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- PDB-3v62: Structure of the S. cerevisiae Srs2 C-terminal domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 3v62
TitleStructure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164
Components
  • ATP-dependent DNA helicase SRS2
  • 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 REDUCTIVE METHYLATION OF ALL LYSINE RESIDUES ON SMT3 / NUCLEAR / PROTEIN BINDING-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


DNA recombinase disassembly / 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 ...DNA recombinase disassembly / 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 / negative regulation of DNA recombination / DNA protection / establishment of mitotic sister chromatid cohesion / meiosis I / 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 / recombinational repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA polymerase processivity factor activity / leading strand elongation / ubiquitin-like protein ligase binding / Dual incision in TC-NER / protein sumoylation / negative regulation of double-strand break repair via homologous recombination / 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 / enzyme activator activity / double-strand break repair via nonhomologous end joining / protein tag activity / mitotic cell cycle / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Box / Proliferating Cell Nuclear Antigen ...DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
N-ETHYLMALEIMIDE / ATP-dependent DNA helicase SRS2 / Proliferating cell nuclear antigen / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Oct 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 1.3Sep 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_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_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
C: ATP-dependent DNA helicase SRS2
D: Ubiquitin-like protein SMT3
E: Proliferating cell nuclear antigen
F: ATP-dependent DNA helicase SRS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,80114
Polymers92,9166
Non-polymers8858
Water91951
1
A: Ubiquitin-like protein SMT3
B: Proliferating cell nuclear antigen
C: ATP-dependent DNA helicase SRS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9007
Polymers46,4583
Non-polymers4424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area18620 Å2
MethodPISA
2
D: Ubiquitin-like protein SMT3
E: Proliferating cell nuclear antigen
F: ATP-dependent DNA helicase SRS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9007
Polymers46,4583
Non-polymers4424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.817, 62.256, 139.247
Angle α, β, γ (deg.)90.00, 135.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
12A
22D
13C
23F
14C
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 255
2112D1 - 255
1122A20 - 98
2122D20 - 98
1132C1148 - 1161
2132F1148 - 1161
1142C1168 - 1174
2142F1168 - 1174

NCS ensembles :
ID
1
2
3
4
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 COMPOSED OF 4 SUBUNITS THE ASU HAS 2 AND THE UNIT CELL CONTAINS ONE TURN OF THIS HELICAL SCREW WITH 4 PROTOMERS

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Ubiquitin-like protein SMT3


Mass: 9882.258 Da / Num. of mol.: 2 / Fragment: unp residues 20-98 / Mutation: GSH from N-tag after thrombin cleavage, K19R
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.: 2 / 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: Protein ATP-dependent DNA helicase SRS2


Mass: 7703.804 Da / Num. of mol.: 2 / Fragment: unp residues 1107-1174 / Mutation: S at N-terminal after Ulp1 cleavage
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W3031A / Gene: HPR5, J0913, RADH, SRS2, YJL092W / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP RIL / References: UniProt: P12954, DNA helicase

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Non-polymers , 3 types, 59 molecules

#4: Chemical
ChemComp-NEQ / N-ETHYLMALEIMIDE


Mass: 125.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H7NO2
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUES A98 AND B164; D98 AND E164

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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: 3.26 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9 M AMMONIUM SULFATE 4% PEG 400 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 101080 / Num. obs: 26583 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-2.953.50.632199.4
2.95-33.50.569199.5
3-3.063.60.455199.1
3.06-3.123.70.386199.9
3.12-3.193.70.333199.8
3.19-3.273.70.2821100
3.27-3.353.70.208199.5
3.35-3.443.80.175199.9
3.44-3.543.80.136199.8
3.54-3.653.80.115199.6
3.65-3.783.90.096199.8
3.78-3.943.90.078199.8
3.94-4.113.90.066199.6
4.11-4.3340.053199.8
4.33-4.640.042199.8
4.6-4.9640.039199.9
4.96-5.463.90.0471100
5.46-6.243.90.047199.8
6.24-7.863.70.036199.5
7.86-503.90.025198.9

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Processing

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

1plq

1euv


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.141 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.862 / ESU R Free: 0.334 / 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
Rfree0.23656 1342 5.1 %RANDOM
Rwork0.18423 ---
obs0.18702 25191 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.556 Å2
Baniso -1Baniso -2Baniso -3
1--4.62 Å20 Å2-3.11 Å2
2--4.61 Å20 Å2
3----4.39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 56 51 5723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6972.0097726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89425.308260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.123151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7921530
X-RAY DIFFRACTIONr_chiral_restr0.1570.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214234
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7431.53526
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42925696
X-RAY DIFFRACTIONr_scbond_it1.66132224
X-RAY DIFFRACTIONr_scangle_it2.9894.52030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1020TIGHT POSITIONAL0.080.05
1B979MEDIUM POSITIONAL0.180.5
1B1020TIGHT THERMAL0.160.5
1B979MEDIUM THERMAL0.282
2A316TIGHT POSITIONAL0.010.05
2A328MEDIUM POSITIONAL0.020.5
2A316TIGHT THERMAL0.020.5
2A328MEDIUM THERMAL0.042
3C56TIGHT POSITIONAL0.010.05
3C57MEDIUM POSITIONAL0.020.5
3C56TIGHT THERMAL0.010.5
3C57MEDIUM THERMAL0.032
4C28TIGHT POSITIONAL0.110.05
4C25MEDIUM POSITIONAL0.190.5
4C28TIGHT THERMAL0.110.5
4C25MEDIUM THERMAL0.112
LS refinement shellResolution: 2.899→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 84 -
Rwork0.344 1652 -
obs--90.61 %

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