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- PDB-5jne: E2-SUMO-Siz1 E3-SUMO-PCNA complex -

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Basic information

Entry
Database: PDB / ID: 5jne
TitleE2-SUMO-Siz1 E3-SUMO-PCNA complex
Components
  • E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
  • Proliferating cell nuclear antigen
  • SUMO-conjugating enzyme UBC9
  • Ubiquitin-like protein SMT3
Keywordsligase/signaling protein / ubiquitin / ubiquitin-like / SUMO / E3 ligase / substrate complex / E2 conjugating enzyme / ligase-signaling protein complex / SIZ / PIAS
Function / homology
Function and homology information


SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / mitotic spindle elongation / meiotic mismatch repair / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / mitotic spindle elongation / meiotic mismatch repair / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Processive synthesis on the lagging strand / SUMO is proteolytically processed / Removal of the Flap Intermediate / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / : / septin ring / Polymerase switching / 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 / : / : / : / cellular bud neck / establishment of mitotic sister chromatid cohesion / SUMOylation of SUMOylation proteins / PCNA complex / : / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / lagging strand elongation / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / 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 / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / negative regulation of protein ubiquitination / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / condensed nuclear chromosome / nucleotide-excision repair / chromosome segregation / protein tag activity / mitotic cell cycle / double-stranded DNA binding / chromosome, telomeric region / cell division / chromatin / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
PINIT domain / E3 SUMO-protein ligase SIZ1, plant / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Box ...PINIT domain / E3 SUMO-protein ligase SIZ1, plant / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / SAP domain superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / SAP motif profile. / SAP domain / : / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Proliferating cell nuclear antigen signature 2. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Jelly Rolls / Roll / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ethane-1,2-dithiol / Proliferating cell nuclear antigen / SUMO-conjugating enzyme UBC9 / E3 SUMO-protein ligase SIZ1 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLima, C.D. / Streich Jr., F.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065872 United States
CitationJournal: Nature / Year: 2016
Title: Capturing a substrate in an activated RING E3/E2-SUMO complex.
Authors: Streich, F.C. / Lima, C.D.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.7May 1, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._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
Revision 1.8Oct 9, 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: E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
B: SUMO-conjugating enzyme UBC9
C: Ubiquitin-like protein SMT3
D: Proliferating cell nuclear antigen
E: E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
F: SUMO-conjugating enzyme UBC9
G: Ubiquitin-like protein SMT3
H: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,28022
Polymers198,0408
Non-polymers1,24014
Water4,882271
1
A: E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
B: SUMO-conjugating enzyme UBC9
C: Ubiquitin-like protein SMT3
D: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,73212
Polymers99,0204
Non-polymers7128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-26 kcal/mol
Surface area40750 Å2
MethodPISA
2
E: E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
F: SUMO-conjugating enzyme UBC9
G: Ubiquitin-like protein SMT3
H: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,54810
Polymers99,0204
Non-polymers5286
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-26 kcal/mol
Surface area40620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.421, 205.882, 142.501
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 / SAP and Miz-finger domain-containing protein 1 / Ubiquitin-like protein ligase 1


Mass: 42195.371 Da / Num. of mol.: 2 / Fragment: unp residues 167-445 / Mutation: Siz1 C361D, Smt3 Delta N-terminus 1-18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIZ1, ULL1, YDR409W, SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04195, UniProt: Q12306, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein SUMO-conjugating enzyme UBC9 / Ubiquitin carrier protein 9 / Ubiquitin-conjugating enzyme E2-18 kDa / Ubiquitin-protein ligase


Mass: 18288.750 Da / Num. of mol.: 2 / Fragment: unp residues 20-98 / Mutation: C5S, A129K, K153R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBC9, YDL064W / Production host: Escherichia coli (E. coli)
References: UniProt: P50623, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein Ubiquitin-like protein SMT3


Mass: 9719.982 Da / Num. of mol.: 2 / Mutation: N-terminal 1-18 delete, K19R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306
#4: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28815.656 Da / Num. of mol.: 2 / Mutation: K77D, C81E, R110D, K127G, K164C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: POL30, YBR088C, YBR0811 / Production host: Escherichia coli (E. coli) / References: UniProt: P15873

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Non-polymers , 4 types, 285 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-6LN / ethane-1,2-dithiol


Mass: 94.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.45 Å3/Da / Density % sol: 64.34 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→48.385 Å / Num. obs: 61981 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.1
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.82 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3id2, 1plq, 2eke

3id2

1plq

2eke


Resolution: 2.85→48.385 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 3139 5.07 %
Rwork0.2115 --
obs0.2135 61968 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13403 0 70 271 13744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213746
X-RAY DIFFRACTIONf_angle_d0.41118537
X-RAY DIFFRACTIONf_dihedral_angle_d7.8668433
X-RAY DIFFRACTIONf_chiral_restr0.0412049
X-RAY DIFFRACTIONf_plane_restr0.0032397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.89450.38371410.33422618X-RAY DIFFRACTION98
2.8945-2.9420.34391230.32962619X-RAY DIFFRACTION98
2.942-2.99270.36411510.30982661X-RAY DIFFRACTION99
2.9927-3.04710.34341340.29792671X-RAY DIFFRACTION99
3.0471-3.10570.33851420.28692634X-RAY DIFFRACTION99
3.1057-3.16910.30571500.26062635X-RAY DIFFRACTION99
3.1691-3.2380.33371320.26192712X-RAY DIFFRACTION99
3.238-3.31330.29931470.25082653X-RAY DIFFRACTION100
3.3133-3.39610.29831350.23862660X-RAY DIFFRACTION100
3.3961-3.48790.25141270.22952717X-RAY DIFFRACTION99
3.4879-3.59050.26521220.22942668X-RAY DIFFRACTION100
3.5905-3.70640.26561400.21482685X-RAY DIFFRACTION100
3.7064-3.83880.26851570.20422638X-RAY DIFFRACTION100
3.8388-3.99240.22761510.20692672X-RAY DIFFRACTION99
3.9924-4.1740.26121600.1942697X-RAY DIFFRACTION100
4.174-4.3940.20791500.18222670X-RAY DIFFRACTION100
4.394-4.66910.20041470.16382702X-RAY DIFFRACTION100
4.6691-5.02920.19391580.16142666X-RAY DIFFRACTION100
5.0292-5.53470.21191470.17262697X-RAY DIFFRACTION100
5.5347-6.3340.2141460.18592694X-RAY DIFFRACTION100
6.334-7.97440.23071330.20322720X-RAY DIFFRACTION100
7.9744-48.39240.21291460.17942740X-RAY DIFFRACTION100

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