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

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Basic information

Entry
Database: PDB / ID: 3uio
TitleComplex between human RanGAP1-SUMO2, 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 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 / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMO ligase activity / annulate lamellae / SUMOylation of nuclear envelope proteins / transferase complex ...cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMO ligase activity / annulate lamellae / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / nuclear pore cytoplasmic filaments / small protein activating enzyme binding / synaptonemal complex / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / SUMOylation of DNA methylation proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Maturation of nucleoprotein / activation of GTPase activity / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / nuclear export / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / aggresome / Maturation of nucleoprotein / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / transcription factor binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / response to axon injury / mRNA transport / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / response to amphetamine / Meiotic synapsis / GTPase activator activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / HCMV Late Events / Regulation of endogenous retroelements by KRAB-ZFP proteins / transcription coregulator binding / chromosome segregation / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / PML body / mitotic spindle / ISG15 antiviral mechanism / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / HCMV Early Events / Separation of Sister Chromatids / protein tag activity / Signaling by ALK fusions and activated point mutants / protein folding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / snRNP Assembly / Processing of DNA double-strand break ends
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 domain / Ran binding protein RanBP1-like / 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 domain / Ran binding protein RanBP1-like / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine rich repeat, ribonuclease inhibitor type / Zinc finger domain / Leucine Rich repeat / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeats / 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. / Ubiquitin-like domain / PH-like domain superfamily / 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: 2.602 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)53,6044
Polymers53,6044
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.351, 151.351, 57.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 18094.812 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: 7759.584 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: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Keywords: A2642V, Q2644E, L2647K, T2649D, K2650T / References: UniProt: P49792
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, 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 15, 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: 2.602→35 Å / Num. all: 23446 / Num. obs: 23329 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 4.8 % / Biso Wilson estimate: 42.92 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.3
Reflection shellResolution: 2.602→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2262 / % possible all: 99

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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: 2.602→34.775 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1198 5.14 %RANDOM
Rwork0.2036 ---
obs0.2061 23318 99.52 %-
all-23430 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.022 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 133.81 Å2 / Biso mean: 53.3471 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.9393 Å20 Å20 Å2
2---1.9393 Å20 Å2
3---3.8786 Å2
Refinement stepCycle: LAST / Resolution: 2.602→34.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 0 143 3768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093706
X-RAY DIFFRACTIONf_angle_d1.1845019
X-RAY DIFFRACTIONf_chiral_restr0.082555
X-RAY DIFFRACTIONf_plane_restr0.005653
X-RAY DIFFRACTIONf_dihedral_angle_d18.2891412
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 (%)
2.602-2.7060.36611340.29722399253399
2.706-2.82910.33091360.26982404254099
2.8291-2.97820.32291370.25892423256099
2.9782-3.16470.32411080.24224732581100
3.1647-3.40880.29631470.240424372584100
3.4088-3.75150.23361240.205124612585100
3.7515-4.29350.24091420.175624602602100
4.2935-5.40610.21961300.165725072637100
5.4061-34.77810.1761400.168525562696100

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