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- PDB-5hb1: Crystal structure of Chaetomium thermophilum Nup170 SOL -

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Basic information

Entry
Database: PDB / ID: 5hb1
TitleCrystal structure of Chaetomium thermophilum Nup170 SOL
ComponentsNucleoporin NUP170
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / Protein transport
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane
Similarity search - Function
Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.007 Å
AuthorsLin, 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
A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)92,2591
Polymers92,2591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area40780 Å2
2
A: Nucleoporin NUP170

A: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)184,5182
Polymers184,5182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2250 Å2
ΔGint-29 kcal/mol
Surface area79300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 138.620, 89.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 92259.148 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: NUP170, CTHT_0036270 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7B6

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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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.1 M HEPES (pH 7.1), 0.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4→40 Å / Num. obs: 10614 / % possible obs: 99.7 % / Redundancy: 12.8 % / Net I/σ(I): 18.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 4.007→40 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 50.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3524 789 10.03 %
Rwork0.3035 --
obs0.3087 7867 75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.007→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 0 0 5895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035992
X-RAY DIFFRACTIONf_angle_d0.4628119
X-RAY DIFFRACTIONf_dihedral_angle_d10.4113645
X-RAY DIFFRACTIONf_chiral_restr0.025933
X-RAY DIFFRACTIONf_plane_restr0.0031056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0072-4.2580.3724440.4214432X-RAY DIFFRACTION28
4.258-4.58640.4718950.4006796X-RAY DIFFRACTION52
4.5864-5.04710.42841280.37281123X-RAY DIFFRACTION73
5.0471-5.77570.39861610.39821490X-RAY DIFFRACTION95
5.7757-7.26980.37581770.37311583X-RAY DIFFRACTION100
7.2698-40.48510.31721840.24761654X-RAY DIFFRACTION99

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