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Open data
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Basic information
Entry | Database: PDB / ID: 5jne | ||||||
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Title | E2-SUMO-Siz1 E3-SUMO-PCNA complex | ||||||
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![]() | ligase/signaling protein / ubiquitin / ubiquitin-like / SUMO / E3 ligase / substrate complex / E2 conjugating enzyme / ligase-signaling protein complex / SIZ / PIAS | ||||||
Function / homology | ![]() SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO ligase activity / SUMO is proteolytically processed / mitotic spindle elongation / SUMOylation of transcription factors / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO ligase activity / SUMO is proteolytically processed / mitotic spindle elongation / SUMOylation of transcription factors / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / SUMOylation of DNA damage response and repair proteins / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / septin ring / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / cellular bud neck / PCNA complex / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / lagging strand elongation / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / postreplication repair / SUMO transferase activity / 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 / protein sumoylation / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / negative regulation of protein ubiquitination / positive regulation of DNA repair / condensed nuclear chromosome / positive regulation of DNA replication / replication fork / chromosome segregation / nucleotide-excision repair / transcription coregulator activity / PML body / protein tag activity / mitotic cell cycle / chromosome, telomeric region / cell division / chromatin / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lima, C.D. / Streich Jr., F.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Capturing a substrate in an activated RING E3/E2-SUMO complex. Authors: Streich, F.C. / Lima, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.7 KB | Display | ![]() |
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PDB format | ![]() | 281.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.1 KB | Display | ![]() |
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Full document | ![]() | 524.7 KB | Display | |
Data in XML | ![]() | 59.4 KB | Display | |
Data in CIF | ![]() | 80.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SIZ1, ULL1, YDR409W, SMT3, YDR510W, D9719.15 / Production host: ![]() ![]() References: UniProt: Q04195, UniProt: Q12306, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: UBC9, YDL064W / Production host: ![]() ![]() References: UniProt: P50623, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: Protein | 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: ![]() ![]() #4: Protein | 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: POL30, YBR088C, YBR0811 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 285 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/HOH.gif)
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.34 % / Description: Plates |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.385 Å
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Refine LS restraints |
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LS refinement shell |
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