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- PDB-2mk3: Solution NMR structure of gp41 ectodomain monomer on a DPC micelle -

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Basic information

Entry
Database: PDB / ID: 2mk3
TitleSolution NMR structure of gp41 ectodomain monomer on a DPC micelle
ComponentsTransmembrane glycoprotein, chimeric construct
KeywordsIMMUNE SYSTEM / HIV-1 ENV / membrane fusion / gp41 ectodomain / pre-hairpin / CoreS
Function / homologyHelix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Transmembrane glycoprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsRoche, J. / Louis, J.M. / Grishaev, A. / Ying, J. / Bax, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion.
Authors: Roche, J. / Louis, J.M. / Grishaev, A. / Ying, J. / Bax, A.
History
DepositionJan 23, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane glycoprotein, chimeric construct


Theoretical massNumber of molelcules
Total (without water)8,2931
Polymers8,2931
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)20 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Transmembrane glycoprotein, chimeric construct


Mass: 8293.226 Da / Num. of mol.: 1 / Fragment: unp residues 93-126; unp residues 138-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCO
1313D 1H-15N NOESY
1413D (H)CCH-TOCSY
1512D 1H-1H NOESY
1622D 1H-15N Artsy
1722D 1H-15N TROSY-HSQC
1823D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM [U-99% 2H] DPC, 50 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
2100 mM [U-99% 2H] DPC, 50 mM potassium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMDPC-1[U-99% 2H]1
50 mMsodium phosphate-21
100 mMDPC-3[U-99% 2H]2
50 mMpotassium phosphate-42
Sample conditionsIonic strength: 0.05 / pH: 4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 465 / NOE intraresidue total count: 48 / NOE long range total count: 0 / NOE medium range total count: 186 / NOE sequential total count: 231 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 57
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 3.6 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 8.4 ° / Maximum upper distance constraint violation: 0.55 Å / Torsion angle constraint violation method: TalosN
NMR ensemble rmsDistance rms dev: 0.08 Å / Distance rms dev error: 0.01 Å

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