BMRB Entry 30769

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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/BMR30769
MolProbity Validation Chart

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Title:
Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A
Deposition date:
2020-07-09
Original release date:
2021-11-09
Authors:
Byeon, I.-J.; Calero, G.; Wu, Y.; Byeon, C.; Gronenborn, A.
Citation:

Citation: Byeon, I.-J.; Calero, G.; Wu, Y.; Byeon, C.; Jung, J.; DeLucia, M.; Zhou, X.; Weiss, S.; Ahn, J.; Hao, C.; Skowronski, J.; Gronenborn, A.. "Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A"  Nat. Commun. 12, 6864-6864 (2021).
PubMed: 34824204

Assembly members:

Assembly members:
entity_1, polymer, 234 residues, 26792.789 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: HIV-1   Taxonomy ID: 11698   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: MEQAPEDQGPQREPYNEWTL ELLEELKSEAVRHFPRIWLH NLGQHIYETYGDTWAGVEAI IRILQQLLFIHFRIGCRHSG GSGGSATEAAGENPLEFLRD QPQFQNMRQVIQQNPALLPA LLQQLGQENPQLLQQISRHQ EQFIQMLNEPPGELADISDV EGEVGAIGEEAPQMNYIQVT PQEKEAIERLKALGFPESLV IQAYFACEKNENLAANFLLS QNFDDELEHHHHHH

Data sets:
Data typeCount
13C chemical shifts756
15N chemical shifts248
1H chemical shifts1565

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 234 residues - 26792.789 Da.

1   METGLUGLNALAPROGLUASPGLNGLYPRO
2   GLNARGGLUPROTYRASNGLUTRPTHRLEU
3   GLULEULEUGLUGLULEULYSSERGLUALA
4   VALARGHISPHEPROARGILETRPLEUHIS
5   ASNLEUGLYGLNHISILETYRGLUTHRTYR
6   GLYASPTHRTRPALAGLYVALGLUALAILE
7   ILEARGILELEUGLNGLNLEULEUPHEILE
8   HISPHEARGILEGLYCYSARGHISSERGLY
9   GLYSERGLYGLYSERALATHRGLUALAALA
10   GLYGLUASNPROLEUGLUPHELEUARGASP
11   GLNPROGLNPHEGLNASNMETARGGLNVAL
12   ILEGLNGLNASNPROALALEULEUPROALA
13   LEULEUGLNGLNLEUGLYGLNGLUASNPRO
14   GLNLEULEUGLNGLNILESERARGHISGLN
15   GLUGLNPHEILEGLNMETLEUASNGLUPRO
16   PROGLYGLULEUALAASPILESERASPVAL
17   GLUGLYGLUVALGLYALAILEGLYGLUGLU
18   ALAPROGLNMETASNTYRILEGLNVALTHR
19   PROGLNGLULYSGLUALAILEGLUARGLEU
20   LYSALALEUGLYPHEPROGLUSERLEUVAL
21   ILEGLNALATYRPHEALACYSGLULYSASN
22   GLUASNLEUALAALAASNPHELEULEUSER
23   GLNASNPHEASPASPGLULEUGLUHISHIS
24   HISHISHISHIS

Entity 2, unit_2 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Vpr-hHR23A complex, [U-100% 2H; U-100% 13C; U-100% 15N], 927 ± 10 uM; sodium phosphate 25 ± 1 mM; sodium chloride 50 ± 2 mM; DTT 2 ± 0.2 mM; TCEP 1 ± 0.01 mM; ZnSO4 0.1 ± 0.001 mM; EDTA 0.1 ± 0.001 mM; sodium azide 0.02 ± 0.0002 %

sample_2: Vpr-hHR23A complex, [U-100% 13C; U-100% 15N], 1100 ± 10 uM; sodium phosphate 25 ± 1 mM; sodium chloride 50 ± 2 mM; DTT 2 ± 0.02 mM; TCEP 1 ± 0.01 mM; ZnSO4 0.1 ± 0.001 mM; EDTA 0.1 ± 0.001 mM; sodium azide 0.02 ± 0.0002 %

sample_3: Vpr-hHR23A complex, [U-100% 15N], 1110 ± 10 uM; sodium phosphate 25 ± 1 mM; sodium chloride 50 ± 2 mM; DTT 2 ± 0.02 mM; TCEP 1 ± 0.01 mM; ZnSO4 0.1 ± 0.001 mM; EDTA 0.1 ± 0.001 mM; sodium azide 0.02 ± 0.0002 %

sample_4: Vpr-hHR23A complex, [U-100% 15N], 1000 ± 10 uM; sodium phosphate 25 ± 1 mM; sodium chloride 50 ± 2 mM; DTT 2 ± 0.02 mM; TCEP 1 ± 0.01 mM; ZnSO4 0.1 ± 0.001 mM; EDTA 0.1 ± 0.001 mM; sodium azide 0.02 ± 0.0002 %

sample_5: Vpr-hHR23A complex, [U-100% 13C; U-100% 15N], 745 ± 10 uM; sodium phosphate 25 ± 1 mM; sodium chloride 50 ± 2 mM; DTT 2 ± 0.02 mM; TCEP 1 ± 0.01 mM; ZnSO4 0.1 ± 0.001 mM; EDTA 0.1 ± 0.001 mM; sodium azide 0.02 ± 0.0002 %

sample_conditions_1: ionic strength: 100 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D TROSY-HNCACBsample_1isotropicsample_conditions_1
3D TROSY-HNCOCACBsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D similtaneously 13C/15C-edited NOESY (aliphatic)sample_2isotropicsample_conditions_1
3D similtaneously 13C/15C-edited NOESY (aliphatic)sample_5isotropicsample_conditions_2
3D similtaneously 13C/15C-edited NOESY (aromatic)sample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_2
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
2D NOESYsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1

Software:

TopSpin v3.1, Bruker Biospin - collection

NMRPipe v8.7, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNmr Analysis v2.3.1, CCPN - chemical shift assignment

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

TALOS+, Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax - data analysis

NMR spectrometers:

  • Bruker AVANCE 900 MHz
  • Bruker AVANCE 800 MHz
  • Bruker AVANCE 700 MHz
  • Bruker AVANCE 600 MHz

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