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- PDB-5cww: Crystal structure of the Chaetomium thermophilum heterotrimeric N... -

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Basic information

Entry
Database: PDB / ID: 5cww
TitleCrystal structure of the Chaetomium thermophilum heterotrimeric Nup82 NTD-Nup159 TAIL-Nup145N APD complex
Components
  • Nucleoporin NUP145N
  • Nucleoporin NUP159
  • Nucleoporin NUP82
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nuclear localization sequence binding / RNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore ...telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nuclear localization sequence binding / RNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / mRNA export from nucleus / ribosomal small subunit export from nucleus / protein import into nucleus / nuclear membrane / hydrolase activity / RNA binding
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein / 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 ...Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Trp-Asp (WD) repeats signature. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoporin NUP82 / Nucleoporin NUP145 / Nucleoporin NUP159
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsStuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. ...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. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / 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
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 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 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP145N
B: Nucleoporin NUP82
C: Nucleoporin NUP159


Theoretical massNumber of molelcules
Total (without water)85,0963
Polymers85,0963
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-16 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.300, 107.960, 69.590
Angle α, β, γ (deg.)90.00, 108.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleoporin NUP145N / Nuclear pore protein NUP145


Mass: 15693.921 Da / Num. of mol.: 1 / Fragment: UNP residues 858-993
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: Protein Nucleoporin NUP82 / Nuclear pore protein NUP82


Mass: 65644.664 Da / Num. of mol.: 1 / Fragment: UNP residues 1-595
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: NUP82, CTHT_0022610 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4F3
#3: Protein/peptide Nucleoporin NUP159 / Nuclear pore protein NUP159


Mass: 3757.468 Da / Num. of mol.: 1 / Fragment: UNP residues 1449-1480
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: NUP159, CTHT_0054650 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SBS8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM lithium citrate 20 % (w/v) PEG 3,350 3 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 43372 / Num. obs: 43372 / % possible obs: 99 % / Redundancy: 6.9 % / Rsym value: 0.084 / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.187 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2959 6.85 %Random selection
Rwork0.1846 ---
obs0.1865 43203 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 0 164 5717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035770
X-RAY DIFFRACTIONf_angle_d0.7567884
X-RAY DIFFRACTIONf_dihedral_angle_d10.4422144
X-RAY DIFFRACTIONf_chiral_restr0.029877
X-RAY DIFFRACTIONf_plane_restr0.0041033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23610.36271390.3411891X-RAY DIFFRACTION99
2.2361-2.27460.3391390.31591895X-RAY DIFFRACTION99
2.2746-2.3160.341400.30441899X-RAY DIFFRACTION99
2.316-2.36050.34331370.29291878X-RAY DIFFRACTION99
2.3605-2.40870.31621420.27941929X-RAY DIFFRACTION99
2.4087-2.4610.30951400.25841899X-RAY DIFFRACTION99
2.461-2.51820.26951410.24871892X-RAY DIFFRACTION99
2.5182-2.58120.26871370.25161906X-RAY DIFFRACTION99
2.5812-2.65090.2851420.24641921X-RAY DIFFRACTION99
2.6509-2.72890.27711400.23251913X-RAY DIFFRACTION99
2.7289-2.81690.26371420.21711909X-RAY DIFFRACTION100
2.8169-2.91750.24851440.22861929X-RAY DIFFRACTION99
2.9175-3.03420.24061410.21431905X-RAY DIFFRACTION100
3.0342-3.17210.23481410.20731915X-RAY DIFFRACTION100
3.1721-3.33910.23171410.20341910X-RAY DIFFRACTION100
3.3391-3.5480.22631370.18971936X-RAY DIFFRACTION100
3.548-3.82140.19831420.1671921X-RAY DIFFRACTION100
3.8214-4.20490.18871440.15281923X-RAY DIFFRACTION100
4.2049-4.8110.161430.12971953X-RAY DIFFRACTION100
4.811-6.05250.18481420.15421933X-RAY DIFFRACTION100
6.0525-29.18950.16331450.15781987X-RAY DIFFRACTION100
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)
13.8821-4.6193-5.23927.12036.44457.09790.64931.0110.0751-1.6064-0.73370.4279-0.11051.4033-0.10050.63860.1091-0.0770.56930.15020.710262.178236.55216.3718
25.7499-4.10120.99446.706-1.37662.17330.00240.1806-0.06890.0371-0.0455-0.43880.25180.37450.05060.45440.1147-0.02850.5788-0.01850.572360.01531.97115.2144
33.7814-0.5123-0.67198.1116-0.41263.5046-0.3596-0.3540.89280.52130.0944-0.4612-0.28630.04310.2060.55580.1159-0.15620.7089-0.18340.815955.571349.020523.0097
43.9373-0.2002-1.44681.96110.392.4633-0.2383-0.4646-0.50950.44620.07390.61970.3002-0.51140.19170.50940.02610.13960.57170.13830.658315.330340.633222.068
52.191-0.5243-0.14292.32040.07442.1159-0.10980.20670.1012-0.24340.0979-0.1028-0.09590.03230.01750.43410.02210.02890.36860.01290.485333.982952.38292.5503
61.74650.9907-0.80013.536-2.17394.0059-0.1684-0.32150.20340.35440.30690.356-0.2394-0.1929-0.1660.54550.18070.03970.5191-0.03080.662822.697564.808119.8291
75.4966-3.48563.38845.768-2.64259.9451-0.11480.42260.386-0.1831-0.1725-0.79440.01670.49580.25180.7226-0.00560.10210.49420.05810.993333.148775.5647-0.3022
87.26452.1397-3.66924.0487-5.52128.4640.3894-0.12520.98630.2791-0.67070.2662-3.38742.0450.1741.0696-0.0481-0.01550.8547-0.16160.879233.521573.54128.0177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 854 through 865 )
2X-RAY DIFFRACTION2chain 'A' and (resid 866 through 957 )
3X-RAY DIFFRACTION3chain 'A' and (resid 958 through 993 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 216 )
5X-RAY DIFFRACTION5chain 'B' and (resid 217 through 461 )
6X-RAY DIFFRACTION6chain 'B' and (resid 462 through 593 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1440 through 1461 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1462 through 1471 )

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