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- PDB-5tvz: Solution NMR structure of Saccharomyces cerevisiae Pom152 Ig-like... -

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Entry
Database: PDB / ID: 5tvz
TitleSolution NMR structure of Saccharomyces cerevisiae Pom152 Ig-like repeat, residues 718-820
ComponentsNucleoporin POM152
KeywordsTRANSPORT PROTEIN / Nuclear Pore Complex / Ig-like fold / nuclear envelope membrane / cadherin like fold
Function / homology
Function and homology information


nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery ...nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery / cell periphery / protein import into nucleus / nuclear envelope / nuclear membrane / mitochondrion
Similarity search - Function
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsDutta, K. / Sampathkumar, P. / Cowburn, D. / Almo, S.C. / Rout, M.P. / Fernandez-Martinez, J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112108 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM109824 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM103511 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 117212 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM074945 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094662 United States
CitationJournal: Structure / Year: 2017
Title: Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.
Authors: Paula Upla / Seung Joong Kim / Parthasarathy Sampathkumar / Kaushik Dutta / Sean M Cahill / Ilan E Chemmama / Rosemary Williams / Jeffrey B Bonanno / William J Rice / David L Stokes / David ...Authors: Paula Upla / Seung Joong Kim / Parthasarathy Sampathkumar / Kaushik Dutta / Sean M Cahill / Ilan E Chemmama / Rosemary Williams / Jeffrey B Bonanno / William J Rice / David L Stokes / David Cowburn / Steven C Almo / Andrej Sali / Michael P Rout / Javier Fernandez-Martinez /
Abstract: The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or ...The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals that the luminal domain is formed by a flexible string-of-pearls arrangement of nine repetitive cadherin-like Ig-like domains, indicating an evolutionary connection between NPCs and the cell adhesion machinery. The 16 copies of Pom152 known to be present in the yeast NPC are long enough to form the observed membrane ring, suggesting how interactions between Pom152 molecules help establish and maintain the NPC architecture.
History
DepositionNov 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: Nucleoporin POM152


Theoretical massNumber of molelcules
Total (without water)12,7421
Polymers12,7421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2048structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleoporin POM152 / Nuclear pore protein POM152 / P150 / Pore membrane protein POM152


Mass: 12741.649 Da / Num. of mol.: 1 / Fragment: UNP residues 718-820
Source method: isolated from a genetically manipulated source
Details: Nuclear Pore Complex Assembly: Pore membrane protein (POM)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POM152 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlusRIL / References: UniProt: P39685

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13d HN(CA)CO
141isotropic33D HNCA
151isotropic33D HN(CO)CA
161isotropic33D HN(CA)CB
172isotropic13D CBCA(CO)NH
182isotropic23D HBHA(CO)NH
192isotropic23D 1H-15N NOESY
1103isotropic13D H(CCO)NH
1114isotropic13D C(CO)NH
1125isotropic22D 1H-13C HSQC aliphatic
1135isotropic22D 1H-13C HSQC aromatic
1145isotropic23D (H)CCH-TOCSY
1155isotropic33D 1H-13C NOESY aliphatic
1165isotropic33D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1235 uM [U-100% 13C; U-100% 15N] POM152, 90% H2O/10% D2O10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTTcn-15152a14p290% H2O/10% D2O
solution2402 uM [U-100% 13C; U-100% 15N] POM152, 90% H2O/10% D2O10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTTcn-15152a14p290% H2O/10% D2O
solution3300 uM [U-100% 13C; U-100% 15N] POM152, 90% H2O/10% D2O10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTTcn-15152a14p290% H2O/10% D2O
solution41.2 mM [U-100% 13C; U-100% 15N] POM152, 90% H2O/10% D2O10mM Hepes, 150mM NaCl, pH=6.8, NO DTTcn-15152a14p290% H2O/10% D2O
solution5324 uM [U-100% 13C; U-100% 15N] POM152, 100% D2O10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTTcnD-15152a14p2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
235 uMPOM152[U-100% 13C; U-100% 15N]1
402 uMPOM152[U-100% 13C; U-100% 15N]2
300 uMPOM152[U-100% 13C; U-100% 15N]3
1.2 mMPOM152[U-100% 13C; U-100% 15N]4
324 uMPOM152[U-100% 13C; U-100% 15N]5
Sample conditionsDetails: 10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTT / Ionic strength: 160 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA6002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2048 / Conformers submitted total number: 20

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