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- PDB-5hb8: Crystal structure of Chaetomium thermophilum Nup53 RRM (space gro... -

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Basic information

Entry
Database: PDB / ID: 5hb8
TitleCrystal structure of Chaetomium thermophilum Nup53 RRM (space group P3121)
ComponentsNucleoporin NUP53
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / protein transport
Function / homologymRNA transport / nuclear pore / protein transport / nuclear membrane / Nucleotide-binding alpha-beta plait domain superfamily / SUCCINIC ACID / Nucleoporin NUP53
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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
B: Nucleoporin NUP53
C: Nucleoporin NUP53
D: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,54115
Polymers57,3724
Non-polymers1,16911
Water8,359464
1
A: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6714
Polymers14,3431
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6714
Polymers14,3431
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5533
Polymers14,3431
Non-polymers2102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6454
Polymers14,3431
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.660, 94.660, 115.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 14342.988 Da / Num. of mol.: 4
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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4 % Tacsimate (pH 4.1), 15 % (w/v) PEG 3350

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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 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 60735 / % possible obs: 91.1 % / Redundancy: 35.7 % / Net I/σ(I): 37.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.7→47.33 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 1813 3.03 %
Rwork0.1628 --
obs0.1643 59805 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 78 464 4045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013809
X-RAY DIFFRACTIONf_angle_d0.9995186
X-RAY DIFFRACTIONf_dihedral_angle_d12.2222326
X-RAY DIFFRACTIONf_chiral_restr0.049522
X-RAY DIFFRACTIONf_plane_restr0.006711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7460.29711440.21554657X-RAY DIFFRACTION95
1.746-1.79730.23741510.16684812X-RAY DIFFRACTION99
1.7973-1.85540.20721530.16794907X-RAY DIFFRACTION100
1.8554-1.92170.50071100.36523427X-RAY DIFFRACTION70
1.9217-1.99860.34321230.27813813X-RAY DIFFRACTION78
1.9986-2.08960.25891520.18534849X-RAY DIFFRACTION99
2.0896-2.19970.19481500.13974930X-RAY DIFFRACTION100
2.1997-2.33760.17211110.13463528X-RAY DIFFRACTION72
2.3376-2.5180.17691520.12854924X-RAY DIFFRACTION100
2.518-2.77140.20761240.14933901X-RAY DIFFRACTION79
2.7714-3.17240.21451570.15494977X-RAY DIFFRACTION100
3.1724-3.99650.17881300.1494073X-RAY DIFFRACTION81
3.9965-47.34830.19331560.16035194X-RAY DIFFRACTION100

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