BMRB Entry 19333

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19333
MolProbity Validation Chart

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Title:
HIV-1 Vif SOCS-box and Elongin BC solution structure
Deposition date:
2013-07-01
Original release date:
2013-12-09
Authors:
LU, Zhisheng; Bergeron, Julien; Atkinson, Andrew; Schaller, Torsten; Veselkov, Dennis; Oregioni, Alain; Yang, Yi; Matthews, Stephen; Malim, Michael; Sanderson, Mark
Citation:

Citation: Lu, Zhisheng; Bergeron, Julien; Atkinson, Andrew; Schaller, Torsten; Veselkov, Dennis; Oregioni, Alain; Yang, Yi; Matthews, Stephen; Malim, Michael; Sanderson, Mark. "Insight into the HIV-1 Vif SOCS-box ElonginBC interaction"  Open Biol. 3, 130100-130100 (2013).
PubMed: 24225024

Assembly members:

Assembly members:
Vif_SOCS, polymer, 36 residues, 3637.402 Da.
Elongin_B, polymer, 118 residues, 13147.898 Da.
Elongin_C, polymer, 91 residues, 10217.753 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Vif_SOCS: HNKVGSLQYLALAALIKPKQ IKPPLPSVRKLTEDRW
Elongin_B: MDVFLMIRRHKTTIFTDAKE SSTVFELKRIVEGILKRPPD EQRLYKDDQLLDDGKTLGEC GFTSQTARPQAPATVGLAFR ADDTFEALCIEPFSSPPELP DVMKPQDSGSSANEQAVQ
Elongin_C: VKLISSDGHEFIVKREHALT SGTIKAMLSGPGQFAENETN EVNFREIPSHVLSKVCMYFT YKVRYTNSSTEIPEFPIAPE IALELLMAANF

Data typeCount
13C chemical shifts417
15N chemical shifts160
1H chemical shifts250

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 36 residues - 3637.402 Da.

1   HISASNLYSVALGLYSERLEUGLNTYRLEU
2   ALALEUALAALALEUILELYSPROLYSGLN
3   ILELYSPROPROLEUPROSERVALARGLYS
4   LEUTHRGLUASPARGTRP

Entity 2, entity_2 118 residues - 13147.898 Da.

1   METASPVALPHELEUMETILEARGARGHIS
2   LYSTHRTHRILEPHETHRASPALALYSGLU
3   SERSERTHRVALPHEGLULEULYSARGILE
4   VALGLUGLYILELEULYSARGPROPROASP
5   GLUGLNARGLEUTYRLYSASPASPGLNLEU
6   LEUASPASPGLYLYSTHRLEUGLYGLUCYS
7   GLYPHETHRSERGLNTHRALAARGPROGLN
8   ALAPROALATHRVALGLYLEUALAPHEARG
9   ALAASPASPTHRPHEGLUALALEUCYSILE
10   GLUPROPHESERSERPROPROGLULEUPRO
11   ASPVALMETLYSPROGLNASPSERGLYSER
12   SERALAASNGLUGLNALAVALGLN

Entity 3, entity_3 91 residues - 10217.753 Da.

1   VALLYSLEUILESERSERASPGLYHISGLU
2   PHEILEVALLYSARGGLUHISALALEUTHR
3   SERGLYTHRILELYSALAMETLEUSERGLY
4   PROGLYGLNPHEALAGLUASNGLUTHRASN
5   GLUVALASNPHEARGGLUILEPROSERHIS
6   VALLEUSERLYSVALCYSMETTYRPHETHR
7   TYRLYSVALARGTYRTHRASNSERSERTHR
8   GLUILEPROGLUPHEPROILEALAPROGLU
9   ILEALALEUGLULEULEUMETALAALAASN
10   PHE

Samples:

sample_1: Vif SOCS, [U-99% 13C; U-99% 15N], 0.2 mM; Elongin B 0.2 mM; Elongin C 0.2 mM; H2O 90%; D2O 10%; Na-phosphate buffer 50 mM

sample_2: Vif SOCS 0.2 mM; Elongin B, [U-99% 13C; U-99% 15N], 0.2 mM; Elongin C, [U-99% 13C; U-99% 15N], 0.2 mM; H2O 90%; D2O 10%; Na-phosphate buffer 50 mM

sample_3: Vif SOCS 0.2 mM; Elongin B, [U-99% 13C; U-99% 15N], 0.2 mM; Elongin C, [U-99% 13C; U-99% 15N], 0.2 mM; H2O 90%; D2O 10%; Na-phosphate buffer 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HNCACOsample_3isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1

Software:

NMRPipe v5.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN v3.0, Bruker Biospin - collection

CCPN v2.2, CCPN - chemical shift assignment, chemical shift calculation, peak picking

CS-Rosetta, Shen, Vernon, Baker and Bax - refinement, structure solution

HADDOCK, Alexandre Bonvin - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Varian INOVA 800 MHz

Related Database Links:

PDB
GB AAA44989 AAB04038 AAB31804 AAB60573 AAC28447 AAA75522 AAA80968 AAC08452 AAH13306 AAH51927 AAA41109 AAA67650 AAH09104 AAH13809 AAH28545
SP P12504 P62869 P62870 Q15370 P83940 P83941 Q15369 Q2KII4
BMRB 15606 15606
DBJ BAB21946 BAB22417 BAB22684 BAB25690 BAB25727 BAB27825 BAB27939 BAB28546 BAB28641 BAC30437
PRF 2119399A 2119399B
REF NP_001029972 NP_009039 NP_080581 NP_112391 NP_996896 NP_001002440 NP_001004673 NP_001007889 NP_001016420 NP_001039958
TPG DAA15620 DAA22672
EMBL CAG32006 CAJ81641 CBN81906 CDQ94726 CDQ97243
AlphaFold P12504 P62869 P62870 Q15370 P83940 P83941 Q15369 Q2KII4

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