BMRB Entry 17614

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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/BMR17614
MolProbity Validation Chart

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Title:
Structure of the mitochondrial uncoupling protein 2 determined by NMR molecular fragment replacement
Deposition date:
2011-04-29
Original release date:
2011-08-02
Authors:
Berardi, Marcelo; Chou, James
Citation:

Citation: Berardi, Marcelo; Shih, William; Harrison, Stephen; Chou, James. "Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching."  Nature 476, 109-113 (2011).
PubMed: 21785437

Assembly members:

Assembly members:
UCP2, polymer, 303 residues, 32227.426 Da.
UCP2-SL1, polymer, 303 residues, 32227.426 Da.
UCP2-SL2, polymer, 303 residues, 32227.426 Da.
UCP2-SL3, polymer, 303 residues, 32227.426 Da.
UCP2-SL4, polymer, 303 residues, 32227.426 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   Vector: pET-21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UCP2: MTVKFLGAGTAACIADLITF PLDTAKVRLQIQGESQGLVR TAASAQYRGVLGTILTMVRT EGPRSLYNGLVAGLQRQMSF ASVRIGLYDSVKQFYTKGSE HAGIGSRLLAGSTTGALAVA VAQPTDVVKVRFQAQARAGG GRRYQSTVEAYKTIAREEGI RGLWKGTSPNVARNAIVNCA ELVTYDLIKDTLLKANLMTD DLPCHFTSAFGAGFCTTVIA SPVDVVKTRYMNSALGQYHS AGHCALTMLRKEGPRAFYKG FMPSFLRLGSWNVVMFVTYE QLKRALMAAYQSREAPFHHH HHH
UCP2-SL1: MTVKFLGAGTAAAIADLITF PLDTAKVRLQIQGESQGLVR TAASAQYRGVLGTILCMVRT EGPRSLYNGLVAGLQRQMSF ASVRIGLYDSVKQFYTKGSE HAGIGSRLLAGSTTGALAVA VAQPTDVVKVRFQAQARAGG GRRYQSTVEAYKTIAREEGI RGLWKGTSPNVARNAIVNSA ELVTYDLIKDTLLKANLMTD DLPSHFTSAFGAGFSTTVIA SPVDVVKTRYMNSALGQYHS AGHSALTMLRKEGPRAFYKG FMPSFLRLGSWNVVMFVTYE QLKRALMAAYQSREAPFHHH HHH
UCP2-SL2: MTVKFLGAGTAAAIADLITF PLDTAKVRLQIQGESQGLVR TAASAQYRGVLGTILTMVRT EGPRSLYNGLVAGLQRQMSF ASVRIGLYDSVKCFYTKGSE HAGIGSRLLAGSTTGALAVA VAQPTDVVKVRFQAQARAGG GRRYQSTVEAYKTIAREEGI RGLWKGTSPNVARNAIVNSA ELVTYDLIKDTLLKANLMTD DLPSHFTSAFGAGFSTTVIA SPVDVVKTRYMNSALGQYHS AGHSALTMLRKEGPRAFYKG FMPSFLRLGSWNVVMFVTYE QLKRALMAAYQSREAPFHHH HHH
UCP2-SL3: MTVKFLGAGTAAAIADLITF PLDTAKVRLQIQGESQGLVR TAASAQYRGVLGTILTMVRT EGPRSLYNGLVAGLQRQMSF ASVRIGLYDSVKQFYTKGSE HAGIGSRLLAGSTTGALAVA VAQPTDVVKVRFQAQARAGG GRRYQSTVEAYKTIAREEGI RGLWKGTSPNVARNAIVNSA ELVTYDLIKCTLLKANLMTD DLPSHFTSAFGAGFSTTVIA SPVDVVKTRYMNSALGQYHS AGHSALTMLRKEGPRAFYKG FMPSFLRLGSWNVVMFVTYE QLKRALMAAYQSREAPFHHH HHH
UCP2-SL4: MTVKFLGAGTAAAIADLITF PLDTAKVRLQIQGESQGLVR TAASAQYRGVLGTILTMVRT EGPRSLYNGLVAGLQRQMSF ASVRIGLYDSVKQFYTKGSE HAGIGSRLLAGSTTGALAVA VAQPTDVVKVRFQAQARAGG GRRYQSTVEAYKTIAREEGI RGLWKGTSPNVARNAIVNSA ELVTYDLIKDTLLKANLMTD DLPSHFTSAFGAGFSTTVIA SPVDVVKTRYMNSALGQYHS AGCSALTMLRKEGPRAFYKG FMPSFLRLGSWNVVMFVTYE QLKRALMAAYQSREAPFHHH HHH

Data sets:
Data typeCount
13C chemical shifts695
15N chemical shifts236
1H chemical shifts249

Additional metadata:

  • Assembly
  • Samples and Experiments
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Assembly:

Entity Assembly IDEntity NameEntity ID
1UCP21
2UCP2-SL12
3UCP2-SL23
4UCP2-SL34
5UCP2-SL45

Entities:

Entity 1, UCP2 303 residues - 32227.426 Da.

Residues 1-12 of the native sequence have been removed for structure determination

1   METTHRVALLYSPHELEUGLYALAGLYTHR
2   ALAALACYSILEALAASPLEUILETHRPHE
3   PROLEUASPTHRALALYSVALARGLEUGLN
4   ILEGLNGLYGLUSERGLNGLYLEUVALARG
5   THRALAALASERALAGLNTYRARGGLYVAL
6   LEUGLYTHRILELEUTHRMETVALARGTHR
7   GLUGLYPROARGSERLEUTYRASNGLYLEU
8   VALALAGLYLEUGLNARGGLNMETSERPHE
9   ALASERVALARGILEGLYLEUTYRASPSER
10   VALLYSGLNPHETYRTHRLYSGLYSERGLU
11   HISALAGLYILEGLYSERARGLEULEUALA
12   GLYSERTHRTHRGLYALALEUALAVALALA
13   VALALAGLNPROTHRASPVALVALLYSVAL
14   ARGPHEGLNALAGLNALAARGALAGLYGLY
15   GLYARGARGTYRGLNSERTHRVALGLUALA
16   TYRLYSTHRILEALAARGGLUGLUGLYILE
17   ARGGLYLEUTRPLYSGLYTHRSERPROASN
18   VALALAARGASNALAILEVALASNCYSALA
19   GLULEUVALTHRTYRASPLEUILELYSASP
20   THRLEULEULYSALAASNLEUMETTHRASP
21   ASPLEUPROCYSHISPHETHRSERALAPHE
22   GLYALAGLYPHECYSTHRTHRVALILEALA
23   SERPROVALASPVALVALLYSTHRARGTYR
24   METASNSERALALEUGLYGLNTYRHISSER
25   ALAGLYHISCYSALALEUTHRMETLEUARG
26   LYSGLUGLYPROARGALAPHETYRLYSGLY
27   PHEMETPROSERPHELEUARGLEUGLYSER
28   TRPASNVALVALMETPHEVALTHRTYRGLU
29   GLNLEULYSARGALALEUMETALAALATYR
30   GLNSERARGGLUALAPROPHEHISHISHIS
31   HISHISHIS

Entity 2, UCP2-SL1 303 residues - 32227.426 Da.

All native Cys have been mutated with C25A, C191S, C217S, C227S, C256S mutations. A single Cys (T68C) was introduced for MTSL labeling.

1   METTHRVALLYSPHELEUGLYALAGLYTHR
2   ALAALAALAILEALAASPLEUILETHRPHE
3   PROLEUASPTHRALALYSVALARGLEUGLN
4   ILEGLNGLYGLUSERGLNGLYLEUVALARG
5   THRALAALASERALAGLNTYRARGGLYVAL
6   LEUGLYTHRILELEUCYSMETVALARGTHR
7   GLUGLYPROARGSERLEUTYRASNGLYLEU
8   VALALAGLYLEUGLNARGGLNMETSERPHE
9   ALASERVALARGILEGLYLEUTYRASPSER
10   VALLYSGLNPHETYRTHRLYSGLYSERGLU
11   HISALAGLYILEGLYSERARGLEULEUALA
12   GLYSERTHRTHRGLYALALEUALAVALALA
13   VALALAGLNPROTHRASPVALVALLYSVAL
14   ARGPHEGLNALAGLNALAARGALAGLYGLY
15   GLYARGARGTYRGLNSERTHRVALGLUALA
16   TYRLYSTHRILEALAARGGLUGLUGLYILE
17   ARGGLYLEUTRPLYSGLYTHRSERPROASN
18   VALALAARGASNALAILEVALASNSERALA
19   GLULEUVALTHRTYRASPLEUILELYSASP
20   THRLEULEULYSALAASNLEUMETTHRASP
21   ASPLEUPROSERHISPHETHRSERALAPHE
22   GLYALAGLYPHESERTHRTHRVALILEALA
23   SERPROVALASPVALVALLYSTHRARGTYR
24   METASNSERALALEUGLYGLNTYRHISSER
25   ALAGLYHISSERALALEUTHRMETLEUARG
26   LYSGLUGLYPROARGALAPHETYRLYSGLY
27   PHEMETPROSERPHELEUARGLEUGLYSER
28   TRPASNVALVALMETPHEVALTHRTYRGLU
29   GLNLEULYSARGALALEUMETALAALATYR
30   GLNSERARGGLUALAPROPHEHISHISHIS
31   HISHISHIS

Entity 3, UCP2-SL2 303 residues - 32227.426 Da.

All native Cys have been mutated with C25A, C191S, C217S, C227S, C256S mutations. A single Cys (Q105C) was introduced for MTSL labeling.

1   METTHRVALLYSPHELEUGLYALAGLYTHR
2   ALAALAALAILEALAASPLEUILETHRPHE
3   PROLEUASPTHRALALYSVALARGLEUGLN
4   ILEGLNGLYGLUSERGLNGLYLEUVALARG
5   THRALAALASERALAGLNTYRARGGLYVAL
6   LEUGLYTHRILELEUTHRMETVALARGTHR
7   GLUGLYPROARGSERLEUTYRASNGLYLEU
8   VALALAGLYLEUGLNARGGLNMETSERPHE
9   ALASERVALARGILEGLYLEUTYRASPSER
10   VALLYSCYSPHETYRTHRLYSGLYSERGLU
11   HISALAGLYILEGLYSERARGLEULEUALA
12   GLYSERTHRTHRGLYALALEUALAVALALA
13   VALALAGLNPROTHRASPVALVALLYSVAL
14   ARGPHEGLNALAGLNALAARGALAGLYGLY
15   GLYARGARGTYRGLNSERTHRVALGLUALA
16   TYRLYSTHRILEALAARGGLUGLUGLYILE
17   ARGGLYLEUTRPLYSGLYTHRSERPROASN
18   VALALAARGASNALAILEVALASNSERALA
19   GLULEUVALTHRTYRASPLEUILELYSASP
20   THRLEULEULYSALAASNLEUMETTHRASP
21   ASPLEUPROSERHISPHETHRSERALAPHE
22   GLYALAGLYPHESERTHRTHRVALILEALA
23   SERPROVALASPVALVALLYSTHRARGTYR
24   METASNSERALALEUGLYGLNTYRHISSER
25   ALAGLYHISSERALALEUTHRMETLEUARG
26   LYSGLUGLYPROARGALAPHETYRLYSGLY
27   PHEMETPROSERPHELEUARGLEUGLYSER
28   TRPASNVALVALMETPHEVALTHRTYRGLU
29   GLNLEULYSARGALALEUMETALAALATYR
30   GLNSERARGGLUALAPROPHEHISHISHIS
31   HISHISHIS

Entity 4, UCP2-SL3 303 residues - 32227.426 Da.

All native Cys have been mutated with C25A, C191S, C217S, C227S, C256S mutations. A single Cys (D202C) was introduced for MTSL labeling.

1   METTHRVALLYSPHELEUGLYALAGLYTHR
2   ALAALAALAILEALAASPLEUILETHRPHE
3   PROLEUASPTHRALALYSVALARGLEUGLN
4   ILEGLNGLYGLUSERGLNGLYLEUVALARG
5   THRALAALASERALAGLNTYRARGGLYVAL
6   LEUGLYTHRILELEUTHRMETVALARGTHR
7   GLUGLYPROARGSERLEUTYRASNGLYLEU
8   VALALAGLYLEUGLNARGGLNMETSERPHE
9   ALASERVALARGILEGLYLEUTYRASPSER
10   VALLYSGLNPHETYRTHRLYSGLYSERGLU
11   HISALAGLYILEGLYSERARGLEULEUALA
12   GLYSERTHRTHRGLYALALEUALAVALALA
13   VALALAGLNPROTHRASPVALVALLYSVAL
14   ARGPHEGLNALAGLNALAARGALAGLYGLY
15   GLYARGARGTYRGLNSERTHRVALGLUALA
16   TYRLYSTHRILEALAARGGLUGLUGLYILE
17   ARGGLYLEUTRPLYSGLYTHRSERPROASN
18   VALALAARGASNALAILEVALASNSERALA
19   GLULEUVALTHRTYRASPLEUILELYSCYS
20   THRLEULEULYSALAASNLEUMETTHRASP
21   ASPLEUPROSERHISPHETHRSERALAPHE
22   GLYALAGLYPHESERTHRTHRVALILEALA
23   SERPROVALASPVALVALLYSTHRARGTYR
24   METASNSERALALEUGLYGLNTYRHISSER
25   ALAGLYHISSERALALEUTHRMETLEUARG
26   LYSGLUGLYPROARGALAPHETYRLYSGLY
27   PHEMETPROSERPHELEUARGLEUGLYSER
28   TRPASNVALVALMETPHEVALTHRTYRGLU
29   GLNLEULYSARGALALEUMETALAALATYR
30   GLNSERARGGLUALAPROPHEHISHISHIS
31   HISHISHIS

Entity 5, UCP2-SL4 303 residues - 32227.426 Da.

All native Cys have been mutated with C25A, C191S, C217S, C227S, C256S mutations. A single Cys (H255C) was introduced for MTSL labeling.

1   METTHRVALLYSPHELEUGLYALAGLYTHR
2   ALAALAALAILEALAASPLEUILETHRPHE
3   PROLEUASPTHRALALYSVALARGLEUGLN
4   ILEGLNGLYGLUSERGLNGLYLEUVALARG
5   THRALAALASERALAGLNTYRARGGLYVAL
6   LEUGLYTHRILELEUTHRMETVALARGTHR
7   GLUGLYPROARGSERLEUTYRASNGLYLEU
8   VALALAGLYLEUGLNARGGLNMETSERPHE
9   ALASERVALARGILEGLYLEUTYRASPSER
10   VALLYSGLNPHETYRTHRLYSGLYSERGLU
11   HISALAGLYILEGLYSERARGLEULEUALA
12   GLYSERTHRTHRGLYALALEUALAVALALA
13   VALALAGLNPROTHRASPVALVALLYSVAL
14   ARGPHEGLNALAGLNALAARGALAGLYGLY
15   GLYARGARGTYRGLNSERTHRVALGLUALA
16   TYRLYSTHRILEALAARGGLUGLUGLYILE
17   ARGGLYLEUTRPLYSGLYTHRSERPROASN
18   VALALAARGASNALAILEVALASNSERALA
19   GLULEUVALTHRTYRASPLEUILELYSASP
20   THRLEULEULYSALAASNLEUMETTHRASP
21   ASPLEUPROSERHISPHETHRSERALAPHE
22   GLYALAGLYPHESERTHRTHRVALILEALA
23   SERPROVALASPVALVALLYSTHRARGTYR
24   METASNSERALALEUGLYGLNTYRHISSER
25   ALAGLYCYSSERALALEUTHRMETLEUARG
26   LYSGLUGLYPROARGALAPHETYRLYSGLY
27   PHEMETPROSERPHELEUARGLEUGLYSER
28   TRPASNVALVALMETPHEVALTHRTYRGLU
29   GLNLEULYSARGALALEUMETALAALATYR
30   GLNSERARGGLUALAPROPHEHISHISHIS
31   HISHISHIS

Samples:

sample_1: UCP2, [U-100% 13C; U-100% 15N; U-80% 2H], 0.8 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; H2O 95%; D2O 5%

sample_2: UCP2, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; DNA nanotube 2 ± 0.2 w/v; H2O 95%; D20 5%

sample_3: UCP2-SL1, [U-100% 13C; U-100% 15N; U-80% 2H], 0.8 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; H2O 95%; D2O 5%

sample_4: UCP2-SL2, [U-100% 13C; U-100% 15N; U-80% 2H], 0.8 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; H2O 95%; D2O 5%

sample_5: UCP2-SL3, [U-100% 13C; U-100% 15N; U-80% 2H], 0.8 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; H2O 95%; D2O 5%

sample_6: UCP2-SL4, [U-100% 13C; U-100% 15N; U-80% 2H], 0.8 mM; guanosine diphosphate 5 mM; dodecylphosphocholine 150 mM; cardiolipin 1 mM; dimyristoyl-phosphatidylcholine 2 mM; beta-mercatpoethanol 5 mM; potassium phosphate 30 mM; sodium chloride 80 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 150 mM; pH: 6.5; pressure: 1 atm; temperature: 306 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQCsample_1isotropicsample_conditions_1
3D TROSY-HNCAsample_1isotropicsample_conditions_1
3D TROSY-HN(CO)CAsample_1isotropicsample_conditions_1
3D TROSY-HNCACBsample_1isotropicsample_conditions_1
3D TROSY-HN(CO)CACBsample_1isotropicsample_conditions_1
3D TROSY-HN(CA)COsample_1isotropicsample_conditions_1
3D TROSY-HNCOsample_1isotropicsample_conditions_1
3D (HN,HN)-HMQC-NOESY-TROSYsample_1isotropicsample_conditions_1
3D J(NH)-scaled TROSY-HNCOsample_1isotropicsample_conditions_1
3D J(NH)-scaled TROSY-HNCOsample_2anisotropicsample_conditions_1
3D quantitative J(C'Ca) TROSY-HNCOsample_1isotropicsample_conditions_1
3D quantitative J(C'Ca) TROSY-HNCOsample_2anisotropicsample_conditions_1
3D quantitative J(C'N) TROSY-HNCOsample_1isotropicsample_conditions_1
3D quantitative J(C'N) TROSY-HNCOsample_2anisotropicsample_conditions_1
3D TROSY-HNCOsample_3isotropicsample_conditions_1
3D TROSY-HNCOsample_4isotropicsample_conditions_1
3D TROSY-HNCOsample_5isotropicsample_conditions_1
3D TROSY-HNCOsample_6isotropicsample_conditions_1

Software:

NMRPipe v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

XEASY, Bartels et al. - chemical shift assignment

X-PLOR NIH v2.26, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAA23383 BAA25698 BAA28832 BAA32532 BAC29021 BAA23383 BAA28832 BAA32532 BAC29021 BAC35641 BAA23383 BAA28832 BAA32532 BAC29021 BAC35641 BAA23383 BAA28832 BAA32532 BAC29021 BAC35641 BAA23383 BAA28832 BAA32532 BAC29021 BAC35641
GB AAB17666 AAB53092 AAC98733 AAD17198 AAD17199 AAB17666 AAB53092 AAC98733 AAD17198 AAD17199 AAB17666 AAB53092 AAC98733 AAD17198 AAD17199 AAB17666 AAB53092 AAC98733 AAD17198 AAD17199 AAB17666 AAB53092 AAC98733 AAD17198 AAD17199
REF NP_035801 NP_062227 XP_003511817 XP_005357555 XP_006507642 NP_035801 NP_062227 XP_006507642 XP_006982207 NP_035801 NP_062227 XP_006507642 XP_006982207 NP_035801 NP_062227 XP_006507642 XP_006982207 NP_035801 NP_062227 XP_006507642 XP_006982207
SP P56500 P70406 P56500 P70406 P56500 P70406 P56500 P70406 P56500 P70406
AlphaFold P56500 P70406 P56500 P70406 P56500 P70406 P56500 P70406 P56500 P70406

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