BMRB Entry 25914

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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/BMR25914
MolProbity Validation Chart

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Title:
Solution structure of RNF126 N-terminal zinc finger domain in complex with BAG6 Ubiquitin-like domain
Deposition date:
2015-12-01
Original release date:
2016-05-23
Authors:
Martinez-Lumbreras, Santiago; Krysztofinska, Ewelina; Thapaliya, Arjun; Isaacson, Rivka
Citation:

Citation: Krysztofinska, Ewelina; Martinez-Lumbreras, Santiago; Thapaliya, Arjun; Evans, Nicola; High, Stephen; Isaacson, Rivka. "Structural and functional insights into the E3 ligase, RNF126"  Sci. Rep. 6, 26433-26433 (2016).
PubMed: 27193484

Assembly members:

Assembly members:
entity_1, polymer, 42 residues, 4705.417 Da.
entity_2, polymer, 100 residues, 11276.897 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSMAEASPHPGRYFCHCCSV EIVPRLPDYICPRCESGFIE EL
entity_2: MAHHHHHHVDDDDKMLEVLV KTLDSQTRTFIVGAQMNVKE FKEHIAASVSIPSEKQRLIY QGRVLQDDKKLQEYNVGGKV IHLVERAPPQTHLPSGASSG

Data sets:
Data typeCount
13C chemical shifts548
15N chemical shifts136
1H chemical shifts862

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3ZINC ION3

Entities:

Entity 1, entity_1 42 residues - 4705.417 Da.

'GS' correspond to TEV cleavage tag

1   GLYSERMETALAGLUALASERPROHISPRO
2   GLYARGTYRPHECYSHISCYSCYSSERVAL
3   GLUILEVALPROARGLEUPROASPTYRILE
4   CYSPROARGCYSGLUSERGLYPHEILEGLU
5   GLULEU

Entity 2, entity_2 100 residues - 11276.897 Da.

'MAHHHHHHDDDDKM' correspond to His-tag

1   METALAHISHISHISHISHISHISVALASP
2   ASPASPASPLYSMETLEUGLUVALLEUVAL
3   LYSTHRLEUASPSERGLNTHRARGTHRPHE
4   ILEVALGLYALAGLNMETASNVALLYSGLU
5   PHELYSGLUHISILEALAALASERVALSER
6   ILEPROSERGLULYSGLNARGLEUILETYR
7   GLNGLYARGVALLEUGLNASPASPLYSLYS
8   LEUGLNGLUTYRASNVALGLYGLYLYSVAL
9   ILEHISLEUVALGLUARGALAPROPROGLN
10   THRHISLEUPROSERGLYALASERSERGLY

Entity 3, ZINC ION - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 600 uM; entity_2 800 uM; potassium phosphate 10 mM; sodium chloride 100 mM; TCEP 250 uM; DSS 10 uM; H2O 90%; D2O 10%

sample_2: entity_1, [U-99% 13C; U-99% 15N], 600 uM; entity_2 800 uM; potassium phosphate 10 mM; sodium chloride 100 mM; TCEP 250 uM; DSS 10 uM; D2O 100%

sample_3: entity_1 600 uM; entity_2, [U-99% 13C; U-99% 15N], 400 uM; potassium phosphate 10 mM; sodium chloride 100 mM; TCEP 250 uM; DSS 10 uM; H2O 90%; D2O 10%

sample_4: entity_1 600 uM; entity_2, [U-99% 13C; U-99% 15N], 400 uM; potassium phosphate 10 mM; sodium chloride 100 mM; TCEP 250 uM; DSS 10 uM; D2O 100%

sample_conditions_1: ionic strength: 0.12 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 12C14N filtered 13C edited NOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
3D 12C14N filtered 13C edited NOESYsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1

Software:

TOPSPIN v3.2, Bruker Biospin - collection, processing

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

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

ARIA v2.1, Linge, O'Donoghue and Nilges - refinement, structure solution

CcpNMR_Analysis v2.3, CCPN - chemical shift assignment, peak picking, structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 500 MHz

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