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- PDB-4xmn: Structure of the yeast coat nucleoporin complex, space group P212121 -

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Basic information

Entry
Database: PDB / ID: 4xmn
TitleStructure of the yeast coat nucleoporin complex, space group P212121
Components
  • Antibody 87 heavy chain
  • Antibody 87 light chain
  • Nucleoporin NUP120
  • Nucleoporin NUP145
  • Nucleoporin NUP84
  • Nucleoporin NUP85
  • Protein transport protein SEC13
KeywordsPROTEIN TRANSPORT / STRUCTURAL 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 / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling ...mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel / nuclear pore outer ring / telomere tethering at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / tRNA export from nucleus / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / nuclear localization sequence binding / RNA export from nucleus / SUMOylation of chromatin organization proteins / vacuolar membrane / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / subtelomeric heterochromatin formation / nuclear pore / mRNA export from nucleus / ERAD pathway / positive regulation of TORC1 signaling / protein export from nucleus / 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 / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region ...: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / 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. / 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
Similarity search - Domain/homology
Nucleoporin NUP120 / Nucleoporin NUP85 / Nucleoporin NUP145 / Nucleoporin NUP84 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.6 Å
AuthorsStuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A.
CitationJournal: Science / Year: 2015
Title: Nuclear pores. Architecture of the nuclear pore complex coat.
Authors: Stuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Structure summary
Revision 1.2Feb 3, 2016Group: Source and taxonomy
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_oper_list.symmetry_operation
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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein transport protein SEC13
B: Nucleoporin NUP145
F: Nucleoporin NUP84
E: Nucleoporin NUP120
D: Nucleoporin NUP85
L: Antibody 87 light chain
H: Antibody 87 heavy chain


Theoretical massNumber of molelcules
Total (without water)413,5257
Polymers413,5257
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.130, 179.950, 441.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 5 molecules ABFED

#1: Protein Protein transport protein SEC13


Mass: 33129.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04491
#2: Protein Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 75087.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NUP145, RAT10, YGL092W / Production host: Escherichia coli (E. coli)
References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 52434.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / References: UniProt: P52891
#4: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 121607.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729
#5: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 79188.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP85, RAT9, YJR042W, J1624 / Production host: Escherichia coli (E. coli) / References: UniProt: P46673

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Antibody , 2 types, 2 molecules LH

#6: Antibody Antibody 87 light chain


Mass: 23461.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Description: phage display library / Production host: Escherichia coli (E. coli)
#7: Antibody Antibody 87 heavy chain


Mass: 28615.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Description: obtained from phage display library / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.62 Å3/Da / Density % sol: 78.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 20000, ethanol, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 7.6→50 Å / Num. obs: 22082 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1809)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IKO, 3F7F, 3PGF

3iko

3f7f

3pgf


Resolution: 7.6→49.606 Å / SU ML: 1.02 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3473 2193 9.94 %
Rwork0.3183 --
obs0.3212 22065 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.6→49.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19816 0 0 0 19816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520176
X-RAY DIFFRACTIONf_angle_d1.12327431
X-RAY DIFFRACTIONf_dihedral_angle_d15.8626928
X-RAY DIFFRACTIONf_chiral_restr0.0423226
X-RAY DIFFRACTIONf_plane_restr0.0063504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.6-7.75690.43611300.36661198X-RAY DIFFRACTION94
7.7569-7.93660.34861330.33971236X-RAY DIFFRACTION100
7.9366-8.13420.30911390.32161217X-RAY DIFFRACTION100
8.1342-8.35320.32631410.30881270X-RAY DIFFRACTION100
8.3532-8.59780.3111340.29221254X-RAY DIFFRACTION100
8.5978-8.87370.2821320.2871228X-RAY DIFFRACTION100
8.8737-9.1890.31521420.27641261X-RAY DIFFRACTION100
9.189-9.55440.34531370.26441257X-RAY DIFFRACTION100
9.5544-9.98590.26641450.24841246X-RAY DIFFRACTION100
9.9859-10.50760.22161370.24241253X-RAY DIFFRACTION100
10.5076-11.1590.23291380.2621237X-RAY DIFFRACTION100
11.159-12.00930.28881370.24751253X-RAY DIFFRACTION100
12.0093-13.19710.31581420.2971239X-RAY DIFFRACTION100
13.1971-15.05980.35021370.32471239X-RAY DIFFRACTION100
15.0598-18.80050.41951350.38851248X-RAY DIFFRACTION100
18.8005-49.60730.52961340.43681236X-RAY DIFFRACTION99

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