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- PDB-4ga1: Structure of the N-terminal domain of Nup358 -

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Basic information

Entry
Database: PDB / ID: 4ga1
TitleStructure of the N-terminal domain of Nup358
ComponentsE3 SUMO-PROTEIN LIGASE RANBP2
KeywordsTRANSPORT PROTEIN / TPR motif / Nuclear pore complex component Nucleocytoplasmic transport
Function / homology
Function and homology information


annulate lamellae / Transferases; Acyltransferases; Aminoacyltransferases / NLS-bearing protein import into nucleus / protein sumoylation / mRNA transport / nuclear pore / peptidyl-prolyl cis-trans isomerase activity / protein folding / nuclear envelope / transferase activity ...annulate lamellae / Transferases; Acyltransferases; Aminoacyltransferases / NLS-bearing protein import into nucleus / protein sumoylation / mRNA transport / nuclear pore / peptidyl-prolyl cis-trans isomerase activity / protein folding / nuclear envelope / transferase activity / nuclear membrane / RNA binding / metal ion binding / 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 / Zn-finger in Ran binding protein and others / Tetratricopeptide repeat 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 / Zinc finger domain / Zn-finger in Ran binding protein and others / Tetratricopeptide repeat domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsHoelz, A. / Kassube, S.A. / Lin, D.H. / Stuwe, T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal structure of the N-terminal domain of Nup358/RanBP2.
Authors: Kassube, S.A. / Stuwe, T. / Lin, D.H. / Antonuk, C.D. / Napetschnig, J. / Blobel, G. / Hoelz, A.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-PROTEIN LIGASE RANBP2


Theoretical massNumber of molelcules
Total (without water)17,5131
Polymers17,5131
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.387, 83.641, 29.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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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: 17512.523 Da / Num. of mol.: 1 / Fragment: unp residues 1-145 / Mutation: I27(MSE), Y37(MSE), T92(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Gene: ENSG00000153201 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) RIL / References: UniProt: H2QII6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 18 % (w/v) PEG 3350 200 mM lithium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→47.9 Å / Num. obs: 99452 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.067 / Net I/σ(I): 25.5
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / % possible all: 93.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→47.876 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.11 / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 5019 5.05 %
Rwork0.1932 --
obs0.1947 99449 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9438 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.15→47.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 0 231 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131232
X-RAY DIFFRACTIONf_angle_d1.3961667
X-RAY DIFFRACTIONf_dihedral_angle_d13.186491
X-RAY DIFFRACTIONf_chiral_restr0.075177
X-RAY DIFFRACTIONf_plane_restr0.009217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1492-1.16230.3821620.27692645X-RAY DIFFRACTION84
1.1623-1.17590.24891610.26312952X-RAY DIFFRACTION94
1.1759-1.19030.26591450.24253212X-RAY DIFFRACTION98
1.1903-1.20540.2961490.24483177X-RAY DIFFRACTION99
1.2054-1.22120.26741820.23353130X-RAY DIFFRACTION99
1.2212-1.2380.26581440.22583214X-RAY DIFFRACTION99
1.238-1.25560.24711780.21953159X-RAY DIFFRACTION99
1.2556-1.27440.27421650.2033131X-RAY DIFFRACTION99
1.2744-1.29430.22141860.21043185X-RAY DIFFRACTION99
1.2943-1.31550.24241750.20483098X-RAY DIFFRACTION99
1.3155-1.33820.25981550.20113182X-RAY DIFFRACTION99
1.3382-1.36250.23741750.20313254X-RAY DIFFRACTION99
1.3625-1.38870.24321570.19873121X-RAY DIFFRACTION99
1.3887-1.41710.23711310.1953257X-RAY DIFFRACTION99
1.4171-1.44790.24341530.20123148X-RAY DIFFRACTION99
1.4479-1.48160.2312170.19913125X-RAY DIFFRACTION99
1.4816-1.51860.25861720.18993184X-RAY DIFFRACTION99
1.5186-1.55970.22341700.17893205X-RAY DIFFRACTION100
1.5597-1.60560.17061780.1783155X-RAY DIFFRACTION100
1.6056-1.65740.23051580.1783202X-RAY DIFFRACTION100
1.6574-1.71670.21961940.18113168X-RAY DIFFRACTION100
1.7167-1.78540.18141900.18033180X-RAY DIFFRACTION100
1.7854-1.86670.24041800.17883164X-RAY DIFFRACTION99
1.8667-1.96510.21161340.18223222X-RAY DIFFRACTION100
1.9651-2.08820.22411670.1873178X-RAY DIFFRACTION100
2.0882-2.24940.20771920.17343154X-RAY DIFFRACTION100
2.2494-2.47580.18331580.18473225X-RAY DIFFRACTION100
2.4758-2.8340.23811560.1933196X-RAY DIFFRACTION100
2.834-3.57040.22721610.18323095X-RAY DIFFRACTION97
3.5704-47.91750.22251740.21613112X-RAY DIFFRACTION97

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