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- PDB-2pe6: Non-covalent complex between human SUMO-1 and human Ubc9 -

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Basic information

Entry
Database: PDB / ID: 2pe6
TitleNon-covalent complex between human SUMO-1 and human Ubc9
Components
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 1
KeywordsPROTEIN BINDING / LIGASE / SUMO / UBIQUITIN-LIKE / CONJUGATION / SMT3 / UBC9
Function / homology
Function and homology information


SUMO conjugating enzyme activity / SUMO ligase complex / RING-like zinc finger domain binding / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / HLH domain binding / SUMO is conjugated to E1 (UBA2:SAE1) / transferase complex / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...SUMO conjugating enzyme activity / SUMO ligase complex / RING-like zinc finger domain binding / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / HLH domain binding / SUMO is conjugated to E1 (UBA2:SAE1) / transferase complex / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / negative regulation of action potential / import into nucleus / nuclear stress granule / negative regulation of transcription initiation by RNA polymerase II / mitotic nuclear membrane reassembly / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / synaptonemal complex / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / negative regulation of protein import into nucleus / SUMOylation of DNA methylation proteins / Maturation of nucleoprotein / nuclear export / SUMOylation of RNA binding proteins / SUMO transferase activity / regulation of cardiac muscle cell contraction / Transferases; Acyltransferases; Aminoacyltransferases / Postmitotic nuclear pore complex (NPC) reformation / transcription factor binding / roof of mouth development / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / cellular response to cadmium ion / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA replication proteins / ubiquitin-like protein ligase binding / protein sumoylation / Regulation of IFNG signaling / postsynaptic cytosol / transporter activator activity / nuclear pore / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / protein modification process / transcription coregulator binding / SUMOylation of chromatin organization proteins / Meiotic synapsis / SUMOylation of intracellular receptors / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / regulation of protein stability / Maturation of DENV proteins / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / protein tag activity / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear envelope / cellular response to heat / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Dengue Virus-Host Interactions / ubiquitin-dependent protein catabolic process / nuclear body / nuclear speck / protein stabilization / positive regulation of cell migration / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Small ubiquitin-related modifier 1, Ubl domain / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCapili, A.D. / Lima, C.D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Analysis of a Complex between SUMO and Ubc9 Illustrates Features of a Conserved E2-Ubl Interaction.
Authors: Capili, A.D. / Lima, C.D.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)29,4632
Polymers29,4632
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.700, 38.600, 83.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-165-

HOH

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Components

#1: Protein SUMO-conjugating enzyme UBC9 / SUMO-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin ...SUMO-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / Ubiquitin carrier protein 9 / p18


Mass: 18313.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Small ubiquitin-related modifier 1 / SUMO-1 / Sentrin / Ubiquitin-like protein SMT3C / SMT3 homolog 3 / Ubiquitin-homology domain ...SUMO-1 / Sentrin / Ubiquitin-like protein SMT3C / SMT3 homolog 3 / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / GAP-modifying protein 1 / GMP1


Mass: 11149.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1 / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 100 mM Tris-HCl, pH 8.5, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2005 / Details: KB FOCUSING MIRROR
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11142 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.9 / % possible all: 92.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3S

1a3s


Resolution: 2.4→38.47 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 228860.344 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 561 5 %RANDOM
Rwork0.225 ---
obs0.225 11127 96.7 %-
all-11127 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.55 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.94 Å20 Å20 Å2
2---2.9 Å20 Å2
3----3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 0 67 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scbond_it2.822
X-RAY DIFFRACTIONc_scangle_it4.132.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 40 3.8 %
Rwork0.324 1004 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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