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- PDB-5cws: Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup4... -

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Basic information

Entry
Database: PDB / ID: 5cws
TitleCrystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57 channel nucleoporin heterotrimer bound to its Nic96 nuclear pore complex attachment site
Components
  • Nucleoporin NIC96
  • Nucleoporin NSP1
  • Nucleoporin NUP49
  • Nucleoporin NUP57
  • sAB-158 Fab Heavy Chain
  • sAB-158 Fab Light Chain
KeywordsPROTEIN TRANSPORT / nucleocytoplasmic transport
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore ...protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / phospholipid binding / protein import into nucleus / protein transport / nuclear membrane
Similarity search - Function
Nucleoporin Nup49 C-terminal helical region / NUP57/Nup54 C-terminal domain / Nucleoporin p58/p45 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin interacting component Nup93/Nic96 ...Nucleoporin Nup49 C-terminal helical region / NUP57/Nup54 C-terminal domain / Nucleoporin p58/p45 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
OSMIUM ION / Nucleoporin NIC96 / Nucleoporin NUP57 / Nucleoporin NUP49 / Nucleoporin NSP1
Similarity search - Component
Biological speciesHomo sapiens (human)
Chaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.77 Å
AuthorsBley, C.J. / Petrovic, S. / Paduch, M. / Lu, V. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 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
The Camille & Henry Dreyfus FoundationCamille-Dreyfus Teacher Scholar Award United States
Edward Mallinckrodt Jr. Foundation54th Mallinckrodt Scholar Award United States
Sidney Kimmel Foundation for Cancer ResearchKimmel Scholar Award United States
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 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Sep 13, 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 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: sAB-158 Fab Light Chain
B: sAB-158 Fab Heavy Chain
C: Nucleoporin NSP1
D: Nucleoporin NUP49
E: Nucleoporin NUP57
F: Nucleoporin NIC96
G: sAB-158 Fab Light Chain
H: sAB-158 Fab Heavy Chain
I: Nucleoporin NSP1
J: Nucleoporin NUP49
K: Nucleoporin NUP57
L: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,74414
Polymers277,36412
Non-polymers3802
Water00
1
A: sAB-158 Fab Light Chain
B: sAB-158 Fab Heavy Chain
C: Nucleoporin NSP1
D: Nucleoporin NUP49
E: Nucleoporin NUP57
F: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8727
Polymers138,6826
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: sAB-158 Fab Light Chain
H: sAB-158 Fab Heavy Chain
I: Nucleoporin NSP1
J: Nucleoporin NUP49
K: Nucleoporin NUP57
L: Nucleoporin NIC96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8727
Polymers138,6826
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.180, 162.820, 212.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules CIDJEKFL

#3: Protein Nucleoporin NSP1 / Nuclear pore protein NSP1 / Nucleoskeletal-like protein


Mass: 23558.211 Da / Num. of mol.: 2 / Fragment: UNP residues 467-674
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: NSP1, CTHT_0054390 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SBQ3
#4: Protein Nucleoporin NUP49 / Nuclear pore protein NUP49


Mass: 24536.504 Da / Num. of mol.: 2 / Fragment: UNP residues 246-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP49, CTHT_0031980 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4X2
#5: Protein Nucleoporin NUP57 / Nuclear pore protein NUP57


Mass: 28792.684 Da / Num. of mol.: 2 / Fragment: UNP residues 74-319
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
#6: Protein Nucleoporin NIC96 / Nuclear pore protein NIC96


Mass: 7793.831 Da / Num. of mol.: 2 / Fragment: UNP residues 139-211
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: NIC96, CTHT_0008480 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S024

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Antibody , 2 types, 4 molecules AGBH

#1: Antibody sAB-158 Fab Light Chain


Mass: 25394.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody sAB-158 Fab Heavy Chain


Mass: 28606.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os

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Details

Has protein modificationY

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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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1M TRIS, pH 8.7 5.7 % (w/v) PEG 20,000 1 % (v/v) 1-propanol
PH range: 8.7 - 8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.14 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 3.77→50 Å / Num. obs: 43896 / % possible obs: 99.9 % / Redundancy: 40.2 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 17
Reflection shellHighest resolution: 3.77 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.77→49.666 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 2000 4.55 %Random selection
Rwork0.2293 ---
obs0.2309 43896 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.77→49.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16524 0 2 0 16526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316864
X-RAY DIFFRACTIONf_angle_d0.67822818
X-RAY DIFFRACTIONf_dihedral_angle_d11.2416264
X-RAY DIFFRACTIONf_chiral_restr0.0292580
X-RAY DIFFRACTIONf_plane_restr0.0032956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.77-3.81770.42961380.4032910X-RAY DIFFRACTION100
3.8177-3.86790.39981400.37512988X-RAY DIFFRACTION100
3.8679-3.92090.41641390.37962927X-RAY DIFFRACTION100
3.9209-3.97690.44181410.36242970X-RAY DIFFRACTION100
3.9769-4.03620.36281360.33662949X-RAY DIFFRACTION100
4.0362-4.09930.37151410.32582994X-RAY DIFFRACTION100
4.0993-4.16640.31031410.29362919X-RAY DIFFRACTION100
4.1664-4.23830.35271370.27842925X-RAY DIFFRACTION100
4.2383-4.31530.24751420.26012922X-RAY DIFFRACTION100
4.3153-4.39820.29461480.23913007X-RAY DIFFRACTION100
4.3982-4.48790.26421410.2332876X-RAY DIFFRACTION100
4.4879-4.58550.25181440.23432972X-RAY DIFFRACTION100
4.5855-4.69210.29811430.22592936X-RAY DIFFRACTION100
4.6921-4.80930.28171410.22782922X-RAY DIFFRACTION100
4.8093-4.93920.29231360.22752989X-RAY DIFFRACTION100
4.9392-5.08440.27161360.20562975X-RAY DIFFRACTION100
5.0844-5.24840.26931460.20742931X-RAY DIFFRACTION100
5.2484-5.43570.28131410.21762948X-RAY DIFFRACTION100
5.4357-5.65310.2821430.22522911X-RAY DIFFRACTION100
5.6531-5.910.30161440.23022972X-RAY DIFFRACTION100
5.91-6.2210.29161350.21692941X-RAY DIFFRACTION100
6.221-6.60990.31831430.21362932X-RAY DIFFRACTION100
6.6099-7.11890.24731370.21162951X-RAY DIFFRACTION100
7.1189-7.83280.20751360.18112962X-RAY DIFFRACTION100
7.8328-8.96050.14861460.16572958X-RAY DIFFRACTION100
8.9605-11.26750.19871390.16562943X-RAY DIFFRACTION100
11.2675-49.67050.30441350.28582923X-RAY DIFFRACTION99

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