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- PDB-5cwv: Crystal structure of Chaetomium thermophilum Nup192 TAIL domain -

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Basic information

Entry
Database: PDB / ID: 5cwv
TitleCrystal structure of Chaetomium thermophilum Nup192 TAIL domain
ComponentsNucleoporin NUP192
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic 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 / Nucleoporin NUP192
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.155 Å
AuthorsStuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. ...Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM111461 United States
V Foundation for Cancer ResearchAlbert Wyrick V Scholar Award United States
Edward Mallinckrodt Jr. Foundation54th Mallinckrodt Scholar Award United States
Sidney Kimmel Foundation for Cancer ResearchKimmel Scholar Award United States
The Camille & Henry Dreyfus FoundationCamille-Dreyfus Teacher Scholar Award United States
CitationJournal: Science / Year: 2015
Title: Architecture of the fungal nuclear pore inner ring complex.
Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP192
B: Nucleoporin NUP192


Theoretical massNumber of molelcules
Total (without water)78,3102
Polymers78,3102
Non-polymers00
Water00
1
A: Nucleoporin NUP192


Theoretical massNumber of molelcules
Total (without water)39,1551
Polymers39,1551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP192


Theoretical massNumber of molelcules
Total (without water)39,1551
Polymers39,1551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.745, 114.474, 114.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer by SEC-MALS

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Components

#1: Protein Nucleoporin NUP192 / Nuclear pore protein NUP192


Mass: 39154.789 Da / Num. of mol.: 2 / Fragment: UNP residues 1397-1756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP192, CTHT_0023410 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4T0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 50 mM HEPES, pH 7.1 15 % (w/v) PEG 200 340 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. obs: 13043 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rsym value: 0.075 / Net I/σ(I): 21.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.155→19.891 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1453 10.12 %Random selection
Rwork0.1943 ---
obs0.1987 13043 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.155→19.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 0 0 4167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034217
X-RAY DIFFRACTIONf_angle_d0.655706
X-RAY DIFFRACTIONf_dihedral_angle_d11.9731535
X-RAY DIFFRACTIONf_chiral_restr0.034697
X-RAY DIFFRACTIONf_plane_restr0.003718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1545-3.20870.34041510.33611277X-RAY DIFFRACTION98
3.2087-3.26680.36491330.3051252X-RAY DIFFRACTION99
3.2668-3.32930.35991350.33161245X-RAY DIFFRACTION100
3.3293-3.3970.35561370.29321305X-RAY DIFFRACTION100
3.397-3.47040.31571410.27711266X-RAY DIFFRACTION99
3.4704-3.55070.2641410.26911243X-RAY DIFFRACTION100
3.5507-3.6390.39031440.26721273X-RAY DIFFRACTION99
3.639-3.73680.29421320.23511244X-RAY DIFFRACTION100
3.7368-3.8460.29031410.21231291X-RAY DIFFRACTION99
3.846-3.96910.25511490.19331274X-RAY DIFFRACTION100
3.9691-4.10980.25091340.1831265X-RAY DIFFRACTION100
4.1098-4.27280.27171460.18641258X-RAY DIFFRACTION100
4.2728-4.46520.19851450.17231235X-RAY DIFFRACTION99
4.4652-4.69770.20461420.17971293X-RAY DIFFRACTION100
4.6977-4.98760.19941480.15911255X-RAY DIFFRACTION99
4.9876-5.36570.2241440.18271254X-RAY DIFFRACTION100
5.3657-5.89290.27071430.20291259X-RAY DIFFRACTION99
5.8929-6.71670.2351440.21931260X-RAY DIFFRACTION100
6.7167-8.35670.21591430.17971259X-RAY DIFFRACTION100
8.3567-19.89160.18731500.14761244X-RAY DIFFRACTION98

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