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Biological Magnetic Resonance Data Bank


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BMRB Entry 30856

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30856
MolProbity Validation Chart

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Title: Model of the HIV-1 gp41 membrane-proximal external region, transmembrane domain and cytoplasmic tail   PubMed: 33882664

Deposition date: 2021-02-10 Original release date: 2021-04-23

Authors: Piai, A.; Fu, Q.; Sharp, A.; Bighi, B.; Brown, A.; Chou, J.

Citation: Piai, A.; Fu, Q.; Sharp, A.; Bighi, B.; Brown, A.; Chou, J.. "NMR Model of the Entire Membrane-Interacting Region of the HIV-1 Fusion Protein and Its Perturbation of Membrane Morphology"  J. Am. Chem. Soc. 143, 6609-6615 (2021).

Assembly members:
entity_1, polymer, 197 residues, 22979.607 Da.

Natural source:   Common Name: HIV-1   Taxonomy ID: 11676   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus HIV-1

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):
entity_1: LLELDKWASLWNWFDITNWL WYIRIFIIIVGSLIGLRIVF AVLSLVNRVRQGYSPLSFQT HLPTPRGPDRPEGIEEEGGE RDRDRSIRLVNGSLALIWDD LRSLSLFSYHRLRDLLLIVT RIVELLGRRGWEALKYWWNL LQYWSQELKNSAVSLLNATA IAVGEGTDRVIEVVQGASRA IRHIPRRIRQGLERILL

Data sets:
Data typeCount
13C chemical shifts328
15N chemical shifts164
1H chemical shifts164

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21
3unit_31

Entities:

Entity 1, unit_1 197 residues - 22979.607 Da.

1   LEULEUGLULEUASPLYSTRPALASERLEU
2   TRPASNTRPPHEASPILETHRASNTRPLEU
3   TRPTYRILEARGILEPHEILEILEILEVAL
4   GLYSERLEUILEGLYLEUARGILEVALPHE
5   ALAVALLEUSERLEUVALASNARGVALARG
6   GLNGLYTYRSERPROLEUSERPHEGLNTHR
7   HISLEUPROTHRPROARGGLYPROASPARG
8   PROGLUGLYILEGLUGLUGLUGLYGLYGLU
9   ARGASPARGASPARGSERILEARGLEUVAL
10   ASNGLYSERLEUALALEUILETRPASPASP
11   LEUARGSERLEUSERLEUPHESERTYRHIS
12   ARGLEUARGASPLEULEULEUILEVALTHR
13   ARGILEVALGLULEULEUGLYARGARGGLY
14   TRPGLUALALEULYSTYRTRPTRPASNLEU
15   LEUGLNTYRTRPSERGLNGLULEULYSASN
16   SERALAVALSERLEULEUASNALATHRALA
17   ILEALAVALGLYGLUGLYTHRASPARGVAL
18   ILEGLUVALVALGLNGLYALASERARGALA
19   ILEARGHISILEPROARGARGILEARGGLN
20   GLYLEUGLUARGILELEULEU

Samples:

sample_1: HIV-1 gp41 MPER-TMD-CT, [U-100% 13C; U-100% 15N; U-85% 2H], 1.2 mM; DMPC 40 mM; DHPC 80 mM; MES 40 mM; sodium azide 1%

sample_2: HIV-1 gp41 MPER-TMD-CT, [ILV-100% 13C; U-100% 15N; U-85% 2H], 1 mM; DMPC 40 mM; DHPC 80 mM; MES 40 mM; sodium azide 1%

sample_conditions_1: ionic strength: 0 M; pH: 6.7; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY HSQCsample_1isotropicsample_conditions_1
3D TROSY HNCOsample_1isotropicsample_conditions_1
3D TROSY HNCAsample_1isotropicsample_conditions_1
2D 1H-15N TROSY HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D 15N-edited TROSY-NOESY-TROSY-HSQCsample_2isotropicsample_conditions_1
3D 13C-edited NOESYsample_2isotropicsample_conditions_1
3D 15N-edited NOESY-TROSY-HSQCsample_2isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CARA, Keller and Wuthrich - peak picking

XEASY, Bartels et al. - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE III 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts