BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18518

Title: LC3B OPTN-LIR Ptot complex structure   PubMed: 23805866

Deposition date: 2012-06-13 Original release date: 2013-07-15

Authors: Rogov, Vladimir; Rozenknop, Alexis; Loehr, Frank; Guentert, Peter; Doetsch, Volker

Citation: Rogov, Vladimir; Suzuki, Hironori; Fiskin, Evgenij; Wild, Philipp; Kniss, Andreas; Rozenknop, Alexis; Kato, Ryuichi; Kawasaki, Masato; McEwan, David; Lohr, Frank; Guntert, Peter; Dikic, Ivan; Wakatsuki, Soichi; Dotsch, Volker. "Structural basis for phosphorylation-triggered autophagic clearance of Salmonella."  Biochem. J. 454, 459-466 (2013).

Assembly members:
entity_1, polymer, 119 residues, 13965.232 Da.
entity_2, polymer, 17 residues, 2245.827 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pETm60_UB3

Entity Sequences (FASTA):
entity_1: GAMGKTFKQRRTFEQRVEDV RLIREQHPTKIPVIIERYKG EKQLPVLDKTKFLVPDHVNM SELIKIIRRRLQLNANQAFF LLVNGHSMVSVSTPISEVYE SEKDEDGFLYMVYASQETF
entity_2: NXXGXXEDXFVEIRMAE

Data sets:
Data typeCount
13C chemical shifts548
15N chemical shifts141
1H chemical shifts1028

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 119 residues - 13965.232 Da.

Residues 1-4 are expression tag. Residues 5-119 correspond to residues 5-119 of human Microtubule-associated proteins 1A/1B light chain 3B (UniProtKB entry Q9GZQ8)

1   GLYALAMETGLYLYSTHRPHELYSGLNARG
2   ARGTHRPHEGLUGLNARGVALGLUASPVAL
3   ARGLEUILEARGGLUGLNHISPROTHRLYS
4   ILEPROVALILEILEGLUARGTYRLYSGLY
5   GLULYSGLNLEUPROVALLEUASPLYSTHR
6   LYSPHELEUVALPROASPHISVALASNMET
7   SERGLULEUILELYSILEILEARGARGARG
8   LEUGLNLEUASNALAASNGLNALAPHEPHE
9   LEULEUVALASNGLYHISSERMETVALSER
10   VALSERTHRPROILESERGLUVALTYRGLU
11   SERGLULYSASPGLUASPGLYPHELEUTYR
12   METVALTYRALASERGLNGLUTHRPHE

Entity 2, entity_2 17 residues - 2245.827 Da.

Residues 169-185 correspond to residues 169-185 of human Optineurin sequence (UniProtKB entry Q96CV9). All serines in the peptide are phosphoserines (SEP).

1   ASNSEPSEPGLYSEPSEPGLUASPSEPPHE
2   VALGLUILEARGMETALAGLU

Samples:

sample_1: entity_1, [U-98% 13C; U-98% 15N], 0.6 ± 0.05 mM; entity_2 4.9 ± 0.5 mM; sodium phosphate 70 mM; sodium chloride 30 mM; DSS 0.3 mM; Protease inhibitors cocktail 5 mM; H2O 95%; D2O 5%

sample_2: entity_1, [U-98% 13C; U-98% 15N], 2.5 ± 0.05 mM; entity_2 0.4 ± 0.04 mM; sodium phosphate 70 mM; sodium chloride 30 mM; DSS 0.3 mM; Protease inhibitors cocktail 5 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.8; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1sample_1isotropicsample_conditions_1
2D 1H-1H NOESY F1,F2 13C/15N filteredsample_2isotropicsample_conditions_1
3D NOESY-[15N,1H]-FHSQCsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2, Bruker Biospin - chemical shift calculation, collection, processing

SPARKY v3.114, Goddard - chemical shift assignment, data analysis, peak picking

CYANA v2, Guntert, Mumenthaler and Wuthrich - structure solution

OPALp, Koradi, Billeter and Guntert - refinement

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

UNP Q9GZQ8 Q96CV9
BMRB 15877
PDB
DBJ BAB15169 BAB22364 BAB22569 BAB22641 BAB22855
EMBL CAD38970 CAG31435 CAL38438
GB AAA20645 AAB72082 AAG09686 AAG23182 AAH18634
REF NP_001001169 NP_001026632 NP_001078950 NP_001177219 NP_001180554
SP A6NCE7 O41515 Q62625 Q9CQV6 Q9GZQ8
TPG DAA20021

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