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- PDB-5fq2: Crystal structure of human SUMO E1 UFD domain in complex with Ubc... -

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Basic information

Entry
Database: PDB / ID: 5fq2
TitleCrystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group.
Components
  • SUMO-ACTIVATING ENZYME SUBUNIT 2
  • SUMO-CONJUGATING ENZYME UBC9
KeywordsLIGASE / ACTIVATING ENZYME / CONJUGATING ENZYME / SUMO
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
SUMO-conjugating enzyme UBC9 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsLiu, B. / Castano, L. / Lois, M. / Reverter, D.
CitationJournal: To be Published
Title: Crystal Structure of Human Sumo E1 Ufd Domain in Complex with Ubc9.
Authors: Liu, B. / Castano, L. / Lois, M. / Reverter, D.
History
DepositionDec 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)30,0862
Polymers30,0862
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-2.4 kcal/mol
Surface area16320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)129.614, 129.614, 66.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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 / SUMO E2-CONJUGATING ENZYME


Mass: 18340.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LYSINE METHYLATION AT LYS110 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
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 / SUMO E1 ACTIVATING ENZYME


Mass: 11746.217 Da / Num. of mol.: 1 / Fragment: UBIQUITIN FOLD DOMAIN, UNP RESIDUES 446-547
Source method: isolated from a genetically manipulated source
Details: LYSINE METHYLATION AT LYS505 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9UBT2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYSINE METHYLATION AT POSITION LYS110 LYSINE METHYLATION AT POSITION LYS505

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 75.53 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→46.44 Å / Num. obs: 29309 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 11 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.201→46.439 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1488 5.1 %
Rwork0.2293 --
obs0.2303 29254 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→46.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 0 38 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082108
X-RAY DIFFRACTIONf_angle_d1.1142853
X-RAY DIFFRACTIONf_dihedral_angle_d14.191808
X-RAY DIFFRACTIONf_chiral_restr0.048312
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2009-2.2720.31491450.26332408X-RAY DIFFRACTION97
2.272-2.35320.27031270.25832479X-RAY DIFFRACTION100
2.3532-2.44740.33341400.25542479X-RAY DIFFRACTION100
2.4474-2.55880.24821390.24312494X-RAY DIFFRACTION100
2.5588-2.69370.29861290.26042506X-RAY DIFFRACTION100
2.6937-2.86240.2631320.262502X-RAY DIFFRACTION100
2.8624-3.08340.25531410.25582508X-RAY DIFFRACTION100
3.0834-3.39360.28411350.25242530X-RAY DIFFRACTION100
3.3936-3.88440.24851440.22442529X-RAY DIFFRACTION100
3.8844-4.89310.21881260.19812592X-RAY DIFFRACTION100
4.8931-46.44930.23171300.22282739X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.6666 Å / Origin y: 124.7904 Å / Origin z: 13.2245 Å
111213212223313233
T0.408 Å2-0.0283 Å20.0617 Å2-0.4243 Å2-0.0141 Å2--0.4343 Å2
L0.6376 °2-1.8015 °20.1082 °2-5.073 °20.113 °2--0.3453 °2
S-0.0723 Å °-0.0809 Å °-0.0548 Å °0.0106 Å °0.057 Å °0.105 Å °-0.0032 Å °0.0477 Å °0.0253 Å °
Refinement TLS groupSelection details: ALL

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