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- PDB-4xmm: Structure of the yeast coat nucleoporin complex, space group C2 -

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Basic information

Entry
Database: PDB / ID: 4xmm
TitleStructure of the yeast coat nucleoporin complex, space group C2
Components
  • Antibody 57 heavy chain
  • Antibody 57 light chain
  • Nucleoporin NUP120
  • Nucleoporin NUP145
  • Nucleoporin NUP84
  • Nucleoporin NUP85
  • Nucleoporin SEH1
  • Protein transport protein SEC13
KeywordsTransport Protein/Immune System / Structural protein / Immune System / Transport Protein-Immune System complex
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / subtelomeric heterochromatin formation / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein export from nucleus / cell periphery / protein import into nucleus / double-strand break repair / protein transport / nuclear envelope / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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 Nup120/160 / 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 ...Nucleoporin Nup120/160 / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / 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
Similarity search - Domain/homology
Nucleoporin NUP120 / Nucleoporin NUP85 / Nucleoporin NUP145 / Nucleoporin NUP84 / Nucleoporin SEH1 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.384 Å
AuthorsStuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM07616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM094588 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 United States
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: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 NUP145
C: Nucleoporin SEH1
D: Nucleoporin NUP85
E: Nucleoporin NUP120
F: Nucleoporin NUP84
H: Antibody 57 heavy chain
L: Antibody 57 light chain


Theoretical massNumber of molelcules
Total (without water)454,6448
Polymers454,6448
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-131 kcal/mol
Surface area164350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.645, 186.297, 199.570
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 6 types, 6 molecules ABCDEF

#1: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: 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: 74618.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: 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 SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39170.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SEH1, YGL100W / Production host: Escherichia coli (E. coli) / References: UniProt: P53011
#4: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 81568.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP85, RAT9, YJR042W, J1624 / Production host: Escherichia coli (E. coli) / References: UniProt: P46673
#5: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 121577.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729
#6: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 52059.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / References: UniProt: P52891

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Antibody , 2 types, 2 molecules HL

#7: Antibody Antibody 57 heavy chain


Mass: 28977.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#8: Antibody Antibody 57 light chain


Mass: 23588.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 20000, ethanol, MES / PH range: 6.7

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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: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 7.384→70 Å / Num. obs: 10375 / % possible obs: 99 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.3
Reflection shellResolution: 7.384→7.8 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.4 / % possible all: 94.9

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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, 3F3F, 3F7F, and 3PGF

3iko

3f3f

3f7f

3pgf


Resolution: 7.384→67.516 Å / SU ML: 1.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3527 1022 9.99 %Random selection
Rwork0.3299 ---
obs0.3322 10227 99.47 %-
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.384→67.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26139 0 0 0 26139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626637
X-RAY DIFFRACTIONf_angle_d1.21736184
X-RAY DIFFRACTIONf_dihedral_angle_d15.7619280
X-RAY DIFFRACTIONf_chiral_restr0.0514198
X-RAY DIFFRACTIONf_plane_restr0.0074616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.384-7.77250.39961420.39081265X-RAY DIFFRACTION98
7.7725-8.25860.37751450.36661325X-RAY DIFFRACTION100
8.2586-8.8950.37961450.3121298X-RAY DIFFRACTION100
8.895-9.78770.36381470.29641323X-RAY DIFFRACTION100
9.7877-11.19850.27921470.27761315X-RAY DIFFRACTION100
11.1985-14.08780.33381480.31991332X-RAY DIFFRACTION100
14.0878-67.51910.3821480.35981347X-RAY DIFFRACTION99

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