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- PDB-6gis: Structural basis of human clamp sliding on DNA -

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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 / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / 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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / 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 / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / 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 / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / male germ cell nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / replication fork / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / 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 / 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 / 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
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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
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: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

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

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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


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

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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: 2.59 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

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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

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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 °

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