BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 50108

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50108

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Title: 1H, 13C and 15N chemical shift assignments for VARP 687-747   PubMed: 33024112

Deposition date: 2019-11-29 Original release date: 2020-10-16

Authors: Owen, David; Neuhaus, David; Yang, Ji-Chun; Crawley-Snowdon, Harriet

Citation: Crawley-Snowdon, Harriet; Yang, Ji-Chun; Zaccai, Nathan; Davis, Luther; Wartosch, Lena; Herman, Emily; Bright, Nicholas; Swarbrick, James; Collins, Brett; Jackson, Lauren; Seaman, Matthew; Luzio, J Paul; Dacks, Joel; Neuhaus, David; Owen, David. "Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29"  Nat. Commun. 11, 5031-5031 (2020).

Assembly members:
entity_1, polymer, 61 residues, Formula weight is not available
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEXVARPfingernail2

Entity Sequences (FASTA):
entity_1: GPLGSTEEDLEDAEDTVSAA DPEFCHPLCQCPKCAPAQKR LAKVPASGLGVNVTSQDGSS W

Data sets:
Data typeCount
13C chemical shifts181
15N chemical shifts58
1H chemical shifts359

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1VARP 687-7471
2zinc ion2

Entities:

Entity 1, VARP 687-747 61 residues - Formula weight is not available

1   GLYPROLEUGLYSERTHRGLUGLUASPLEU
2   GLUASPALAGLUASPTHRVALSERALAALA
3   ASPPROGLUPHECYSHISPROLEUCYSGLN
4   CYSPROLYSCYSALAPROALAGLNLYSARG
5   LEUALALYSVALPROALASERGLYLEUGLY
6   VALASNVALTHRSERGLNASPGLYSERSER
7   TRP

Entity 2, zinc ion - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: VARP 687-747, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_2: VARP 687-747, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC full-widthsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic constant timesample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromatic constant timesample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D [1H-13C-1H] HCCH-COSYsample_1isotropicsample_conditions_1
3D [1H-13C-1H] HCCH-TOCSYsample_1isotropicsample_conditions_1
3D [13C-13C-1H] HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HACAHBsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D 15N NOESY-HSQC (50ms mixing time)sample_1isotropicsample_conditions_1
3D 15N NOESY-HSQC (150ms mixing time)sample_1isotropicsample_conditions_1
3D 13C NOESY-HSQC aliphatic (150ms mixing time)sample_1isotropicsample_conditions_1
3D 13C NOESY-HSQC aromatic (150ms mixing time)sample_2isotropicsample_conditions_1

Software:

TOPSPIN v3.5, Bruker Biospin - processing

CcpNMR v2.4.2, CCPN - chemical shift assignment

NMR spectrometers:

  • Bruker Avance-III 800 MHz
  • Bruker Avance-1 600 MHz

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