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- PDB-3v61: Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 -

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Basic information

Entry
Database: PDB / ID: 3v61
TitleStructure of S. cerevisiae PCNA conjugated to SUMO on lysine 164
Components
  • Proliferating cell nuclear antigen
  • Ubiquitin-like protein SMT3
KeywordsPROTEIN BINDING/DNA BINDING PROTEIN / UBIQUITIN-LIKE PROTEIN PCNA / POST-TRANSLATIONAL MODIFICATION / DNA REPLICATION / DNA DAMAGE RESPONSE / SRS2 / NEM MODIFICATION ON PCNA CYS22 AND CYS81 / NUCLEAR / PROTEIN BINDING-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / SUMO is conjugated to E1 (UBA2:SAE1) / meiotic mismatch repair / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / Processive synthesis on the lagging strand / SUMOylation of transcription factors / Removal of the Flap Intermediate ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / SUMO is conjugated to E1 (UBA2:SAE1) / meiotic mismatch repair / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / Processive synthesis on the lagging strand / SUMOylation of transcription factors / Removal of the Flap Intermediate / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / Polymerase switching / septin ring / E3 ubiquitin ligases ubiquitinate target proteins / SUMOylation of DNA damage response and repair proteins / maintenance of DNA trinucleotide repeats / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / SUMOylation of SUMOylation proteins / Termination of translesion DNA synthesis / PCNA complex / lagging strand elongation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / DNA damage tolerance / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / ubiquitin-like protein ligase binding / Dual incision in TC-NER / protein sumoylation / subtelomeric heterochromatin formation / translesion synthesis / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / condensed nuclear chromosome / nucleotide-excision repair / protein tag activity / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / : / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / N-ETHYLMALEIMIDE / Proliferating cell nuclear antigen / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArmstrong, A.A. / Mohideen, F. / Lima, C.D.
CitationJournal: Nature / Year: 2012
Title: Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2.
Authors: Armstrong, A.A. / Mohideen, F. / Lima, C.D.
History
DepositionDec 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Other
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3
B: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,62717
Polymers38,5922
Non-polymers2,03615
Water1,62190
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)140.060, 140.060, 52.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
DetailsPCNA IS NORMALLY A TRIMER BUT NEM MODIFICATION DISRUPTS THE TRIMER AND CAUSES PCNA TO RUN AS A MONOMER ON GEL FILTRATION THIS SUMO-PCNA MONOMER CRYSTALLIZES BY REFORMING THE PCNA:PCNA PROTOMER BUT WITH A RIGHT HANDED HELICAL SCREW COINCIDENT WITH THE I41 SCREW AXIS THE UNIT CELL CONTAINS ONE TURN OF THIS HELICAL SCREW

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Components

#1: Protein Ubiquitin-like protein SMT3


Mass: 9719.982 Da / Num. of mol.: 1 / Fragment: unp residues 20-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W3031A / Gene: D9719.15, SMT3, YDR510W / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q12306
#2: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28871.922 Da / Num. of mol.: 1 / Mutation: K127G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W3031A / Gene: POL30, YBR0811, YBR088C / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP RIL / References: UniProt: P15873
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-NEQ / N-ETHYLMALEIMIDE


Mass: 125.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUES A98 AND B164

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% MPD, 100 mM BaCl2, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 73601 / Num. obs: 23649 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Χ2: 1.54 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.92.40.37621800.63189.4
2.9-3.022.60.30623170.647194.2
3.02-3.152.90.23423030.741195.7
3.15-3.3230.17223840.806197.6
3.32-3.533.10.1223811.011198.1
3.53-3.83.30.09724071.198198.9
3.8-4.183.30.07823851.483199.2
4.18-4.793.50.06324352.122199.6
4.79-6.033.40.07324462.854199.7
6.03-503.50.04424112.638199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1PLQ and 1EUV

1plq

1euv


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.592 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.997 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: NEM molecule has occupancy of 1 as mass spec suggested that this ligand is fully modified in the studied samples.
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 617 4.9 %RANDOM
Rwork0.2142 ---
obs0.2163 12550 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 197.13 Å2 / Biso mean: 57.4447 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 31 90 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222663
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9953581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63425.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4721514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211978
X-RAY DIFFRACTIONr_mcbond_it0.6081.51647
X-RAY DIFFRACTIONr_mcangle_it1.14722663
X-RAY DIFFRACTIONr_scbond_it1.25131016
X-RAY DIFFRACTIONr_scangle_it2.1784.5918
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 49 -
Rwork0.309 842 -
all-891 -
obs--93.79 %

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