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- PDB-3uin: Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from... -

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Basic information

Entry
Database: PDB / ID: 3uin
TitleComplex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2
Components
  • E3 SUMO-protein ligase RanBP2
  • Ran GTPase-activating protein 1
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 2
KeywordsLigase/Isomerase/Protein Binding / E3 / ligase / SUMO / UBC9 / RanBP2 / nuclear pore complex / Ligase-Isomerase-Protein Binding complex
Function / homology
Function and homology information


cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMO ligase activity / annulate lamellae / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding ...cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMO ligase activity / annulate lamellae / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / SUMO is proteolytically processed / 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) / Vitamin D (calciferol) metabolism / nuclear pore cytoplasmic filaments / mitotic nuclear membrane reassembly / synaptonemal complex / Nuclear Pore Complex (NPC) Disassembly / small protein activating enzyme binding / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / activation of GTPase activity / Transport of the SLBP independent Mature mRNA / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Maturation of nucleoprotein / negative regulation of protein export from nucleus / Nuclear import of Rev protein / nuclear export / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / kinase activator activity / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / aggresome / nucleocytoplasmic transport / Maturation of nucleoprotein / centrosome localization / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / transcription factor binding / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / postsynaptic cytosol / nuclear pore / response to axon injury / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / axon cytoplasm / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / GTPase activator activity / SUMOylation of transcription cofactors / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / response to amphetamine / hippocampal mossy fiber to CA3 synapse / HCMV Late Events / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / PML body / PKR-mediated signaling / modulation of chemical synaptic transmission / GABA-ergic synapse / kinetochore / protein modification process / small GTPase binding / ISG15 antiviral mechanism / Schaffer collateral - CA1 synapse / protein tag activity / Formation of Incision Complex in GG-NER / HCMV Early Events / mitotic spindle
Similarity search - Function
Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain ...Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Leucine rich repeat, ribonuclease inhibitor type / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / : / Zinc finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Leucine Rich repeat / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / PH-like domain superfamily / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / E3 SUMO-protein ligase RanBP2 / Small ubiquitin-related modifier 2 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsGareau, J.R. / Reverter, D. / Lima, C.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2.
Authors: Gareau, J.R. / Reverter, D. / Lima, C.D.
History
DepositionNov 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Sep 13, 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 2
C: Ran GTPase-activating protein 1
D: E3 SUMO-protein ligase RanBP2


Theoretical massNumber of molelcules
Total (without water)53,7074
Polymers53,7074
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.407, 155.407, 57.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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


Mass: 18030.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC9, UBCE9, UBE2I / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / 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 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 9177.270 Da / Num. of mol.: 1 / Fragment: UNP residues 14-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3A, SMT3H2, SUMO2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61956
#3: Protein Ran GTPase-activating protein 1 / RanGAP1


Mass: 18572.506 Da / Num. of mol.: 1 / Fragment: UNP residues 419-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1835, RANGAP1, SD / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46060
#4: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


Mass: 7926.794 Da / Num. of mol.: 1 / Fragment: UNP residues 2629-2695
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP358, RANBP2 / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49792
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVAL TO MET CONFLICT IN UNP ENTRY P61956

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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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.597→25 Å / Num. all: 25030 / Num. obs: 24830 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 63.73 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 2.597→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.8 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z5S

1z5s


Resolution: 2.597→24.411 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1263 5.09 %RANDOM
Rwork0.2113 ---
obs0.2139 24821 99.19 %-
all-25024 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.633 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso mean: 79.1316 Å2
Baniso -1Baniso -2Baniso -3
1--4.1551 Å2-0 Å20 Å2
2---4.1551 Å20 Å2
3---8.3102 Å2
Refinement stepCycle: LAST / Resolution: 2.597→24.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 42 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093690
X-RAY DIFFRACTIONf_angle_d1.1764996
X-RAY DIFFRACTIONf_dihedral_angle_d18.041403
X-RAY DIFFRACTIONf_chiral_restr0.081553
X-RAY DIFFRACTIONf_plane_restr0.006651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.597-2.7010.41510.35912511266297
2.701-2.82380.34781470.32762568271599
2.8238-2.97240.32451400.30252580272099
2.9724-3.15830.3531280.283926122740100
3.1583-3.40160.32871270.259826662793100
3.4016-3.74280.27981400.211826092749100
3.7428-4.28190.22971470.186526182765100
4.2819-5.38510.23181400.17226722812100
5.3851-24.41190.22291430.17292722286599

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