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 18521

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18521
MolProbity Validation Chart

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Title: The NMR structure of the Vta1-Vps60 complex   PubMed: 23105107

Deposition date: 2012-06-13 Original release date: 2012-11-05

Authors: Yang, Zhongzheng; Vild, Cody; Ju, Jiaying; Zhang, Xu; Liu, Jianping; Shen, Jie; Zhao, Bin; Lan, Wenxian; Gong, Fuchun; Liu, Maili; Cao, Chunyang; Xu, Zhaohui

Citation: Yang, Zhongzheng; Vild, Cody; Ju, Jiaying; Zhang, Xu; Liu, Jianping; Shen, Jie; Zhao, Bin; Lan, Wenxian; Gong, Fuchun; Liu, Maili; Cao, Chunyang; Xu, Zhaohui. "Structural basis of molecular recognition between ESCRT-III-like protein Vps60 and AAA-ATPase regulator Vta1 in the multivesicular body pathway."  J. Biol. Chem. 287, 43899-43908 (2012).

Assembly members:
entity_1, polymer, 167 residues, 19062.176 Da.
entity_2, polymer, 59 residues, 6609.143 Da.

Natural source:   Common Name: baker   Taxonomy ID: 4932   Superkingdom: not available   Kingdom: not available   Genus/species: Eukaryota Fungi

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

Entity Sequences (FASTA):
entity_1: MASNAARVVATAKDFDKVGL GIIGYYLQLYAVELILSEED RSQEMTALATELLDTIEAFK KEIGGESEAEDSDKSLHVMN TLIHDQEKAKIYMLNFTMSL YNEKLKQLKDGPWDVMLKRS LWCCIDLFSCILHLWKENIS ETSTNSLQKRIKYCKIYLSK LAKGEIG
entity_2: INIDKLQDMQDEMLDLIEQG DELQEVLAMNNNSGELDDIS DAELDAELDALAQEDFTLP

Data sets:
Data typeCount
13C chemical shifts926
15N chemical shifts232
1H chemical shifts1605

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 167 residues - 19062.176 Da.

1   METALASERASNALAALAARGVALVALALA
2   THRALALYSASPPHEASPLYSVALGLYLEU
3   GLYILEILEGLYTYRTYRLEUGLNLEUTYR
4   ALAVALGLULEUILELEUSERGLUGLUASP
5   ARGSERGLNGLUMETTHRALALEUALATHR
6   GLULEULEUASPTHRILEGLUALAPHELYS
7   LYSGLUILEGLYGLYGLUSERGLUALAGLU
8   ASPSERASPLYSSERLEUHISVALMETASN
9   THRLEUILEHISASPGLNGLULYSALALYS
10   ILETYRMETLEUASNPHETHRMETSERLEU
11   TYRASNGLULYSLEULYSGLNLEULYSASP
12   GLYPROTRPASPVALMETLEULYSARGSER
13   LEUTRPCYSCYSILEASPLEUPHESERCYS
14   ILELEUHISLEUTRPLYSGLUASNILESER
15   GLUTHRSERTHRASNSERLEUGLNLYSARG
16   ILELYSTYRCYSLYSILETYRLEUSERLYS
17   LEUALALYSGLYGLUILEGLY

Entity 2, entity_2 59 residues - 6609.143 Da.

1   ILEASNILEASPLYSLEUGLNASPMETGLN
2   ASPGLUMETLEUASPLEUILEGLUGLNGLY
3   ASPGLULEUGLNGLUVALLEUALAMETASN
4   ASNASNSERGLYGLULEUASPASPILESER
5   ASPALAGLULEUASPALAGLULEUASPALA
6   LEUALAGLNGLUASPPHETHRLEUPRO

Samples:

sample_1: entity_1, [U-13C; U-15N], 1.0-1.2 mM; entity_2 1.0-1.2 mM

sample_2: entity_1, [U-13C; U-15N], 1.0-1.2 mM; entity_2 1.0-1.2 mM

sample_3: entity_1 1.0-1.2 mM; entity_2, [U-13C; U-15N], 1.0-1.2 mM

sample_4: entity_1 1.0-1.2 mM; entity_2, [U-13C; U-15N], 1.0-1.2 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.0; pressure: 1 atm; temperature: 293.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_4isotropicsample_conditions_1

Software:

X-PLOR NIH vNIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

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

SPARKY, Goddard - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

VNMRJ, Varian - collection

ProcheckNMR, Laskowski and MacArthur - structure analysis

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ GAA25057 GAA22697
EMBL CAY81418 CAY78983
GB AAA66933 AAB67473 AHY78560 AJP40335 AJV46241 AAB64922 AAS56499 AHY75433 EDN60805 EDV07859
REF NP_013282 NP_010774
SP Q06263 Q03390
TPG DAA09501 DAA12319

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