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- PDB-5hb3: Crystal structure of Chaetomium thermophilum Nic96 SOL-Nup53 complex -

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Basic information

Entry
Database: PDB / ID: 5hb3
TitleCrystal structure of Chaetomium thermophilum Nic96 SOL-Nup53 complex
Components
  • Nucleoporin NIC96
  • Nucleoporin NUP53
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic Transport / Protein Transport
Function / homology
Function and homology information


structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / protein import into nucleus / protein transport / nuclear membrane
Similarity search - Function
Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nucleoporin NIC96 / Nucleoporin NUP53
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 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 NIC96
B: Nucleoporin NUP53
C: Nucleoporin NIC96
D: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,1197
Polymers175,0134
Non-polymers1063
Water1,27971
1
A: Nucleoporin NIC96
B: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5423
Polymers87,5062
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-23 kcal/mol
Surface area34830 Å2
MethodPISA
2
C: Nucleoporin NIC96
D: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5774
Polymers87,5062
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-33 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.520, 86.950, 98.010
Angle α, β, γ (deg.)100.69, 99.59, 95.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleoporin NIC96 / Nuclear pore protein NIC96


Mass: 81516.734 Da / Num. of mol.: 2
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
#2: Protein Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 5989.653 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M TRIS (pH 7.0), 12 % (w/v) PEG 6000, 1.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 48566 / % possible obs: 88.6 % / Redundancy: 3.9 % / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.65→47.285 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2368 4.88 %
Rwork0.2116 --
obs0.2134 48535 88.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→47.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11477 0 3 71 11551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211718
X-RAY DIFFRACTIONf_angle_d0.56215851
X-RAY DIFFRACTIONf_dihedral_angle_d13.8934410
X-RAY DIFFRACTIONf_chiral_restr0.0361735
X-RAY DIFFRACTIONf_plane_restr0.0022087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6499-2.7040.33281340.29632511X-RAY DIFFRACTION82
2.704-2.76280.37961410.29812596X-RAY DIFFRACTION86
2.7628-2.8270.33181370.28322820X-RAY DIFFRACTION92
2.827-2.89770.3731400.26392796X-RAY DIFFRACTION91
2.8977-2.97610.30341480.27062826X-RAY DIFFRACTION91
2.9761-3.06360.31521300.26732714X-RAY DIFFRACTION89
3.0636-3.16250.31611470.26812720X-RAY DIFFRACTION89
3.1625-3.27550.3441390.25942599X-RAY DIFFRACTION85
3.2755-3.40660.27991220.23752543X-RAY DIFFRACTION83
3.4066-3.56160.29151540.22972829X-RAY DIFFRACTION92
3.5616-3.74930.2391290.22012815X-RAY DIFFRACTION91
3.7493-3.98410.2331410.20312784X-RAY DIFFRACTION90
3.9841-4.29150.21721360.18612656X-RAY DIFFRACTION87
4.2915-4.7230.20341440.17832674X-RAY DIFFRACTION88
4.723-5.40560.2081420.18042848X-RAY DIFFRACTION92
5.4056-6.80730.21881390.21012648X-RAY DIFFRACTION87
6.8073-47.29290.20771450.16962788X-RAY DIFFRACTION91

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