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BMRB Entry 17738

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17738
MolProbity Validation Chart

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Title: Structure of a monomeric mutant of the HIV-1 capsid protein   PubMed: 21995733

Deposition date: 2011-06-28 Original release date: 2011-10-25

Authors: Shin, Ronald; Tzou, Ywh-Min; Krishna, N. Rama

Citation: Shin, Ronald; Tzou, Ywh-Min; Krishna, N. Rama. "Structure of a monomeric mutant of the HIV-1 capsid protein."  Biochemistry 50, 9457-9467 (2011).

Assembly members:
HIV-1_CA, polymer, 240 residues, 26609.50 Da.

Natural source:   Common Name: Human Immunodeficiency Virus   Taxonomy ID: 12721   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus HIV

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

Entity Sequences (FASTA):
HIV-1_CA: MPIVQNLQGQMVHQAISPRT LNAWVKVVEEKAFSPEVIPM FSALSEGATPQDLNTMLNTV GGHQAAMQMLKETINEEAAE WDRLHPVHAGPIAPGQMREP RGSDIAGTTSTLQEQIGWMT HNPPIPVGEIYKRWIILGLN KIVRMYSPTSILDIRQGPKE PFRDYVDRFYKTLRAEQASQ EVKNAATETLLVQNANPDCK TILKALGPGATLEEMMTACQ GVGGPGHKARVLVEHHHHHH

Data sets:
Data typeCount
13C chemical shifts902
15N chemical shifts214
1H chemical shifts1484

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1HIV-1_CA1

Entities:

Entity 1, HIV-1_CA 240 residues - 26609.50 Da.

The start codon MET is listed as residue #0 in the sequence. The first PRO is listed as residue #1. The final 8 residues are the 6xhis tag, and are not included in the final structure.

1   METPROILEVALGLNASNLEUGLNGLYGLN
2   METVALHISGLNALAILESERPROARGTHR
3   LEUASNALATRPVALLYSVALVALGLUGLU
4   LYSALAPHESERPROGLUVALILEPROMET
5   PHESERALALEUSERGLUGLYALATHRPRO
6   GLNASPLEUASNTHRMETLEUASNTHRVAL
7   GLYGLYHISGLNALAALAMETGLNMETLEU
8   LYSGLUTHRILEASNGLUGLUALAALAGLU
9   TRPASPARGLEUHISPROVALHISALAGLY
10   PROILEALAPROGLYGLNMETARGGLUPRO
11   ARGGLYSERASPILEALAGLYTHRTHRSER
12   THRLEUGLNGLUGLNILEGLYTRPMETTHR
13   HISASNPROPROILEPROVALGLYGLUILE
14   TYRLYSARGTRPILEILELEUGLYLEUASN
15   LYSILEVALARGMETTYRSERPROTHRSER
16   ILELEUASPILEARGGLNGLYPROLYSGLU
17   PROPHEARGASPTYRVALASPARGPHETYR
18   LYSTHRLEUARGALAGLUGLNALASERGLN
19   GLUVALLYSASNALAALATHRGLUTHRLEU
20   LEUVALGLNASNALAASNPROASPCYSLYS
21   THRILELEULYSALALEUGLYPROGLYALA
22   THRLEUGLUGLUMETMETTHRALACYSGLN
23   GLYVALGLYGLYPROGLYHISLYSALAARG
24   VALLEUVALGLUHISHISHISHISHISHIS

Samples:

15N: HIV-1 CA, [U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; H2O 90%; D2O 10%

13C_-_15N_(H2O): HIV-1 CA, [U-98% 13C; U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; H2O 90%; D2O 10%

13C_-_15N_(D2O): HIV-1 CA, [U-98% 13C; U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; D2O 100%

13C_-_15N_-_2H_(H2O): HIV-1 CA, [U-98% 13C; U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; H2O 90%; D2O 10%

13C_-_15N_-_2H_(D2O): HIV-1 CA, [U-98% 13C; U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; D2O 100%

15N_(D2O): HIV-1 CA, [U-98% 13C; U-98% 15N], 2 mM; sodium chloride 25 mM; sodium acetate, [U-99% 2H], 25 mM; DTT, [U-99% 2H], 10 mM; sodium azide 0.02%; AEBSF protease inhibitor 0.1 mM; EDTA, [U-99% 2H], 1 mM; D2O 100%

Sample_conditions: pH: 5.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15NisotropicSample_conditions
2D 1H-15N SOFAST HMQC15N_(D2O)isotropicSample_conditions
2D 1H-13C HSQC13C_-_15N_(D2O)isotropicSample_conditions
3D CBCA(CO)NH13C_-_15N_(H2O)isotropicSample_conditions
3D HNCO13C_-_15N_(H2O)isotropicSample_conditions
3D HNCA13C_-_15N_(H2O)isotropicSample_conditions
3D HNCACB13C_-_15N_-_2H_(H2O)isotropicSample_conditions
3D HCCH-TOCSY13C_-_15N_(D2O)isotropicSample_conditions
3D HCCH-TOCSY13C_-_15N_-_2H_(D2O)isotropicSample_conditions
3D HCCH-COSY13C_-_15N_(D2O)isotropicSample_conditions
3D HCCH-COSY13C_-_15N_-_2H_(D2O)isotropicSample_conditions
3D 1H-15N NOESY15NisotropicSample_conditions
3D 1H-13C NOESY13C_-_15N_(D2O)isotropicSample_conditions

Software:

TOPSPIN v1.3, Bruker Biospin - collection, data analysis, processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, refinement, structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

BMRB 19261 19264 19575 25532
PDB
DBJ BAA00992 BAA12988 BAA12996 BAA93773 BAA93775
EMBL CAA11884 CAA25902 CAA65355 CAA76038 CAB85858
GB AAA44201 AAA44652 AAA44987 AAA45003 AAA76686
PIR FOVWLV
PRF 1102247B 1103299C
REF NP_057849 NP_057850 NP_579880
SP P03347 P03348 P03349 P03366 P03367

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