbond_other5.72712.3782838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.31718.3684146
X-RAY DIFFRACTIONr_long_range_B_refined13.5325789
X-RAY DIFFRACTIONr_long_range_B_other13.5325788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A822medium positional0.010.5
11C822medium positional0.010.5
11E822medium positional0.010.5
22A84medium positional0.020.5
22C84medium positional0.030.5
22E84medium positional0.030.5
33A129medium positional0.010.5
33C129medium positional0.020.5
33E129medium positional0.010.5
44A454medium positional0.010.5
44C454medium positional0.010.5
44E454medium positional0.010.5
55A601medium positional0.010.5
55C601medium positional0.010.5
55E601medium positional0.010.5
11A535tight thermal10.680.5
11C535tight thermal11.340.5
11E535tight thermal17.970.5
22A60tight thermal14.650.5
22C60tight thermal5.350.5
22E60tight thermal15.730.5
33A72tight thermal12.890.5
33C72tight thermal8.050.5
33E72tight thermal12.810.5
44A317tight thermal10.030.5
44C317tight thermal15.570.5
44E317tight thermal16.840.5
55A379tight thermal7.370.5
55C379tight thermal16.660.5
55E379tight thermal19.980.5
11A822medium thermal11.572
11C822medium thermal10.892
11E822medium thermal17.472
22A84medium thermal13.832
22C84medium thermal6.642
22E84medium thermal13.322
33A129medium thermal12.652
33C129medium thermal8.92
33E129medium thermal13.352
44A454medium thermal10.282
44C454medium thermal14.22
44E454medium thermal14.532
55A601medium thermal7.92
55C601medium thermal16.012
55E601medium thermal18.792
LS refinement shellResolution: 3.22→3.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 46 -
Rwork0.425 808 -
obs--70.87 %

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