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- PDB-5cwt: Crystal structure of Chaetomium thermophilum Nup57 -

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Basic information

Entry
Database: PDB / ID: 5cwt
TitleCrystal structure of Chaetomium thermophilum Nup57
ComponentsNucleoporin NUP57
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


mRNA transport / nuclear pore / protein transport / nuclear membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3600 / NUP57/Nup54 C-terminal domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.5 Å
AuthorsBley, C.J. / Hoelz, A.
Funding support United States, United Kingdom, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM111461 United States
V Foundation for Cancer ResearchAlbert Wyrick V Scholar Award United States
Edward Mallinckrodt Jr. Foundation54th Mallinckrodt Scholar Award United States
Sidney Kimmel Foundation for Cancer ResearchKimmel Scholar Award United States
The Camille & Henry Dreyfus FoundationCamille-Dreyfus Teacher Scholar Award United Kingdom
CitationJournal: Science / Year: 2015
Title: Architecture of the fungal nuclear pore inner ring complex.
Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Mar 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 NUP57
B: Nucleoporin NUP57
C: Nucleoporin NUP57
D: Nucleoporin NUP57


Theoretical massNumber of molelcules
Total (without water)25,2004
Polymers25,2004
Non-polymers00
Water32418
1
A: Nucleoporin NUP57
B: Nucleoporin NUP57


Theoretical massNumber of molelcules
Total (without water)12,6002
Polymers12,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-16 kcal/mol
Surface area6690 Å2
MethodPISA
2
C: Nucleoporin NUP57
D: Nucleoporin NUP57


Theoretical massNumber of molelcules
Total (without water)12,6002
Polymers12,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-15 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.252, 42.361, 138.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsNup57 is a homo-dimer in solution by SEC-MALS

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Components

#1: Protein
Nucleoporin NUP57 / Nuclear pore protein NUP57


Mass: 6299.908 Da / Num. of mol.: 4 / Fragment: UNP residues 265-317
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: NUP57, CTHT_0010940 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0R2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5 % (w/v) PEG 1,000 12 % (w/v) PEG 8,000

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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: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 8970 / Num. obs: 8970 / % possible obs: 98 % / Redundancy: 15.2 % / Rsym value: 0.043 / Net I/σ(I): 58.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.5→19.256 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 809 9.96 %Random selection
Rwork0.241 ---
obs0.2461 8126 86.9 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 18 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021321
X-RAY DIFFRACTIONf_angle_d0.4431749
X-RAY DIFFRACTIONf_dihedral_angle_d14.238541
X-RAY DIFFRACTIONf_chiral_restr0.031174
X-RAY DIFFRACTIONf_plane_restr0.001226
LS refinement shellResolution: 2.5→2.6549 Å /
RfactorNum. reflection
Rfree0.3117 -
obs0.2514 655

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