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- PDB-1z5s: Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and ... -

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Basic information

Entry
Database: PDB / ID: 1z5s
TitleCrystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2
Components
  • Ran GTPase-activating protein 1
  • Ran-binding protein 2
  • Ubiquitin-conjugating enzyme E2 I
  • Ubiquitin-like protein SMT3C
KeywordsLIGASE / E3 / SUMO / UBC9 / NUCLEAR PORE 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 / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / annulate lamellae ...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 / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / annulate lamellae / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / negative regulation of action potential / 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) / regulation of calcium ion transmembrane transport / 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 / XY body / 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 / regulation of cardiac muscle cell contraction / 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 / negative regulation of protein import into nucleus / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / transcription factor binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / 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 / potassium channel regulator activity / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Regulation of IFNG signaling / 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 / cellular response to cadmium ion / 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 / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / protein modification process
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 domain / Ran binding protein RanBP1-like ...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 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 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Nature / Year: 2005
Title: Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.
Authors: Reverter, D. / Lima, C.D.
History
DepositionMar 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / struct_conn / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE COVALENT ISOPEPTIDE BOND BETWEEN RANGAP1 LYS524 AND SUMO C-TERMINUS GLY97.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 I
B: Ubiquitin-like protein SMT3C
C: Ran GTPase-activating protein 1
D: Ran-binding protein 2


Theoretical massNumber of molelcules
Total (without water)55,7364
Polymers55,7364
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.123, 157.123, 59.613
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 Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO- 1 ...Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO- 1 conjugating enzyme / Ubiquitin carrier protein 9 / p18


Mass: 18030.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P63279, ubiquitin-protein ligase
#2: Protein Ubiquitin-like protein SMT3C / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein ...Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein SUMO-1 / GAP modifying protein 1 / GMP1 / Sentrin / OK/SW-cl.43


Mass: 9473.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL1, SMT3C, SMT3H3 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P63165
#3: Protein Ran GTPase-activating protein 1


Mass: 18686.607 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1 / Plasmid: PSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P46060
#4: Protein Ran-binding protein 2 / RanBP2 / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / 358 kDa nucleoporin / P270


Mass: 9544.638 Da / Num. of mol.: 1 / Fragment: IR1-M domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Plasmid: PSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P49792
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16464 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.1 / % possible all: 91.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RANGAP1-UBC9 COMPLEX

Resolution: 3.01→29.69 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2281669.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 832 5.1 %RANDOM
Rwork0.247 ---
obs0.247 16461 96.5 %-
all-17058 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.936 Å2 / ksol: 0.267286 e/Å3
Displacement parametersBiso mean: 90 Å2
Baniso -1Baniso -2Baniso -3
1--15.45 Å217.61 Å20 Å2
2---15.45 Å20 Å2
3---30.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.47 Å
Luzzati d res low-8 Å
Luzzati sigma a1.16 Å0.99 Å
Refinement stepCycle: LAST / Resolution: 3.01→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 0 28 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.272
X-RAY DIFFRACTIONc_mcangle_it3.983.5
X-RAY DIFFRACTIONc_scbond_it2.82.5
X-RAY DIFFRACTIONc_scangle_it4.724
LS refinement shellResolution: 3.01→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 122 5 %
Rwork0.425 2299 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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