+Open data
-Basic information
Entry | Database: PDB / ID: 3kyc | ||||||
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Title | Human SUMO E1 complex with a SUMO1-AMP mimic | ||||||
Components |
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Keywords | LIGASE / E1 / SUMO / UBIQUITIN / THIOESTER / ADENYLATION / INHIBITOR / ACYL-ADENYLATE INTERMEDIATE / Acetylation / Nucleus / Phosphoprotein / Ubl conjugation pathway / ATP-binding / Nucleotide-binding / Polymorphism / Cytoplasm / Isopeptide bond / Membrane | ||||||
Function / homology | Function and homology information SUMO activating enzyme complex / SUMO activating enzyme activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / ubiquitin activating enzyme activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO activating enzyme complex / SUMO activating enzyme activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / ubiquitin activating enzyme activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / positive regulation of protein sumoylation / SUMO binding / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / ATP-dependent protein binding / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Transferases; Acyltransferases; Aminoacyltransferases / ubiquitin-like protein conjugating enzyme binding / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / positive regulation of protein targeting to mitochondrion / SUMOylation of chromatin organization proteins / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / roof of mouth development / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / transcription factor binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / cellular response to cadmium ion / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / enzyme activator activity / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / transferase activity / nuclear membrane / nuclear body / protein stabilization / nuclear speck / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Lima, C.D. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Active site remodelling accompanies thioester bond formation in the SUMO E1. Authors: Olsen, S.K. / Capili, A.D. / Lu, X. / Tan, D.S. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kyc.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kyc.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kyc_validation.pdf.gz | 767.9 KB | Display | wwPDB validaton report |
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Full document | 3kyc_full_validation.pdf.gz | 795.7 KB | Display | |
Data in XML | 3kyc_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 3kyc_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/3kyc ftp://data.pdbj.org/pub/pdb/validation_reports/ky/3kyc | HTTPS FTP |
-Related structure data
Related structure data | 3kydC 1y8qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a heterotrimer. |
-Components
-SUMO-activating enzyme subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38499.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AOS1, SAE1, SUA1, UBLE1A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: Q9UBE0 |
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#2: Protein | Mass: 73501.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRIHFB2115, SAE2, UBA2, UBLE1B / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL References: UniProt: Q9UBT2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
-Protein , 1 types, 1 molecules D
#3: Protein | Mass: 11151.584 Da / Num. of mol.: 1 / Fragment: UNP residues 1-97 / Mutation: T95C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: P63165 |
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-Non-polymers , 3 types, 255 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-JZU / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | LIGAND CYS-GLY-GLY-AMSN, WHERE AMSN HAS ID JZU IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN-MEDIATED ...LIGAND CYS-GLY-GLY-AMSN, WHERE AMSN HAS ID JZU IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN-MEDIATED LIGATION TO MAKE CHAIN D. |
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Sequence details | CHAIN D IS COMPOSED AS UB/UBI-CYS-GLY-GLY-AMSN, ADENYLATE MIMIC. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1 MES, 24% PEG 3350, 1.3 M AMMONIUM ACETATE, 10 mM ATP, 10 mM MgCl2, 10 mM TCEP, 2.5% PEG 400, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→25 Å / Num. obs: 47106 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.45→2.51 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.2 / % possible all: 98 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y8Q Resolution: 2.45→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.958 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.48 Å2 / Biso mean: 71.486 Å2 / Biso min: 26.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Total num. of bins used: 20
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