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- PDB-5hb7: Crystal structure of Chaetomium thermophilum Nup53 RRM -

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Basic information

Entry
Database: PDB / ID: 5hb7
TitleCrystal structure of Chaetomium thermophilum Nup53 RRM
ComponentsNucleoporin NUP53
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic Transport / Protein transport
Function / homologymRNA transport / nuclear pore / protein transport / nuclear membrane / Nucleotide-binding alpha-beta plait domain superfamily / IODIDE ION / Nucleoporin NUP53
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.819 Å
AuthorsLin, D.H. / Stuwe, T. / 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 NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7244
Polymers14,3431
Non-polymers3813
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-1 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.990, 50.370, 60.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 14342.988 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: NUP53, CTHT_0012410 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S156
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.0), 24 % (w/v) PEG 3350, 0.2 M potassium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.8→40 Å / Num. obs: 92712 / % possible obs: 88.4 % / Redundancy: 9.6 % / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 0.819→38.586 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1315 4651 5.02 %
Rwork0.1179 --
obs0.1186 92709 88.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.819→38.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 3 236 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081241
X-RAY DIFFRACTIONf_angle_d1.0621713
X-RAY DIFFRACTIONf_dihedral_angle_d14.642492
X-RAY DIFFRACTIONf_chiral_restr0.082166
X-RAY DIFFRACTIONf_plane_restr0.009244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8191-0.82850.2911620.26561338X-RAY DIFFRACTION40
0.8285-0.83820.224890.22231742X-RAY DIFFRACTION53
0.8382-0.84840.2425980.20191930X-RAY DIFFRACTION59
0.8484-0.85920.18941060.17952084X-RAY DIFFRACTION63
0.8592-0.87050.16751060.1632358X-RAY DIFFRACTION71
0.8705-0.88240.14061440.14882669X-RAY DIFFRACTION82
0.8824-0.8950.17081540.13782880X-RAY DIFFRACTION88
0.895-0.90840.14391730.12732927X-RAY DIFFRACTION90
0.9084-0.92260.14061650.12152966X-RAY DIFFRACTION89
0.9226-0.93770.1281630.11662959X-RAY DIFFRACTION91
0.9377-0.95390.13291570.1083053X-RAY DIFFRACTION93
0.9539-0.97120.12331650.10532983X-RAY DIFFRACTION91
0.9712-0.98990.12831520.09963094X-RAY DIFFRACTION94
0.9899-1.01010.11291920.09333066X-RAY DIFFRACTION94
1.0101-1.03210.11191580.09173113X-RAY DIFFRACTION94
1.0321-1.05610.09331730.08733159X-RAY DIFFRACTION96
1.0561-1.08250.09381610.08593142X-RAY DIFFRACTION96
1.0825-1.11170.09951720.08443220X-RAY DIFFRACTION97
1.1117-1.14450.09211680.08153138X-RAY DIFFRACTION95
1.1445-1.18140.10051610.08333247X-RAY DIFFRACTION97
1.1814-1.22360.08911790.08733235X-RAY DIFFRACTION98
1.2236-1.27260.10441740.09693216X-RAY DIFFRACTION98
1.2726-1.33050.10651550.10353291X-RAY DIFFRACTION98
1.3305-1.40070.11781680.10763161X-RAY DIFFRACTION95
1.4007-1.48850.12081630.11033283X-RAY DIFFRACTION99
1.4885-1.60340.12151800.11423288X-RAY DIFFRACTION98
1.6034-1.76470.13731660.12133351X-RAY DIFFRACTION99
1.7647-2.02010.14571640.1273290X-RAY DIFFRACTION97
2.0201-2.5450.13582110.12533377X-RAY DIFFRACTION99
2.545-38.62890.15651720.13713498X-RAY DIFFRACTION98

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