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- PDB-3uip: Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from... -

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Basic information

Entry
Database: PDB / ID: 3uip
TitleComplex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II
Components
  • E3 SUMO-protein ligase RanBP2
  • Ran GTPase-activating protein 1
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 1
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 / negative regulation of potassium ion transmembrane transporter activity / SUMO ligase activity / protein localization to nuclear pore / annulate lamellae / : ...cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / SUMO ligase activity / protein localization to nuclear pore / 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) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / 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 / XY body / regulation of calcium ion transmembrane transport / 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 / regulation of cardiac muscle cell contraction / 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 / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / 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 / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / transporter activator activity / nuclear pore / response to axon injury / negative regulation of DNA-binding transcription factor activity / 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 / axon cytoplasm / Mitotic Prometaphase / 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 / response to amphetamine / SUMOylation of chromatin organization proteins / HCMV Late Events / transcription coregulator binding
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 / Small ubiquitin-related modifier 1, Ubl domain / Ran binding protein RanBP1-like / Ran binding 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 / Small ubiquitin-related modifier 1, Ubl 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 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Ran GTPase-activating protein 1
D: E3 SUMO-protein ligase RanBP2


Theoretical massNumber of molelcules
Total (without water)53,8014
Polymers53,8014
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.651, 199.187, 63.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-318-

HOH

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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: 18138.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC9, UBCE9, UBE2I / Plasmid details: 469008 / 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 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 9285.527 Da / Num. of mol.: 1 / Fragment: UNP residues 18-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Plasmid details: 469008 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#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 details: 469008 / 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: 7803.704 Da / Num. of mol.: 1 / Fragment: UNP residues 2631-2695 / Mutation: A2642V, Q2644E, L2647K, T2649D, K2650T
Source method: isolated from a genetically manipulated source
Details: Motif II of RanBP2 IR1 was mutated to IR2 motif II.
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP358, RANBP2 / Plasmid details: 469008 / 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.: 343 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG4000, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.293→35 Å / Num. all: 39176 / Num. obs: 38980 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1
Reflection shellResolution: 2.293→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3840 / % possible all: 99.4

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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: 2.293→33.978 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1949 5 %RANDOM
Rwork0.1915 ---
obs0.1935 38956 99.16 %-
all-39286 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.951 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 135.7 Å2 / Biso mean: 38.8526 Å2 / Biso min: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.2805 Å2-0 Å20 Å2
2---1.5875 Å20 Å2
3---8.868 Å2
Refinement stepCycle: LAST / Resolution: 2.293→33.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 0 343 3954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083693
X-RAY DIFFRACTIONf_angle_d1.1934995
X-RAY DIFFRACTIONf_chiral_restr0.081553
X-RAY DIFFRACTIONf_plane_restr0.006643
X-RAY DIFFRACTIONf_dihedral_angle_d16.0991411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.293-2.35060.30131380.24652508264695
2.3506-2.41420.2431320.22182597272999
2.4142-2.48520.2781580.208926102768100
2.4852-2.56540.26741370.21626172754100
2.5654-2.6570.30391290.216726452774100
2.657-2.76340.25211520.214326092761100
2.7634-2.88910.29991450.209926542799100
2.8891-3.04130.24891470.20926312778100
3.0413-3.23170.23891440.195426322776100
3.2317-3.4810.23471240.198526782802100
3.481-3.83090.24181340.179926632797100
3.8309-4.38420.17581410.15926842825100
4.3842-5.51990.18471370.15962692282999
5.5199-33.98160.21071310.19312787291898

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