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- PDB-5hb2: Crystal Structure of Chaetomium thermophilum Nic96 SOL -

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Basic information

Entry
Database: PDB / ID: 5hb2
TitleCrystal Structure of Chaetomium thermophilum Nic96 SOL
ComponentsNucleoporin NIC96
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / Protein transport
Function / homologyNucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / nuclear pore / protein import into nucleus / nuclear membrane / Nucleoporin NIC96
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsLin, D.H. / Stuwe, T. / Schilbach, S. / Hoelz, A.
Funding support United States, Germany, China, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM111461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM07616 United States
V Foundation for Cancer Research United States
Edward Mallinckrodt Jr. Foundation United States
Sidney Kimmel Foundation for Cancer Research United States
Heritage Medical Research Institute United States
German Research Foundation (DFG) Germany
Boehringer Ingelheim Fonds Germany
China Scholarship Council China
CitationJournal: Science / Year: 2016
Title: Architecture of the symmetric core of the nuclear pore.
Authors: Lin, D.H. / Stuwe, T. / Schilbach, S. / Rundlet, E.J. / Perriches, T. / Mobbs, G. / Fan, Y. / Thierbach, K. / Huber, F.M. / Collins, L.N. / Davenport, A.M. / Jeon, Y.E. / Hoelz, A.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Nucleoporin NIC96


Theoretical massNumber of molelcules
Total (without water)82,5951
Polymers82,5951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.229, 73.007, 122.802
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoporin NIC96 / Nuclear pore protein NIC96


Mass: 82595.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NIC96, CTHT_0008480 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S024
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 4 % Tacsimate (pH 7.4), 14 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 14334 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 3.3→47.664 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 36.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 1410 9.87 %
Rwork0.2306 --
obs0.2354 14284 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→47.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 0 0 5674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035782
X-RAY DIFFRACTIONf_angle_d0.577819
X-RAY DIFFRACTIONf_dihedral_angle_d11.1933533
X-RAY DIFFRACTIONf_chiral_restr0.031853
X-RAY DIFFRACTIONf_plane_restr0.0041034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.41810.42231470.36061251X-RAY DIFFRACTION100
3.4181-3.55490.37921330.32161291X-RAY DIFFRACTION99
3.5549-3.71660.40581320.30091270X-RAY DIFFRACTION99
3.7166-3.91250.32631480.28231277X-RAY DIFFRACTION99
3.9125-4.15750.35111380.25911279X-RAY DIFFRACTION99
4.1575-4.47830.28371400.24231280X-RAY DIFFRACTION100
4.4783-4.92850.29751390.23211294X-RAY DIFFRACTION100
4.9285-5.64070.30181440.24721297X-RAY DIFFRACTION100
5.6407-7.10290.31400.23671290X-RAY DIFFRACTION100
7.1029-47.66860.18621490.16131345X-RAY DIFFRACTION100

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