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- PDB-4gq2: S. pombe Nup120-Nup37 complex -

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Basic information

Entry
Database: PDB / ID: 4gq2
TitleS. pombe Nup120-Nup37 complex
Components
  • Nucleoporin nup120
  • Nup37
KeywordsTRANSPORT PROTEIN / Beta propeller alpha helical / component of nuclear pore complex
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transcriptional regulation by small RNAs / nuclear pore outer ring ...Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transcriptional regulation by small RNAs / nuclear pore outer ring / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear pore / nuclear periphery / nuclear envelope / nucleus / cytosol
Similarity search - Function
: / : / Nucleoporin NUP120, helical domain / Nucleoporin Nup120, HEAT repeats / Nucleoporin Nup37 / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup120/160 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...: / : / Nucleoporin NUP120, helical domain / Nucleoporin Nup120, HEAT repeats / Nucleoporin Nup37 / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup120/160 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Uncharacterized WD repeat-containing protein C4F10.18 / Nucleoporin nup120
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.4 Å
AuthorsLiu, X. / Mitchell, J. / Wozniak, R. / Blobel, G. / Fan, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural evolution of the membrane-coating module of the nuclear pore complex.
Authors: Liu, X. / Mitchell, J.M. / Wozniak, R.W. / Blobel, G. / Fan, J.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Nucleoporin nup120
P: Nup37


Theoretical massNumber of molelcules
Total (without water)151,2962
Polymers151,2962
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-17 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.475, 123.019, 172.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoporin nup120 / Nuclear pore protein nup120


Mass: 108344.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: nup120, SPBC3B9.16c / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: O43044
#2: Protein Nup37 / WD repeat-containing protein C4F10.18


Mass: 42951.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: Nup37, SPAC4F10.18 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: O36030
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 303 K / Method: evaporation / pH: 5.5
Details: 10% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium acetate, EVAPORATION, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 56356 / Num. obs: 56356 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 34
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 4GQ1

4gq1


Resolution: 2.4→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.658 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25814 2995 5 %RANDOM
Rwork0.20971 ---
obs0.21222 56346 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.694 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---0.29 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10114 0 0 122 10236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0210337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.95714055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23251265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23624.891460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.499151747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451533
X-RAY DIFFRACTIONr_chiral_restr0.0850.21624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217716
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 185 -
Rwork0.326 3780 -
obs--98.93 %

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