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- PDB-3ewe: Crystal Structure of the Nup85/Seh1 Complex -

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Basic information

Entry
Database: PDB / ID: 3ewe
TitleCrystal Structure of the Nup85/Seh1 Complex
Components
  • Nucleoporin NUP85
  • Nucleoporin SEH1
KeywordsPROTEIN TRANSPORT / STRUCTURAL PROTEIN / Nucleoporin / Nuclear Pore Complex / mRNA transport / Nucleus / Translocation / Cell membrane / Membrane / Phosphoprotein / Transport / WD repeat / MEMBRANE PROTEIN
Function / homology
Function and homology information


Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / structural constituent of nuclear pore / vacuolar membrane / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / mRNA transport / mRNA export from nucleus ...Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / structural constituent of nuclear pore / vacuolar membrane / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein import into nucleus / protein transport / nuclear envelope / nuclear membrane / positive regulation of DNA-templated transcription
Similarity search - Function
Nucleoporin Nup85-like / Nup85 Nucleoporin / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...Nucleoporin Nup85-like / Nup85 Nucleoporin / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Nucleoporin NUP85 / Nucleoporin SEH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsBrohawn, S.G. / Leksa, N.C. / Rajashankar, K.R. / Schwartz, T.U.
CitationJournal: Science / Year: 2008
Title: Structural evidence for common ancestry of the nuclear pore complex and vesicle coats.
Authors: Brohawn, S.G. / Leksa, N.C. / Spear, E.D. / Rajashankar, K.R. / Schwartz, T.U.
History
DepositionOct 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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 SEH1
B: Nucleoporin NUP85
C: Nucleoporin SEH1
D: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)206,7584
Polymers206,7584
Non-polymers00
Water0
1
A: Nucleoporin SEH1
B: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)103,3792
Polymers103,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-29 kcal/mol
Surface area31660 Å2
MethodPISA
2
C: Nucleoporin SEH1
D: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)103,3792
Polymers103,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-29 kcal/mol
Surface area31850 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-72 kcal/mol
Surface area60820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.559, 112.559, 350.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A OR (CHAIN B AND RESSEQ 1:99)
211CHAIN C OR (CHAIN D AND RESSEQ 1:99)
112CHAIN B AND RESSEQ 216:370)
212CHAIN D AND RESSEQ 216:370)
113CHAIN B AND NOT (RESSEQ 1:99 OR RESSEQ 216:370 OR RESSEQ 531:556)
213CHAIN D AND NOT (RESSEQ 1:99 OR RESSEQ 216:370 OR RESSEQ 531:556)

NCS ensembles :
ID
1
2
3
DetailsHETEROTETRAMER IS NOT OBSERVED IN SOLUTION BY AUTHOR. SEE CITATION FOR DETAILS.

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Components

#1: Protein Nucleoporin SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39170.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEH1, YGL100W / Plasmid: pCola-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P53011
#2: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 64208.402 Da / Num. of mol.: 2 / Fragment: UNP residues 1-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: J1624, NUP85, RAT9, YJR042W / Plasmid: pCola-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P46673

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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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 289 K / pH: 8.5
Details: 18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 29579 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 118 Å2 / Rsym value: 0.107 / Net I/σ(I): 13.7
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 3.3 % / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXC/D/Emodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→29.75 Å / SU ML: 0.59 / σ(F): 1.34 / Phase error: 38.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.369 1405 4.96 %
Rwork0.326 --
obs0.328 28300 96.4 %
all-29360 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.79 Å2 / ksol: 0.26 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9689 0 0 0 9689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089889
X-RAY DIFFRACTIONf_angle_d1.213498
X-RAY DIFFRACTIONf_dihedral_angle_d17.2963172
X-RAY DIFFRACTIONf_chiral_restr0.0791623
X-RAY DIFFRACTIONf_plane_restr0.0051664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2114X-RAY DIFFRACTIONPOSITIONAL
12C2114X-RAY DIFFRACTIONPOSITIONAL0.09
21B876X-RAY DIFFRACTIONPOSITIONAL
22D876X-RAY DIFFRACTIONPOSITIONAL0.109
31B1663X-RAY DIFFRACTIONPOSITIONAL
32D1663X-RAY DIFFRACTIONPOSITIONAL0.101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.62490.46091350.39652703X-RAY DIFFRACTION99
3.6249-3.76980.4331610.33232636X-RAY DIFFRACTION98
3.7698-3.9410.34091310.33562692X-RAY DIFFRACTION98
3.941-4.14830.37461190.31332711X-RAY DIFFRACTION98
4.1483-4.40740.37021310.31432655X-RAY DIFFRACTION97
4.4074-4.74640.34961180.29532707X-RAY DIFFRACTION97
4.7464-5.22180.33911430.29792656X-RAY DIFFRACTION96
5.2218-5.97210.32721490.32362699X-RAY DIFFRACTION96
5.9721-7.50420.38471800.3262721X-RAY DIFFRACTION96
7.5042-29.7560.3381380.29612715X-RAY DIFFRACTION90
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)
13.6136-0.58290.12823.1552-1.13183.66530.0826-0.5344-0.160.57570.52830.96710.0152-0.9733-0.00041.32630.13020.07372.07590.14281.549-43.073760.820162.3163
28.0699-2.7281-3.40132.14230.11311.9958-0.0823-0.4752-0.50830.423-0.20870.1177-0.2740.65310.00091.2592-0.0203-0.30731.8603-0.04920.9677-1.886969.6958.878
35.1405-0.2398-0.12460.77770.36346.0106-0.12740.9238-0.4226-0.64950.2766-0.53650.31532.0529-0.00051.42510.22240.16712.99360.21881.685634.992462.992117.1784
46.38682.6904-2.73680.8945-0.56292.0895-0.22050.1342-0.2473-0.29920.0752-0.2533-0.4216-0.08780.00171.11520.1859-0.24311.60040.21171.1455-6.157471.731821.5158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or (chain B and resseq 1:95)
2X-RAY DIFFRACTION2chain B and not (resseq 1:95)
3X-RAY DIFFRACTION3chain C or (chain D and resseq 1:95)
4X-RAY DIFFRACTION4chain D and not (resseq 1:95)

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