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- PDB-3v60: Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 -

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Basic information

Entry
Database: PDB / ID: 3v60
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 / 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
Proliferating cell nuclear antigen / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Nov 8, 2017Group: Refinement description / Category: 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 1.3Sep 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 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,1688
Polymers38,5922
Non-polymers5766
Water1,802100
1
A: Ubiquitin-like protein SMT3
B: Proliferating cell nuclear antigen
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)117,50524
Polymers115,7766
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
Unit cell
Length a, b, c (Å)268.126, 268.126, 268.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Ubiquitin-like protein SMT3


Mass: 9719.982 Da / Num. of mol.: 1 / Fragment: unp resicues 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUES A98 AND B164
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: 5.2 Å3/Da / Density % sol: 76.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4% PEG 8000, 500 mM LiSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Jun 10, 2007
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: 2.6→50 Å / Num. all: 314610 / Num. obs: 25873 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.052 / Χ2: 1.509 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.696.90.36324881.02199.2
2.69-2.88.40.30525271.045199.5
2.8-2.939.30.24425301.093199.6
2.93-3.0810.60.18525321.174199.8
3.08-3.28120.12825581.24199.8
3.28-3.5313.40.08125731.232199.9
3.53-3.8814.60.05725841.421199.9
3.88-4.4515.30.04226031.4171100
4.45-5.615.50.04226522.4771100
5.6-5014.70.02928261.981199.5

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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: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.95 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1307 5.1 %RANDOM
Rwork0.2103 ---
obs0.2122 25738 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 155.18 Å2 / Biso mean: 62.2473 Å2 / Biso min: 36.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 30 100 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222710
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9963650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09925.36125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74615512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9521514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211981
X-RAY DIFFRACTIONr_mcbond_it0.9971.51667
X-RAY DIFFRACTIONr_mcangle_it1.92222697
X-RAY DIFFRACTIONr_scbond_it2.34131043
X-RAY DIFFRACTIONr_scangle_it4.1224.5953
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 92 -
Rwork0.306 1741 -
all-1833 -
obs--98.44 %

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