BMRB Entry 30741

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR30741
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR
Deposition date:
2020-03-25
Original release date:
2020-08-31
Authors:
Lu, M.; Russell, R.; Bryer, A.; Quinn, C.; Hou, G.; Zhang, H.; Schwieters, C.; Perilla, J.; Gronenborn, A.; Polenova, T.
Citation:

Citation: Lu, M.; Russell, R.; Bryer, A.; Quinn, C.; Hou, G.; Zhang, H.; Schwieters, C.; Perilla, J.; Gronenborn, A.; Polenova, T.. "Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR"  Nat. Struct. Mol. Biol. 27, 863-869 (2020).
PubMed: 32901160

Assembly members:

Assembly members:
entity_1, polymer, 231 residues, 25630.426 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PIVQNLQGQMVHQAISPRTL NAWVKVVEEKAFSPEVIPMF SALSEGATPQDLNTMLNTVG GHQAAMQMLKETINEEAAEW DRLHPVHAGPIAPGQMREPR GSDIAGTTSTLQEQIGWMTH NPPIPVGEIYKRWIILGLNK IVRMYSPTSILDIRQGPKEP FRDYVDRFYKTLRAEQASQE VKNWMTETLLVQNANPDCKT ILKALGPGATLEEMMTACQG VGGPGHKARVL

Data sets:
Data typeCount
13C chemical shifts917
15N chemical shifts209

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 231 residues - 25630.426 Da.

1   PROILEVALGLNASNLEUGLNGLYGLNMET
2   VALHISGLNALAILESERPROARGTHRLEU
3   ASNALATRPVALLYSVALVALGLUGLULYS
4   ALAPHESERPROGLUVALILEPROMETPHE
5   SERALALEUSERGLUGLYALATHRPROGLN
6   ASPLEUASNTHRMETLEUASNTHRVALGLY
7   GLYHISGLNALAALAMETGLNMETLEULYS
8   GLUTHRILEASNGLUGLUALAALAGLUTRP
9   ASPARGLEUHISPROVALHISALAGLYPRO
10   ILEALAPROGLYGLNMETARGGLUPROARG
11   GLYSERASPILEALAGLYTHRTHRSERTHR
12   LEUGLNGLUGLNILEGLYTRPMETTHRHIS
13   ASNPROPROILEPROVALGLYGLUILETYR
14   LYSARGTRPILEILELEUGLYLEUASNLYS
15   ILEVALARGMETTYRSERPROTHRSERILE
16   LEUASPILEARGGLNGLYPROLYSGLUPRO
17   PHEARGASPTYRVALASPARGPHETYRLYS
18   THRLEUARGALAGLUGLNALASERGLNGLU
19   VALLYSASNTRPMETTHRGLUTHRLEULEU
20   VALGLNASNALAASNPROASPCYSLYSTHR
21   ILELEULYSALALEUGLYPROGLYALATHR
22   LEUGLUGLUMETMETTHRALACYSGLNGLY
23   VALGLYGLYPROGLYHISLYSALAARGVAL
24   LEU

Samples:

sample_1: HIV-1 capsid protein, [U-13C; U-15N], 100%

sample_2: HIV-1 capsid protein, [1,6-13C]-Glucose; U-15N, 100%

sample_3: HIV-1 capsid protein, [2-13C]-Glucose; U-15N, 100%

sample_4: HIV-1 capsid protein, [13C,15N-His], 100%

sample_5: HIV-1 capsid protein, [13C,15N-Tyr], 100%

sample_6: 13C,15N-Ala HIV-1 capsid protein, [13C,15N-Ala], 50%; 13C,15N-Ile HIV-1 capsid protein, [13C,15N-Ile], 50%

sample_7: 13C,15N-Ala HIV-1 capsid protein, [13C,15N-Ala], 50%; 13C,15N-Val HIV-1 capsid protein, [13C,15N-Val], 50%

sample_8: HIV-1 capsid protein 86%; U-13C,15N-CA HIV-1 capsid protein, [U-13C; 15N-CA], 14%

sample_9: [U-13C] HIV-1 capsid protein, [U-13C], 50%; [U-15N] HIV-1 capsid protein, [U-15N], 50%

sample_conditions_1: ionic strength: 2.4 M; pH: 6; pressure: 1 atm; temperature: 277 K

Experiments:

NameSampleSample stateSample conditions
Exp1_CORD50mssample_1isotropicsample_conditions_1
Exp2_CORD500mssample_1isotropicsample_conditions_1
Exp3_DARR50mssample_1isotropicsample_conditions_1
Exp4_NCAsample_1isotropicsample_conditions_1
Exp5_NCAsample_1isotropicsample_conditions_1
Exp6_NCACXsample_1isotropicsample_conditions_1
Exp7_NCACXsample_1isotropicsample_conditions_1
Exp8_NCOCXsample_1isotropicsample_conditions_1
Exp9_NCOCX3dsample_1isotropicsample_conditions_1
Exp10_CONCA3dsample_1isotropicsample_conditions_1
Exp11_NCACX3dsample_1isotropicsample_conditions_1
Exp12_NCOCX3dsample_1isotropicsample_conditions_1
Exp13_CORD10mssample_2isotropicsample_conditions_1
Exp14_CORD20mssample_2isotropicsample_conditions_1
Exp15_CORD50mssample_2isotropicsample_conditions_1
Exp16_CORD100mssample_2isotropicsample_conditions_1
Exp17_CORD200mssample_2isotropicsample_conditions_1
Exp18_CORD300mssample_2isotropicsample_conditions_1
Exp19_CORD400mssample_2isotropicsample_conditions_1
Exp20_CORD500mssample_2isotropicsample_conditions_1
Exp21_CORD500mssample_2isotropicsample_conditions_1
Exp22_NCACXsample_2isotropicsample_conditions_1
Exp23_CORD25mssample_3isotropicsample_conditions_1
Exp24_CORD500mssample_3isotropicsample_conditions_1
Exp25_CORD500mssample_3isotropicsample_conditions_1
Exp26_PAINCPsample_3isotropicsample_conditions_1
Exp27_CORD25mssample_4isotropicsample_conditions_1
Exp28_R211sample_5isotropicsample_conditions_1
Exp29_REDOR1mssample_5isotropicsample_conditions_1
Exp30_REDOR1.6mssample_5isotropicsample_conditions_1
Exp31_REDOR2mssample_5isotropicsample_conditions_1
Exp32_CORD50mssample_6isotropicsample_conditions_1
Exp33_PDSD1ssample_6isotropicsample_conditions_1
Exp34_CORD50mssample_7isotropicsample_conditions_1
Exp35_CORD500mssample_8isotropicsample_conditions_1
Exp36_NHHC3mssample_9isotropicsample_conditions_1
Exp37_NHHC5mssample_9isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

Sparky, Goddard - data analysis

TALOS, Cornilescu, Delaglio and Bax - structure calculation

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

NMR spectrometers:

  • Bruker AVANCE III 850 MHz
  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 500 MHz
  • NHMFL NHMFL 900 MHz