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- PDB-5hb5: Crystal structure of Chaetomium thermophilum Nup145N APD -

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Basic information

Entry
Database: PDB / ID: 5hb5
TitleCrystal structure of Chaetomium thermophilum Nup145N APD
ComponentsNucleoporin NUP145
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / Protein transport
Function / homology
Function and homology information


structural constituent of nuclear pore / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / mRNA transport / nuclear pore / protein transport / nuclear membrane / hydrolase activity / RNA binding
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin FG repeat / Nucleoporin FG repeat region / 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 autopeptidase / NUP C-terminal domain profile. ...Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin FG repeat / Nucleoporin FG repeat region / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Nucleoporin NUP145
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP145
B: Nucleoporin NUP145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7129
Polymers31,3882
Non-polymers1,3247
Water5,819323
1
A: Nucleoporin NUP145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0723
Polymers15,6941
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6396
Polymers15,6941
Non-polymers9455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.082, 34.856, 78.179
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 15693.921 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: NUP145, CTHT_0042590 / Production host: Escherichia coli (E. coli)
References: UniProt: G0SAK3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid (pH 3.0), 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 38743 / % possible obs: 97.2 % / Redundancy: 6.6 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.5→27.663 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 2012 5.2 %
Rwork0.1612 --
obs0.1627 38683 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→27.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 91 323 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052490
X-RAY DIFFRACTIONf_angle_d0.8083407
X-RAY DIFFRACTIONf_dihedral_angle_d16.8261037
X-RAY DIFFRACTIONf_chiral_restr0.065348
X-RAY DIFFRACTIONf_plane_restr0.005462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4982-1.53570.30241350.27782458X-RAY DIFFRACTION92
1.5357-1.57720.28761380.2212505X-RAY DIFFRACTION94
1.5772-1.62360.21461430.18452574X-RAY DIFFRACTION97
1.6236-1.6760.21621440.17772626X-RAY DIFFRACTION98
1.676-1.73590.2121460.16242655X-RAY DIFFRACTION99
1.7359-1.80540.21541430.15522607X-RAY DIFFRACTION98
1.8054-1.88750.19081390.15472546X-RAY DIFFRACTION95
1.8875-1.9870.19791440.15062675X-RAY DIFFRACTION99
1.987-2.11150.19211460.14392649X-RAY DIFFRACTION99
2.1115-2.27440.19711450.14442652X-RAY DIFFRACTION99
2.2744-2.50320.18371440.15012619X-RAY DIFFRACTION97
2.5032-2.86510.15961470.15652700X-RAY DIFFRACTION99
2.8651-3.60840.1721470.15222646X-RAY DIFFRACTION97
3.6084-27.66730.17141510.16832759X-RAY DIFFRACTION98

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