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- PDB-5hb4: Crystal structure of Chaetomium thermophilum Nup192 -

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Basic information

Entry
Database: PDB / ID: 5hb4
TitleCrystal structure of Chaetomium thermophilum Nup192
ComponentsNup192,Nucleoporin NUP192
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic Transport / Protein transport
Function / homologyNucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / nuclear pore inner ring / nuclear pore organization / structural constituent of nuclear pore / mRNA transport / protein transport / OSMIUM ION / Nucleoporin NUP192
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsStuwe, T. / Lin, D.H. / 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 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Nup192,Nucleoporin NUP192
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,3806
Polymers178,4291
Non-polymers9515
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-21 kcal/mol
Surface area63710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.740, 53.500, 171.790
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nup192,Nucleoporin NUP192 / Nuclear pore protein NUP192


Mass: 178429.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus), (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP192, CTHT_0023410 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4T0
#2: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Os

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1 M TRIS (pH 7.9), 6 % (w/v) PEG 4000, 5 % (v/v) polypropylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.125 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.125 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27800 / % possible obs: 98.6 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.208 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 3.2→47.739 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1377 5.01 %
Rwork0.2329 --
obs0.2345 27508 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→47.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11030 0 5 0 11035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211248
X-RAY DIFFRACTIONf_angle_d0.515246
X-RAY DIFFRACTIONf_dihedral_angle_d10.6456795
X-RAY DIFFRACTIONf_chiral_restr0.0281757
X-RAY DIFFRACTIONf_plane_restr0.0031945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31430.4371340.41192547X-RAY DIFFRACTION97
3.3143-3.4470.37321340.35912529X-RAY DIFFRACTION98
3.447-3.60380.35021370.32762605X-RAY DIFFRACTION99
3.6038-3.79370.38251370.30172594X-RAY DIFFRACTION99
3.7937-4.03130.30591350.27652571X-RAY DIFFRACTION99
4.0313-4.34240.28391380.2342621X-RAY DIFFRACTION99
4.3424-4.7790.25111380.2162626X-RAY DIFFRACTION99
4.779-5.46970.27081390.22072638X-RAY DIFFRACTION100
5.4697-6.88790.2281390.25392647X-RAY DIFFRACTION99
6.8879-47.74450.21731460.17712753X-RAY DIFFRACTION100

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