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- PDB-5haz: Structure of Chaetomium thermophilum Nup170 CTD -

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Basic information

Entry
Database: PDB / ID: 5haz
TitleStructure of Chaetomium thermophilum Nup170 CTD
ComponentsNucleoporin NUP170
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / protein 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 / structural constituent of nuclear pore / RNA export from nucleus / mRNA transport / protein import into nucleus / nuclear membrane
Similarity search - Function
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, Nup133/Nup155-like, N-terminal / Nup133 N terminal like
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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
Duetsche Forschungsgemeinschaft 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 1.4Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8665
Polymers63,4811
Non-polymers3854
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-3 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.260, 54.770, 108.200
Angle α, β, γ (deg.)90.00, 91.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1503-

EPE

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Components

#1: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 63480.570 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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES (pH 7.0), 1.0 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 47908 / % possible obs: 97.8 % / Redundancy: 6.8 % / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.1→37.255 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 2395 5 %
Rwork0.2056 --
obs0.2068 47882 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 24 378 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054642
X-RAY DIFFRACTIONf_angle_d0.6266328
X-RAY DIFFRACTIONf_dihedral_angle_d12.5842839
X-RAY DIFFRACTIONf_chiral_restr0.032708
X-RAY DIFFRACTIONf_plane_restr0.003839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0965-2.13930.44131300.33452463X-RAY DIFFRACTION91
2.1393-2.18580.35841410.28562684X-RAY DIFFRACTION99
2.1858-2.23670.27461410.26172681X-RAY DIFFRACTION99
2.2367-2.29260.29161420.23452691X-RAY DIFFRACTION98
2.2926-2.35460.26281380.22242617X-RAY DIFFRACTION97
2.3546-2.42390.25011400.20972669X-RAY DIFFRACTION99
2.4239-2.50210.24321410.21112681X-RAY DIFFRACTION99
2.5021-2.59150.25931430.20872713X-RAY DIFFRACTION99
2.5915-2.69520.28211400.21432655X-RAY DIFFRACTION98
2.6952-2.81780.29061400.21012657X-RAY DIFFRACTION98
2.8178-2.96630.23291390.21152658X-RAY DIFFRACTION97
2.9663-3.15210.24611430.222707X-RAY DIFFRACTION99
3.1521-3.39530.2281430.21242710X-RAY DIFFRACTION99
3.3953-3.73670.22041400.20712662X-RAY DIFFRACTION97
3.7367-4.27680.20631440.18992736X-RAY DIFFRACTION99
4.2768-5.38570.19351420.17352705X-RAY DIFFRACTION98
5.3857-37.26070.21021480.20192798X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.29910.2539-2.01613.60510.44733.5084-0.15031.0637-0.31790.08190.0174-0.0473-0.0656-0.81850.0610.27810.0114-0.05760.7666-0.06620.4212-159.1167-72.952-53.3411
23.7877-0.7488-1.6951.92872.06444.12430.1169-0.40970.20920.2556-0.16590.5421-0.2203-0.52120.0160.52850.0860.09910.52660.00120.5348-133.2574-100.4758-82.9409
30.999-0.2572-0.17120.9689-0.04351.3418-0.0704-0.0708-0.07870.05750.08580.06960.0021-0.07370.010.3539-0.0372-0.03610.25490.00430.313-103.9715-121.0675-92.7711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 851:1032
2X-RAY DIFFRACTION2chain A and resid 1033:1193
3X-RAY DIFFRACTION3chain A and resid 1194:1402

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