BMRB Entry 34461

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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/BMR34461
MolProbity Validation Chart

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Title:
Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747
Deposition date:
2019-11-29
Original release date:
2020-10-16
Authors:
Owen, D.; Neuhaus, D.; Yang, J.C.; Crawley-Snowdon, H.
Citation:

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).
PubMed: 33024112

Assembly members:

Assembly members:
entity_1, polymer, 192 residues, 21626.832 Da.
entity_2, polymer, 61 residues, 6319.927 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21   Vector: pGEXVPS29

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSPEFGTRDRMLVLVLGDLH IPHRCNSLPAKFKKLLVPGK IQHILCTGNLCTKESYDYLK TLAGDVHIVRGDFDENLNYP EQKVVTVGQFKIGLIHGHQV IPWGDMASLALLQRQFDVDI LISGHTHKFEAFEHENKFYI NPGSATGAYNALETNIIPSF VLMDIQASTVVTYVYQLIGD DVKVERIEYKKS
entity_2: GPLGSTEEDLEDAEDTVSAA DPEFCHPLCQCPKCAPAQKR LAKVPASGLGVNVTSQDGSS W

Data sets:
Data typeCount
13C chemical shifts749
15N chemical shifts239
1H chemical shifts1447

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_1 192 residues - 21626.832 Da.

1   GLYSERPROGLUPHEGLYTHRARGASPARG
2   METLEUVALLEUVALLEUGLYASPLEUHIS
3   ILEPROHISARGCYSASNSERLEUPROALA
4   LYSPHELYSLYSLEULEUVALPROGLYLYS
5   ILEGLNHISILELEUCYSTHRGLYASNLEU
6   CYSTHRLYSGLUSERTYRASPTYRLEULYS
7   THRLEUALAGLYASPVALHISILEVALARG
8   GLYASPPHEASPGLUASNLEUASNTYRPRO
9   GLUGLNLYSVALVALTHRVALGLYGLNPHE
10   LYSILEGLYLEUILEHISGLYHISGLNVAL
11   ILEPROTRPGLYASPMETALASERLEUALA
12   LEULEUGLNARGGLNPHEASPVALASPILE
13   LEUILESERGLYHISTHRHISLYSPHEGLU
14   ALAPHEGLUHISGLUASNLYSPHETYRILE
15   ASNPROGLYSERALATHRGLYALATYRASN
16   ALALEUGLUTHRASNILEILEPROSERPHE
17   VALLEUMETASPILEGLNALASERTHRVAL
18   VALTHRTYRVALTYRGLNLEUILEGLYASP
19   ASPVALLYSVALGLUARGILEGLUTYRLYS
20   LYSSER

Entity 2, entity_2 61 residues - 6319.927 Da.

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

Entity 3, entity_3 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: VPS29, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; VARP 692-746 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_2: VPS29, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; VARP 692-746 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_3: VPS29 0.45 ± 0.15 mM; VARP 692-746, [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_4: VPS29 0.45 ± 0.15 mM; VARP 692-746, [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

sample_conditions_2: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 275 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic constant-timesample_1isotropicsample_conditions_1
2D 1H-1H NOESY (150ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2sample_1isotropicsample_conditions_1
3D 13C NOESY-HSQC aromatic (150ms mixing time)sample_1isotropicsample_conditions_1
3D 13C NOESY-HSQC aliphatic (150ms mixing time)sample_1isotropicsample_conditions_1
3D 15N NOESY-HSQC (150ms mixing time)sample_1isotropicsample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]sample_1isotropicsample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]sample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
2D 1H-1H NOESY (150ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2sample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic constant-timesample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-1H NOESY (70ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2sample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aromatic, filtered to reject 13C-1 and 15N-coupled 1H in F1sample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aromatic, filtered to reject 13C-1 and 15N-coupled 1H in F1sample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aliphatic, filtered to reject 13C-1 and 15N-coupled 1H in F1sample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aliphatic, filtered to reject 13C-1 and 15N-coupled 1H in F1sample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aromaticsample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aromaticsample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aliphaticsample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aliphaticsample_2isotropicsample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]sample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_2
2D 1H-15N HSQCsample_3isotropicsample_conditions_3
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HNHAsample_3isotropicsample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]sample_3isotropicsample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]sample_3isotropicsample_conditions_1
3D 1H-15N NOESY-HSQC (70ms mixing time)sample_3isotropicsample_conditions_1
3D 1H-15N NOESY-HSQC (150ms mixing time)sample_3isotropicsample_conditions_1
3D 1H-15N NOESY-HSQC (50ms mixing time)sample_3isotropicsample_conditions_2
3D 1H-15N NOESY-HSQC (50ms mixing time)sample_3isotropicsample_conditions_3
3D 1H-13C NOESY (70ms mixing time) aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]sample_4isotropicsample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]sample_4isotropicsample_conditions_1
3D 13C NOESY-HSQC aliphatic (50ms mixing time)sample_4isotropicsample_conditions_1
3D 13C NOESY-HSQC aliphatic (70ms mixing time)sample_4isotropicsample_conditions_1
3D 13C NOESY-HSQC aliphatic (120ms mixing time)sample_4isotropicsample_conditions_1
3D 13C NOESY-HSQC aromatic (70ms mixing time)sample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromatic constant-timesample_2isotropicsample_conditions_1

Software:

TopSpin v3.5, Bruker Biospin - processing

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment

X-PLOR NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 800 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