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- PDB-2m7w: Independently verified structure of gp41-M-MAT, a membrane associ... -

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Basic information

Entry
Database: PDB / ID: 2m7w
TitleIndependently verified structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / MPER / gp41
Function / homologyHelix Hairpins - #210 / Fibritin C-terminal / Fibritin C-terminal region / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Envelope glycoprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / complete search, simulated annealing
AuthorsMartin, J.W. / Reardon, P.N. / Sage, H.S. / Moses, D.S. / Munir, A.S. / Haynes, B.F. / Spicer, L.D. / Donald, B.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of an HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer.
Authors: Reardon, P.N. / Sage, H. / Dennison, S.M. / Martin, J.W. / Donald, B.R. / Alam, S.M. / Haynes, B.F. / Spicer, L.D.
History
DepositionMay 1, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Jun 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 1.4May 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:
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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)21,0323
Polymers21,0323
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Envelope glycoprotein


Mass: 7010.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1E4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HN(CO)CA
1513D 1H-15N NOESY

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Sample preparation

DetailsContents: 2 mM protein, 50 mM sodium phosphate, 100 mM [U-99% 2H] DPC, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMprotein-11
50 mMsodium phosphate-21
100 mMDPC-3[U-99% 2H]1
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
DISCO1Martin, Yan, Bailey-Kellogg, Zhou, and Donaldstructure solution
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: complete search, simulated annealing / Software ordinal: 1
Details: DISCO USED TO COMPUTE MPER QUATERNARY STRUCTURE, XPLOR-NIH USED TO COMPUTE MPER SUBUNIT STRUCTURE AND LINKER/FOLDON TRIMER STRUCTURES AND ALSO FOR FULL-LENGTH REFINEMENT.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 18

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