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- PDB-2l00: Solution structure of the non-covalent complex of the ZNF216 A20 ... -

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Basic information

Entry
Database: PDB / ID: 2l00
TitleSolution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin
Components
  • Ubiquitin
  • Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)
KeywordsMETAL BINDING PROTEIN/PEPTIDE BINDING PROTEIN / A20 domain / ZNF216 / ubiquitin / zinc finger / ubiquitin binding / METAL BINDING PROTEIN-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) ...: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Pexophagy / Regulation of pyruvate metabolism / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / smooth muscle tissue development / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / fibroblast migration / Translesion Synthesis by POLH / respiratory system process / Termination of translesion DNA synthesis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Negative regulators of DDX58/IFIH1 signaling / vasculature development / skeletal system morphogenesis / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / face development / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / platelet-derived growth factor receptor signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / modification-dependent protein catabolic process / protein tag activity / peroxisome / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / in utero embryonic development / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers ...: / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
AN1-type zinc finger protein 5 / Polyubiquitin / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Rigid Body Docking, molecular dynamics
Model detailslowest energy, model 1
AuthorsGarner, T.P. / Long, J.E. / Searle, M.S. / Layfield, R.
CitationJournal: To be Published
Title: Co-localisation of ubiquitin receptors ZNF216 and p62 in a ubiquitin-mediated ternary complex
Authors: Garner, T.P. / Strachan, J. / Long, J.E. / Layfield, R. / Searle, M.S.
History
DepositionJun 29, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1723
Polymers15,1072
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a) / ZNF216-A20


Mass: 6538.265 Da / Num. of mol.: 1 / Fragment: A20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: rCG_48158, Zfand5, Zfp216_predicted / Production host: Escherichia coli (E. coli) / Strain (production host): c41 (DE3) / References: UniProt: B5DF11
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1 / Fragment: ubiquitin core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUBI-2, UBI1 / Production host: Escherichia coli (E. coli) / Strain (production host): c41 (DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR derived solution structure of the A20 zinc finger of ZNF216 with ubiquitin derived from NOE, PRE and RDC measurements
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1172D 1H-15N HSQC
1222D 1H-15N HSQC
1313D 1H-15N NOESY
1473D 1H-15N NOESY
1533D CBCA(CO)NH
1633D HNCO
1742D 1H-15N HSQC IPAP
1852D 1H-15N HSQC IPAP
19315N, 13C Half filtered NOESY
110615N, 13C Half filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 1 mM [U-100% 15N] ubiquitin-6, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 15N] ZNF216-A20-7, 50 uM Zinc-8, 4 mM MTSL-9, 5 mM TRIS-10, 50 mM sodium chloride-11, 4 mM ubiquitin-12, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-13, 50 uM Zinc-14, 0.1 mM DSS-15, 5 mM TRIS-16, 50 mM sodium chloride-17, 2 mM ubiquitin-18, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM [U-100% 15N] ZNF216-A20-19, 50 uM Zinc-20, 0.1 mM DSS-21, 5 mM TRIS-22, 50 mM sodium chloride-23, 5 % Polyacrylamide gel-24, 4 mM ubiquitin-25, 90% H2O/10% D2O90% H2O/10% D2O
54 mM ZNF216-A20-26, 50 uM Zinc-27, 0.1 mM DSS-28, 5 mM TRIS-29, 50 mM sodium chloride-30, 5 % Polyacrylamide gel-31, 1 mM [U-100% 15N] ubiquitin-32, 90% H2O/10% D2O90% H2O/10% D2O
62 mM ZNF216-A20-33, 50 uM Zinc-34, 0.1 mM DSS-35, 5 mM TRIS-36, 50 mM sodium chloride-37, 1 mM [U-100% 13C; U-100% 15N] ubiquitin-38, 90% H2O/10% D2O90% H2O/10% D2O
71 mM [U-100% 15N] ZNF216-A20-39, 50 uM Zinc-40, 0.1 mM DSS-41, 5 mM TRIS-42, 50 mM sodium chloride-43, 4 mM ubiquitin-44, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMZNF216-A20-11
50 uMZinc-21
0.1 mMDSS-31
5 mMTRIS-41
50 mMsodium chloride-51
1 mMubiquitin-6[U-100% 15N]1
1.0 mMZNF216-A20-7[U-100% 15N]2
50 uMZinc-82
4 mMMTSL-92
5 mMTRIS-102
50 mMsodium chloride-112
4 mMubiquitin-122
0.8 mMZNF216-A20-13[U-100% 13C; U-100% 15N]3
50 uMZinc-143
0.1 mMDSS-153
5 mMTRIS-163
50 mMsodium chloride-173
2 mMubiquitin-183
1.0 mMZNF216-A20-19[U-100% 15N]4
50 uMZinc-204
0.1 mMDSS-214
5 mMTRIS-224
50 mMsodium chloride-234
5 %Polyacrylamide gel-244
4 mMubiquitin-254
4 mMZNF216-A20-265
50 uMZinc-275
0.1 mMDSS-285
5 mMTRIS-295
50 mMsodium chloride-305
5 %Polyacrylamide gel-315
1 mMubiquitin-32[U-100% 15N]5
2 mMZNF216-A20-336
50 uMZinc-346
0.1 mMDSS-356
5 mMTRIS-366
50 mMsodium chloride-376
1 mMubiquitin-38[U-100% 13C; U-100% 15N]6
1 mMZNF216-A20-39[U-100% 15N]7
50 uMZinc-407
0.1 mMDSS-417
5 mMTRIS-427
50 mMsodium chloride-437
4 mMubiquitin-447
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CcpNMR1.1.15CCPNchemical shift assignment
CcpNMR1.1.15CCPNchemical shift calculation
CcpNMR1.1.15CCPNpeak picking
CcpNMR1.1.15CCPNdata analysis
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
HADDOCK2Cyril Dominguez, Rolf Boelens, Alexandre M.J.J. Bonvinstructure solution
RefinementMethod: Rigid Body Docking, molecular dynamics / Software ordinal: 1
Details: Rigid Body docking using HADDOCK (Standard protocol), Fully flexible docking in HADDOCK by standard protocol with reduced electrostatics
NMR constraintsNOE constraints total: 38 / NOE intraresidue total count: 0 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 0 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 0 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 10 / Representative conformer: 1

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