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- PDB-4fhl: Nucleoporin Nup37 from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 4fhl
TitleNucleoporin Nup37 from Schizosaccharomyces pombe
ComponentsNUCLEOPORIN NUP37
KeywordsSTRUCTURAL PROTEIN / NUCLEAR PORE COMPLEX / MRNA TRANSPORT / PROTEIN TRANSPORT / WD REPEAT / TRANSLOCATION / TRANSPORT
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore outer ring / nucleocytoplasmic transport / nuclear pore ...Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore outer ring / nucleocytoplasmic transport / nuclear pore / nucleus / cytosol
Similarity search - Function
Nucleoporin Nup37 / 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
1,4-BUTANEDIOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Uncharacterized WD repeat-containing protein C4F10.18
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBilokapic, S. / Schwartz, T.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex.
Authors: Bilokapic, S. / Schwartz, T.U.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Structure summary
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: NUCLEOPORIN NUP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,82311
Polymers43,0481
Non-polymers77510
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NUCLEOPORIN NUP37
hetero molecules

A: NUCLEOPORIN NUP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,64622
Polymers86,0972
Non-polymers1,55020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area7320 Å2
ΔGint13 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.726, 131.726, 117.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit is the same as the biological assembly.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NUCLEOPORIN NUP37 / Uncharacterized WD repeat-containing protein C4F10.18 / NUP37


Mass: 43048.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: Nup37, SPAC4F10.18 / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O36030

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 5.94 Å3/Da / Density % sol: 79.31 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 100 mM Tris/HCl pH 7.75-8.25, 4% (v/v) 1,4-butanediol, 400-500 mM Li2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 303.0K

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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: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→46.553 Å / Num. all: 32471 / Num. obs: 32471 / % possible obs: 100 % / Redundancy: 9.5 % / Rsym value: 0.108 / Net I/σ(I): 16.9
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.699.60.73016831301.056100
2.69-2.799.80.92972230230.79100
2.79-2.919.81.32852329110.544100
2.91-3.049.82.12759728080.345100
3.04-3.189.832614926650.246100
3.18-3.369.84.82509525690.155100
3.36-3.569.772376824410.106100
3.56-3.819.79.12209322870.081100
3.81-4.119.6102062721480.071100
4.11-4.59.410.61849919620.062100
4.5-5.049.210.51664618140.06100
5.04-5.81910.51431915960.06299.9
5.81-7.128.711.21195513790.0699.9
7.12-10.078.712.7950910910.04999.9
10.07-46.5537.515.448636470.04198.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.6→46.553 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 1921 6.18 %
Rwork0.1761 --
obs0.1769 31092 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.48 Å2 / Biso mean: 54.3598 Å2 / Biso min: 22.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 47 129 2841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032771
X-RAY DIFFRACTIONf_angle_d0.8343764
X-RAY DIFFRACTIONf_chiral_restr0.057439
X-RAY DIFFRACTIONf_plane_restr0.003474
X-RAY DIFFRACTIONf_dihedral_angle_d12.336982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5998-2.66480.30141170.26961792190984
2.6648-2.73690.25191290.24671900202988
2.7369-2.81740.28651270.23421899202690
2.8174-2.90830.24941300.2251994212493
2.9083-3.01230.24221320.21122037216995
3.0123-3.13280.20741380.2062047218595
3.1328-3.27540.23631360.2012106224297
3.2754-3.4480.19771410.17532121226299
3.448-3.6640.17181390.16142149228899
3.664-3.94670.15591420.157521602302100
3.9467-4.34360.14851440.14221862330100
4.3436-4.97160.14161440.125821862330100
4.9716-6.26120.16921470.172322442391100
6.2612-46.57960.21961550.197423502505100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1869-0.29412.50482.31821.68645.97010.0585-0.3080.03630.1888-0.06480.2988-0.0439-0.8283-0.00250.31530.01220.03710.36620.03610.37410.566550.9163128.208
23.9582-1.7513-0.57144.15442.63424.4334-0.0179-0.1937-0.30010.35640.0672-0.28150.32670.3093-0.02850.24980.0131-0.02460.24550.0570.306720.636339.9914128.5413
35.074-2.78030.12995.43570.66353.99210.13050.3845-0.6186-0.2651-0.11760.18420.45610.0028-0.0260.2808-0.0189-0.02140.3607-0.02810.32234.808338.7497111.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 106 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 272 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 389 )A0

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