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- PDB-4fhm: Nup37-Nup120(aa1-961) complex from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 4fhm
TitleNup37-Nup120(aa1-961) complex from Schizosaccharomyces pombe
Components
  • NUCLEOPORIN NUP37
  • Nucleoporin nup120
KeywordsSTRUCTURAL PROTEIN/OXIDOREDUCTASE / PROTEIN COMPLEX / STRUCTURAL PROTEIN / NUCLEAR PORE COMPLEX / MRNA TRANSPORT / PROTEIN TRANSPORT / WD REPEAT / HELICAL DOMAIN / TRANSLOCATION / TRANSPORT / STRUCTURAL PROTEIN-OXIDOREDUCTASE complex
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transcriptional regulation by small RNAs / nuclear pore outer ring ...Regulation of HSF1-mediated heat shock response / Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 Nup120/160 / Nucleoporin Nup37 / Nucleoporin Nup120/160 / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized WD repeat-containing protein C4F10.18 / Nucleoporin nup120
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.339 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: NUCLEOPORIN NUP37
B: Nucleoporin nup120


Theoretical massNumber of molelcules
Total (without water)152,7752
Polymers152,7752
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-17 kcal/mol
Surface area61240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.053, 164.053, 310.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit is a dimer. The asymmetric unit is the same as the biological assembly.

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Components

#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
#2: Protein Nucleoporin nup120 / Nuclear pore protein nup120


Mass: 109727.008 Da / Num. of mol.: 1 / Fragment: fragment 1-961
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: nup120, SPBC3B9.16c / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43044

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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: 6.83 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM HEPES/NaOH pH7.5, 1.9 M MgOAc , VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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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: Oct 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.339→71.419 Å / Num. obs: 28523 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rsym value: 0.226 / Net I/σ(I): 8.3
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
4.4-4.557.40.51979826581.46799.9
4.55-4.738.80.52249025601.359100
4.73-4.9210.40.62573324741.085100
4.92-5.1412.20.72917823961.059100
5.14-5.3913.50.73095822901.026100
5.39-5.6813.90.83018721730.902100
5.68-6.0214.112894720590.677100
6.02-6.44141.32728319550.549100
6.44-6.9613.822511018250.362100
6.96-7.6213.532281316900.239100
7.62-8.5212.851969415410.143100
8.52-9.8411.671583613690.09199.9
9.84-12.0510.69.31251211800.06899.9
12.05-17.0411.410.6107359420.05999.9
17.04-71.41910.513.758705590.04597.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 4.339→64.497 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 1.34 / Phase error: 42.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.348 1452 5.09 %
Rwork0.3011 --
obs0.3035 28523 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 710.05 Å2 / Biso mean: 319.1173 Å2 / Biso min: 142.52 Å2
Refinement stepCycle: LAST / Resolution: 4.339→64.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10113 0 0 0 10113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510342
X-RAY DIFFRACTIONf_angle_d1.01514058
X-RAY DIFFRACTIONf_chiral_restr0.071628
X-RAY DIFFRACTIONf_plane_restr0.0041769
X-RAY DIFFRACTIONf_dihedral_angle_d14.2413705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.3394-4.49440.45441320.37132439257192
4.4944-4.67430.4271390.363126872826100
4.6743-4.8870.37781420.357926652807100
4.887-5.14450.40511510.363326782829100
5.1445-5.46670.41151370.368427212858100
5.4667-5.88850.41621550.375826872842100
5.8885-6.48060.47011480.383427292877100
6.4806-7.41720.3991610.344627282889100
7.4172-9.34030.32721400.273627872927100
9.3403-64.50380.27241470.24132950309799
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)
15.0695-7.6295-1.04567.34290.27743.7353-0.3035-0.28170.2768-0.2702-1.68950.7651-0.2010.6233.06312.229-0.15040.5382.86490.12013.167932.609670.199-6.0935
28.45120.9783-3.55727.8859-3.833211.49410.02171.09680.9686-1.8539-0.4099-0.20990.5825-0.99130.67042.4095-0.10080.41081.6533-0.08072.45221.489465.295814.1877
34.2968-6.10752.587910.463-2.05017.13521.1050.22290.2561-1.7350.7229-2.0629-0.3416-1.1489-1.88372.99210.23750.1771.5749-0.02232.960229.380949.90040.7922
41.96710.14451.51675.69090.57685.58050.5626-0.0180.07131.51290.2023-0.13760.09880.0164-0.8422.9211-0.0290.58761.2391-0.13522.594436.910415.692657.2246
50.0274-0.72132.98093.596-5.606813.37870.1989-0.64860.35920.6852-0.26321.880.0903-1.35060.04862.86320.03830.83452.1335-0.2072.800623.664637.059244.0915
64.7512-4.6149-1.44373.70540.59976.64420.0829-1.1905-0.007-0.61440.4133-0.5553-0.2071-1.2283-0.23572.9221-0.28250.72.05170.03952.888932.492360.397345.9711
75.7556-0.9635-7.383710.5395-6.13444.74460.78611.3871-0.7421-0.7442-0.0252-0.76450.3651.6516-1.12472.01940.18760.38252.3541-0.64721.663456.57166.630717.7734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 254 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 389 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 345 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 346 through 552 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 553 through 838 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 839 through 961 )B0

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