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- PDB-4i9y: Structure of the C-terminal domain of Nup358 -

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Basic information

Entry
Database: PDB / ID: 4i9y
TitleStructure of the C-terminal domain of Nup358
ComponentsE3 SUMO-protein ligase RanBP2
KeywordsTRANSPORT PROTEIN / Nuclear Pore Complex
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / 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 / Transport of the SLBP independent Mature mRNA / 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 / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / kinase activator activity / NEP/NS2 Interacts with the Cellular Export Machinery / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / nucleocytoplasmic transport / centrosome localization / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ISG15 antiviral mechanism / small GTPase binding / HCMV Early Events / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / nuclear envelope / protein folding / snRNP Assembly / nuclear membrane / intracellular membrane-bounded organelle / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 / Zinc finger domain / Cyclophilin-like / Cyclophilin ...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 / Zinc finger domain / Cyclophilin-like / Cyclophilin / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLin, D.H. / Zimmermann, S. / Stuwe, T. / Stuwe, E. / Hoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and Functional Analysis of the C-Terminal Domain of Nup358/RanBP2.
Authors: Lin, D.H. / Zimmermann, S. / Stuwe, T. / Stuwe, E. / Hoelz, A.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 SUMO-protein ligase RanBP2
B: E3 SUMO-protein ligase RanBP2
C: E3 SUMO-protein ligase RanBP2
D: E3 SUMO-protein ligase RanBP2
E: E3 SUMO-protein ligase RanBP2
F: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,91836
Polymers110,3216
Non-polymers2,59730
Water27,6171533
1
A: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8496
Polymers18,3871
Non-polymers4625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0338
Polymers18,3871
Non-polymers6467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6995
Polymers18,3871
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8837
Polymers18,3871
Non-polymers4966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7575
Polymers18,3871
Non-polymers3704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6995
Polymers18,3871
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.062, 97.132, 108.151
Angle α, β, γ (deg.)90.00, 117.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 / Putative peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18386.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Production host: Escherichia coli (E. coli) / References: UniProt: P49792
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1533 / 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: 4.4 Å3/Da / Density % sol: 72.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationMonochromator: Liquid nitrogen-cooled double Si(111) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 188791 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.34 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→48.566 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1576 9500 5.03 %
Rwork0.123 --
obs0.1248 188714 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8421 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 162 1533 9435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098400
X-RAY DIFFRACTIONf_angle_d1.16411359
X-RAY DIFFRACTIONf_dihedral_angle_d12.7563177
X-RAY DIFFRACTIONf_chiral_restr0.0741214
X-RAY DIFFRACTIONf_plane_restr0.0051520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76530.28332590.23554745X-RAY DIFFRACTION78
1.7653-1.78610.28512770.22345608X-RAY DIFFRACTION92
1.7861-1.80790.23693430.19666080X-RAY DIFFRACTION99
1.8079-1.83070.2523220.17956072X-RAY DIFFRACTION99
1.8307-1.85480.2143410.16626053X-RAY DIFFRACTION99
1.8548-1.88020.21753110.1666036X-RAY DIFFRACTION99
1.8802-1.90710.20783380.16086073X-RAY DIFFRACTION99
1.9071-1.93560.18063090.15466109X-RAY DIFFRACTION99
1.9356-1.96580.19823020.14535993X-RAY DIFFRACTION99
1.9658-1.9980.17683150.14355973X-RAY DIFFRACTION98
1.998-2.03250.17633120.13875922X-RAY DIFFRACTION97
2.0325-2.06950.19393060.13895769X-RAY DIFFRACTION94
2.0695-2.10930.17823000.1246063X-RAY DIFFRACTION99
2.1093-2.15230.16073270.11136048X-RAY DIFFRACTION99
2.1523-2.19910.13893320.10816052X-RAY DIFFRACTION99
2.1991-2.25030.15163330.10596072X-RAY DIFFRACTION99
2.2503-2.30660.14943220.10426058X-RAY DIFFRACTION99
2.3066-2.36890.15173660.10246019X-RAY DIFFRACTION99
2.3689-2.43860.15712840.10485949X-RAY DIFFRACTION97
2.4386-2.51730.1523070.10585766X-RAY DIFFRACTION94
2.5173-2.60730.15123160.11176117X-RAY DIFFRACTION99
2.6073-2.71170.14263230.11436103X-RAY DIFFRACTION99
2.7117-2.83510.16353120.12036111X-RAY DIFFRACTION99
2.8351-2.98450.16483430.12356060X-RAY DIFFRACTION99
2.9845-3.17150.15333200.12156011X-RAY DIFFRACTION98
3.1715-3.41630.13623140.11195916X-RAY DIFFRACTION96
3.4163-3.760.13743210.10596124X-RAY DIFFRACTION99
3.76-4.30380.12583210.10416125X-RAY DIFFRACTION99
4.3038-5.42120.11833320.10175976X-RAY DIFFRACTION97
5.4212-48.58480.18042920.16136211X-RAY DIFFRACTION98

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