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- PDB-3f3p: Crystal structure of the nucleoporin pair Nup85-Seh1, space group... -

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Basic information

Entry
Database: PDB / ID: 3f3p
TitleCrystal structure of the nucleoporin pair Nup85-Seh1, space group P21212
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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / 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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / 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
N-terminal domain of TfIIb - #500 / Nucleoporin Nup85-like / Nup85 Nucleoporin / Sec13/Seh1 family / N-terminal domain of TfIIb / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Single Sheet / Trp-Asp (WD) repeats profile. ...N-terminal domain of TfIIb - #500 / Nucleoporin Nup85-like / Nup85 Nucleoporin / Sec13/Seh1 family / N-terminal domain of TfIIb / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Single Sheet / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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: 3.2 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 31, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
I: Nucleoporin SEH1
J: Nucleoporin SEH1
K: Nucleoporin NUP85
L: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)631,92012
Polymers631,92012
Non-polymers00
Water00
1
A: Nucleoporin SEH1
B: Nucleoporin SEH1
C: Nucleoporin NUP85
D: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)210,6404
Polymers210,6404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-93.1 kcal/mol
Surface area61990 Å2
MethodPISA
2
E: Nucleoporin SEH1
F: Nucleoporin SEH1
G: Nucleoporin NUP85
H: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)210,6404
Polymers210,6404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-90.7 kcal/mol
Surface area62340 Å2
MethodPISA
3
I: Nucleoporin SEH1
J: Nucleoporin SEH1
K: Nucleoporin NUP85
L: Nucleoporin NUP85


Theoretical massNumber of molelcules
Total (without water)210,6404
Polymers210,6404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-87.9 kcal/mol
Surface area63020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.239, 226.476, 190.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsAuthors state that the heterotetramers (ABCD), (EFGH), and (IJKL) constitute the biomolecules that build up the physiologically-relevant heterooctameric conformations represented by the asymmetric units of related entries 3F3F and 3F3G.

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Components

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


Mass: 39640.488 Da / Num. of mol.: 6
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: 65679.570 Da / Num. of mol.: 6 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 152129 / Num. obs: 150912 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.145 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.3 % / Num. unique all: 7406 / Rsym value: 0.729 / % possible all: 97.9

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Processing

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

3f3f


Resolution: 3.2→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 -Random
Rwork0.261 --
obs0.261 123289 -
all-129823 -
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37800 0 0 0 37800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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