[English] 日本語
Yorodumi
- PDB-6gis: Structural basis of human clamp sliding on DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gis
TitleStructural basis of human clamp sliding on DNA
Components
  • DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / Structural analysis human PCNA DNA complex sliding
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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / 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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / 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 / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / 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 / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / 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 / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / 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
DNA / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsDe March, M. / Merino, N. / Barrera-Vilarmau, S. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A.
Citation
Journal: Nat Commun / Year: 2017
Title: Structural basis of human PCNA sliding on DNA.
Authors: De March, M. / Merino, N. / Barrera-Vilarmau, S. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A.
#1: Journal: Nat Commun / Year: 2015
Title: Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.
Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. ...Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. / Montoya, G. / Blanco, F.J.
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 30, 2018ID: 5L7C
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jan 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

-
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: DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
E: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)92,8915
Polymers92,8915
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-29 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.189, 180.189, 76.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA1 - 2542 - 255
21LYSLYSBB1 - 2542 - 255
12PROPROAA1 - 2532 - 254
22PROPROCC1 - 2532 - 254
13PROPROBB1 - 2532 - 254
23PROPROCC1 - 2532 - 254

NCS ensembles :
ID
1
2
3

-
Components

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


Mass: 28933.893 Da / Num. of mol.: 3 / Mutation: H from His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12004
#2: DNA chain DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')


Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')


Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 11% PEG 3350 0.1M Sodium acetate ph 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.82→90.09 Å / Num. obs: 22331 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2G

4d2g


Resolution: 2.82→90.09 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.85 / SU B: 40.337 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.425
Details: STRUCTURE REFINED USING NCS COSTRAINTS, BABINET CORRECTION AND TLS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 1134 5.1 %RANDOM
Rwork0.24657 ---
obs0.24846 21184 99.59 %-
Displacement parametersBiso mean: 64.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.82→90.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 410 0 40 5743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195826
X-RAY DIFFRACTIONr_bond_other_d0.0080.025244
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9068000
X-RAY DIFFRACTIONr_angle_other_deg1.455311980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11924.727165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27415835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4041515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026374
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021219
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_it3.6034.9972970
X-RAY DIFFRACTIONr_mcbond_other3.6044.9972969
X-RAY DIFFRACTIONr_mcangle_it5.7437.4973702
X-RAY DIFFRACTIONr_mcangle_other5.7427.4973703
X-RAY DIFFRACTIONr_scbond_it3.5847.3572856
X-RAY DIFFRACTIONr_scbond_other3.5717.3542855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.68711.0614299
X-RAY DIFFRACTIONr_long_range_B_refined10.1655.7726229
X-RAY DIFFRACTIONr_long_range_B_other10.14355.7556228
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A249940.09
12B249940.09
21A247720.08
22C247720.08
31B244180.08
32C244180.08
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 87 -
Rwork0.258 1570 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: 60.8133 Å / Origin y: 69.9521 Å / Origin z: 60.6321 Å
111213212223313233
T0.1913 Å2-0.0809 Å2-0.03 Å2-0.1366 Å20.0326 Å2--0.0337 Å2
L0.0363 °20.0718 °20.015 °2-0.1509 °20.0302 °2--0.0065 °2
S0.0224 Å °-0.0145 Å °0.0236 Å °0.0825 Å °-0.0249 Å °0.0432 Å °0.0177 Å °-0.0111 Å °0.0026 Å °

+
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