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- PDB-3f3g: Crystal structure of the nucleoporin pair Nup85-Seh1, space group... -

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Basic information

Entry
Database: PDB / ID: 3f3g
TitleCrystal structure of the nucleoporin pair Nup85-Seh1, space group P212121
Components
  • Nucleoporin NUP85
  • Nucleoporin SEH1
KeywordsSTRUCTURAL PROTEIN / Protein Complex / Nucleoporin / Nucleoporin Complex / Nuclear Pore Complex / Macromolecular Assembly / Membrane Coat / Nucleocytoplasmic Transport / beta-propeller / solenoid domain / mRNA transport / Nucleus / Protein transport / Translocation / WD repeat
Function / homology
Function and homology information


Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins ...Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / mRNA export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein import into nucleus / nuclear envelope / protein transport / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsDebler, E.W. / Hseo, H. / Ma, Y. / Blobel, G. / Hoelz, A.
CitationJournal: Mol.Cell / Year: 2008
Title: A fence-like coat for the nuclear pore membrane.
Authors: Debler, E.W. / Ma, Y. / Seo, H.S. / Hsia, K.C. / Noriega, T.R. / Blobel, G. / Hoelz, A.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin SEH1
B: Nucleoporin SEH1
C: Nucleoporin NUP85
D: Nucleoporin NUP85
E: Nucleoporin SEH1
F: Nucleoporin SEH1
G: Nucleoporin NUP85
H: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)417,3418
Polymers417,3418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34790 Å2
ΔGint-179 kcal/mol
Surface area132190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.377, 106.487, 358.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is the complete heterooctamer that is present in the asymmetric unit

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Components

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


Mass: 39406.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEH1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P53011
#2: Protein
Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 64929.242 Da / Num. of mol.: 4 / Fragment: UNP residues 1-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP85, RAT9 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Sodium citrate, Sodium chloride, Tris-HCl buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 3.75→50 Å / Num. all: 48007 / Num. obs: 46183 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.18 / Net I/σ(I): 7.8
Reflection shellResolution: 3.75→3.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.753 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F3F

3f3f


Resolution: 3.75→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1972 Random
Rwork0.243 --
obs0.243 39143 -
all-42355 -
Refinement stepCycle: LAST / Resolution: 3.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25114 0 0 0 25114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4

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