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- PDB-5hb0: Crystal structure of Chaetomium thermophilum Nup170 CTD-Nup145N c... -

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Basic information

Entry
Database: PDB / ID: 5hb0
TitleCrystal structure of Chaetomium thermophilum Nup170 CTD-Nup145N complex
Components
  • Nucleoporin NUP145
  • Nucleoporin NUP170
KeywordsPROTEIN TRANSPORT / Nucleocytoplasmic transport
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear localization sequence binding / structural constituent of nuclear pore / RNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...protein localization to nuclear inner membrane / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear localization sequence binding / structural constituent of nuclear pore / RNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / mRNA transport / protein import into nucleus / nuclear membrane / hydrolase activity / RNA binding
Similarity search - Function
Nucleoporin, helical C-terminal domain / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal ...Nucleoporin, helical C-terminal domain / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP170 / Nucleoporin NUP145
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsLin, D.H. / Mobbs, G. / 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
Chinese 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: Nucleoporin NUP170
A: Nucleoporin NUP170
C: Nucleoporin NUP170
D: Nucleoporin NUP170
E: Nucleoporin NUP145
F: Nucleoporin NUP145
G: Nucleoporin NUP145
H: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)255,9288
Polymers255,9288
Non-polymers00
Water00
1
B: Nucleoporin NUP170
E: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)63,9822
Polymers63,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoporin NUP170
F: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)63,9822
Polymers63,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoporin NUP170
G: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)63,9822
Polymers63,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoporin NUP170
H: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)63,9822
Polymers63,9822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Nucleoporin NUP170
E: Nucleoporin NUP145

C: Nucleoporin NUP170
G: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)127,9644
Polymers127,9644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area6150 Å2
ΔGint-41 kcal/mol
Surface area55940 Å2
MethodPISA
6
A: Nucleoporin NUP170
D: Nucleoporin NUP170
F: Nucleoporin NUP145
H: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)127,9644
Polymers127,9644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-37 kcal/mol
Surface area53880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.590, 111.470, 111.750
Angle α, β, γ (deg.)91.82, 92.47, 91.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 61392.016 Da / Num. of mol.: 4 / Mutation: delta 1375-1377
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
#2: Protein/peptide
Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 2590.007 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SAK3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 12 % (w/v) PEG 3350, 0.2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 45493 / % possible obs: 98.8 % / Redundancy: 7 % / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 3.5→45.364 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 2011 4.42 %
Rwork0.2101 --
obs0.2124 45466 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→45.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16998 0 0 0 16998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517323
X-RAY DIFFRACTIONf_angle_d0.61623525
X-RAY DIFFRACTIONf_dihedral_angle_d11.5310509
X-RAY DIFFRACTIONf_chiral_restr0.032671
X-RAY DIFFRACTIONf_plane_restr0.0043070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.496-3.58340.41691340.32512946X-RAY DIFFRACTION93
3.5834-3.68020.30461330.29213104X-RAY DIFFRACTION99
3.6802-3.78850.32241520.27173107X-RAY DIFFRACTION99
3.7885-3.91070.31121370.26033101X-RAY DIFFRACTION99
3.9107-4.05040.29371370.24593119X-RAY DIFFRACTION99
4.0504-4.21240.29161500.22483127X-RAY DIFFRACTION99
4.2124-4.4040.27621390.20383115X-RAY DIFFRACTION99
4.404-4.6360.2461490.18683112X-RAY DIFFRACTION99
4.636-4.92610.23611390.17943108X-RAY DIFFRACTION99
4.9261-5.30590.21631410.19523157X-RAY DIFFRACTION99
5.3059-5.83890.26481560.21093107X-RAY DIFFRACTION99
5.8389-6.68150.28721460.21773101X-RAY DIFFRACTION99
6.6815-8.40920.20971430.18493144X-RAY DIFFRACTION100
8.4092-45.36770.20181550.15613107X-RAY DIFFRACTION99

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