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- PDB-2lx0: Arced helix (ArcH) NMR structure of the reovirus p14 fusion-assoc... -

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Basic information

Entry
Database: PDB / ID: 2lx0
TitleArced helix (ArcH) NMR structure of the reovirus p14 fusion-associated small transmembrane (FAST) protein transmembrane domain (TMD) in dodecyl phosphocholine (DPC) micelles
ComponentsMembrane fusion protein p14
KeywordsMEMBRANE PROTEIN / Membrane fusion protein transmembrane domain / p14 FAST protein TMD / ArcH / micelle-peptide complex
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSarker, M. / Key, T. / Duncan, R. / Rainey, J.K.
CitationJournal: To be Published
Title: A Cell-Cell Membrane Fusion Module Comprising a Transmembrane Arced Helix (ArcH)
Authors: Sarker, M. / Key, T. / Rainey, J.K. / Duncan, R.
History
DepositionAug 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane fusion protein p14


Theoretical massNumber of molelcules
Total (without water)3,8171
Polymers3,8171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Membrane fusion protein p14


Mass: 3816.661 Da / Num. of mol.: 1 / Fragment: transmembrane domain / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1413D 1H-15N TOCSY
1513D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.75 mM Partial 15N (8 of 32 amino acids) p14 TMD peptide, 150 mM [U-2H] DPC, 0.5 mM DSS, 0.2 mM sodium azide, 20 mM [U-2H] sodium acetate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMp14 TMD peptide-1Partial 15N (8 of 32 amino acids)1
150 mMDPC-2[U-2H]1
0.5 mMDSS-31
0.2 mMsodium azide-41
20 mMsodium acetate-5[U-2H]1
Sample conditionspH: 5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
MOLMOL2k.2Koradi, Billeter and Wuthrichvisualization
MOLMOL2k.2Koradi, Billeter and Wuthrichensemble superposition
MOLMOL2k.2Koradi, Billeter and Wuthrichrmsd calculation
UCSF Chimera1.6.2Pettersen, Goddard, Huang, Couch, Greenblatt, Meng, Ferrinvisualization
UCSF Chimera1.6.2Pettersen, Goddard, Huang, Couch, Greenblatt, Meng, Ferrindistance measurement
ProcheckNMR3.5.4Laskowski and MacArthurstructure validation
ProcheckNMR3.5.4Laskowski and MacArthurramachandran plot statistics
DSSPKabsch, Sander; Joosten, Te Beek, Krieger, Hekkelman, Hooft, Schneider, Sander, Vriendsecondary structure analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 50

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