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- PDB-4w5v: Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in c... -

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Basic information

Entry
Database: PDB / ID: 4w5v
TitleCrystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd)
Components
  • SUMO-activating enzyme subunit 2
  • SUMO-conjugating enzyme UBC9
KeywordsLIGASE / SUMO / E2-activating enzyme / Ubc9 / E1-conjugating enzyme / Uba2 / ubiquitin fold domain / Ufd / ubiquitin
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO activating enzyme complex / SUMO activating enzyme activity / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / SUMO binding / synaptonemal complex / small protein activating enzyme binding / positive regulation of protein sumoylation / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / nuclear export / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / ubiquitin-like protein conjugating enzyme binding / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / chromosome segregation / transcription coregulator binding / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / transferase activity / positive regulation of cell migration / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / : / SUMO-conjugating enzyme UBC9 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBoucher, L.E. / Reiter, K.H. / Matunis, M.J. / Bosch, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM060980 United States
CitationJournal: To Be Published
Title: Crystal structure of human SUMO complex
Authors: Reiter, K.H. / Boucher, L.E. / Bosch, J. / Matunis, M.J.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: SUMO-activating enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9775
Polymers31,8002
Non-polymers1773
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-3 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.273, 35.272, 58.672
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 18442.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein SUMO-activating enzyme subunit 2 / Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like ...Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like modifier-activating enzyme 2


Mass: 13357.964 Da / Num. of mol.: 1 / Fragment: UNP residues 445-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBT2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 4 types, 77 molecules

#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, pH 8.0, 20% PEG MME 550, 200 mM potassium formate, 20% glycerol; seeded

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.5→44.7 Å / Num. obs: 10654 / % possible obs: 91.12 % / Redundancy: 3.5 % / Net I/σ(I): 9.32

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
Blu-Icedata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONG, 1U9B

3ong

1u9b


Resolution: 2.5→44.7 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 553 5.2 %Random selection
Rwork0.2211 ---
obs0.2244 10631 90.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 10 74 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022148
X-RAY DIFFRACTIONf_angle_d0.52903
X-RAY DIFFRACTIONf_dihedral_angle_d8.261821
X-RAY DIFFRACTIONf_chiral_restr0.022317
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75160.41351270.41362362X-RAY DIFFRACTION87
2.7516-3.14970.37341350.32132512X-RAY DIFFRACTION92
3.1497-3.96780.2891420.23842541X-RAY DIFFRACTION92
3.9678-44.71180.25121490.17922663X-RAY DIFFRACTION93

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