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- PDB-3iko: Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucle... -

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Basic information

Entry
Database: PDB / ID: 3iko
TitleCrystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
Components
  • Nucleoporin NUP145C
  • Nucleoporin NUP84
  • Protein transport protein SEC13
KeywordsSTRUCTURAL PROTEIN / PROTEIN TRANSPORT / NPC / TRANSPORT / WD REPEAT / AUTOCATALYTIC CLEAVAGE / MRNA TRANSPORT / NUCLEAR PORE COMPLEX / NUCLEUS / PHOSPHOPROTEIN / TRANSLOCATION / Coiled coil / Membrane / Hydrolase / RNA-binding / Cytoplasmic vesicle / Endoplasmic reticulum / ER-Golgi transport / NUCLEAR PROTEIN
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / COPII-mediated vesicle transport ...mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / COPII-mediated vesicle transport / regulation of TORC1 signaling / telomere tethering at nuclear periphery / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / RNA export from nucleus / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / vacuolar membrane / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / mRNA transport / nuclear pore / mRNA export from nucleus / subtelomeric heterochromatin formation / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding
Similarity search - Function
Hyaluronidase domain-like - #20 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Hyaluronidase domain-like / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region / N-terminal domain of TfIIb / Nuclear pore complex protein NUP96, C-terminal domain ...Hyaluronidase domain-like - #20 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Hyaluronidase domain-like / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region / N-terminal domain of TfIIb / 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 / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Other non-globular / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP145 / Nucleoporin NUP84 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsNagy, V. / Hsia, K.-C. / Debler, E.W. / Davenport, A. / Blobel, G. / Hoelz, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of a trimeric nucleoporin complex reveals alternate oligomerization states.
Authors: Nagy, V. / Hsia, K.C. / Debler, E.W. / Kampmann, M. / Davenport, A.M. / Blobel, G. / Hoelz, A.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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: Protein transport protein SEC13
B: Nucleoporin NUP145C
C: Nucleoporin NUP84
D: Protein transport protein SEC13
E: Nucleoporin NUP145C
F: Nucleoporin NUP84
G: Protein transport protein SEC13
H: Nucleoporin NUP145C
I: Nucleoporin NUP84


Theoretical massNumber of molelcules
Total (without water)410,8859
Polymers410,8859
Non-polymers00
Water00
1
A: Protein transport protein SEC13
B: Nucleoporin NUP145C
C: Nucleoporin NUP84


Theoretical massNumber of molelcules
Total (without water)136,9623
Polymers136,9623
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-49 kcal/mol
Surface area51440 Å2
MethodPISA
2
D: Protein transport protein SEC13
E: Nucleoporin NUP145C
F: Nucleoporin NUP84


Theoretical massNumber of molelcules
Total (without water)136,9623
Polymers136,9623
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-55 kcal/mol
Surface area50140 Å2
MethodPISA
3
G: Protein transport protein SEC13
H: Nucleoporin NUP145C
I: Nucleoporin NUP84


Theoretical massNumber of molelcules
Total (without water)136,9623
Polymers136,9623
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-53 kcal/mol
Surface area49410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.397, 194.050, 327.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 3 / Fragment: UNP residues 1-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)-RIL / References: UniProt: Q04491
#2: Protein Nucleoporin NUP145C / Nucleoporin NUP145C / C-NUP145


Mass: 51013.898 Da / Num. of mol.: 3 / Fragment: UNP residues 731-1158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP145, RAT10, YGL092W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)-RIL
References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 52864.793 Da / Num. of mol.: 3 / Fragment: UNP residues 1-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)-RIL / References: UniProt: P52891

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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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.14 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 108829 / Num. obs: 105020 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.115 / Net I/σ(I): 16.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.525 / % possible all: 75.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 9887 -9.2
Rwork0.234 ---
obs-97899 91.1 %-
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27032 0 0 0 27032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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