BMRB Entry 17024

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17024
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin
Deposition date:
2010-06-29
Original release date:
2012-08-02
Authors:
Garner, Thomas; Long, Jed; Searle, Mark; Layfield, Robert
Citation:

Citation: Garner, Thomas; Strachan, Joanna; Long, Jed; Layfield, Robert; Searle, Mark. "Co-localisation of ubiquitin receptors ZNF216 and p62 in a ubiquitin-mediated ternary complex"  Nat. Struct. Biol. ., .-..

Assembly members:

Assembly members:
ZNF216-A20, polymer, 62 residues, 3868.3 Da.
ubiquitin, polymer, 76 residues, 8017.1 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Norway rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PGEX-4T1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ZNF216-A20: GSMAQETNQTPGPMLCSTGC GFYGNPRTNGMCSVCYKEHL QRQQNSGRMSPMGTASGSNS PT
ubiquitin: MQIFVKTLTGKTITLEVESS DTIDNVKSKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts178
15N chemical shifts65
1H chemical shifts210

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Znf_A201
2Zinc3
3Ubiquitin2

Entities:

Entity 1, Znf_A20 62 residues - 3868.3 Da.

Only residue numbers 12 to 47 were included during the final docking protocol, the flexible termini were removed as per the recommendations for the docking program HADDOCK. Quoted Mwt is for the presented fragment not the full sequence

1   GLYSERMETALAGLNGLUTHRASNGLNTHR
2   PROGLYPROMETLEUCYSSERTHRGLYCYS
3   GLYPHETYRGLYASNPROARGTHRASNGLY
4   METCYSSERVALCYSTYRLYSGLUHISLEU
5   GLNARGGLNGLNASNSERGLYARGMETSER
6   PROMETGLYTHRALASERGLYSERASNSER
7   PROTHR

Entity 3, Zinc - Zn - 65.409 Da.

1   ZN

Entity 2, Ubiquitin 76 residues - 8017.1 Da.

native yeast ubiquitin with the flexible C terminus removed (5 residues) Mwt is given for the fragment used for docking

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUSERSER
3   ASPTHRILEASPASNVALLYSSERLYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Samples:

sample_1: ZNF216-A20 4 ± 0.1 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; ubiquitin, [U-100% 15N], 1 ± 0.1 mM; H2O 90%; D2O 10%

sample_2: ZNF216-A20, [U-100% 15N], 1.0 ± 0.1 mM; ZnCl2 50 ± 0.2 uM; MTSL 4 ± 0.1 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; ubiquitin 4 ± 0.1 mM; H2O 90%; D2O 10%

sample_3: ZNF216-A20, [U-100% 13C; U-100% 15N], 0.8 ± 0.2 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; ubiquitin 2 ± 0.1 mM; H2O 90%; D2O 10%

sample_4: ZNF216-A20, [U-100% 15N], 1.0 ± 0.1 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; Polyacrylamide gel 5 ± 0.5 %; ubiquitin 4 ± 0.1 mM; H2O 90%; D2O 10%

sample_5: ZNF216-A20 4 ± 0.1 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; Polyacrylamide gel 5 ± 0.5 %; ubiquitin, [U-100% 15N], 1 ± 0.1 mM; H2O 90%; D2O 10%

sample_6: ZNF216-A20 2 ± 0.2 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; ubiquitin, [U-100% 13C; U-100% 15N], 1 ± 0.1 mM; H2O 90%; D2O 10%

sample_2a: ZNF216-A20, [U-100% 15N], 1 ± 0.1 mM; ZnCl2 50 ± 0.2 uM; DSS 0.1 ± 0.01 mM; TRIS 5 ± 0.5 mM; sodium chloride 50 ± 5 mM; ubiquitin 4 ± 0.1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2aisotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2aisotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_4anisotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_5anisotropicsample_conditions_1
15N, 13C Half filtered NOESYsample_3isotropicsample_conditions_1
15N, 13C Half filtered NOESYsample_6isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CcpNMR v1.1.15, CCPN - chemical shift assignment, chemical shift calculation, data analysis, peak picking

X-PLOR NIH v2.14, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

HADDOCK v2.0, Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

UNP B5DF11-1
BMRB 17023 15592 4769 4983
PDB
DBJ BAC36321 BAF83538 BAG73932 BAA02154 BAA03764 BAA05085 BAA05670 BAA76889
GB AAC42600 AAC42601 AAC42602 AAC61801 AAH11018 AAA03351 AAA19247 AAA32904 AAA32905 AAA32906
REF NP_001090975 NP_001094515 NP_001095890 NP_001095891 NP_001157077 NP_001031585 NP_001031824 NP_001042915 NP_001045980 NP_001049479
SP B5DF11 O76080 O88878 B9DHA6 P05759 P0C016 P0C224 P0C8R3
TPG DAA26877 DAA08405 DAA09244 DAA09283 DAA09489 DAA39608
EMBL CAA07773 CAA10056 CAA11267 CAA11268 CAA21278
PIR G85036 JS0657 S28426 S42643 S49332
PRF 1101405A 1207189A 1515347A 1603402A 1604470A
TPD FAA00316 FAA00317 FAA00318 FAA00319
TPE CBF76581 CBF85986
AlphaFold B5DF11 B5DF11 O76080 O88878 B9DHA6 P05759 P0C016 P0C224 P0C8R3

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