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- PDB-2m9a: Solution NMR Structure of E3 ubiquitin-protein ligase ZFP91 from ... -

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Basic information

Entry
Database: PDB / ID: 2m9a
TitleSolution NMR Structure of E3 ubiquitin-protein ligase ZFP91 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7784A
ComponentsE3 ubiquitin-protein ligase ZFP91
KeywordsMETAL BINDING PROTEIN / PSI:Biology / C2H2 / Hr7784A / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


activation of NF-kappaB-inducing kinase activity / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ZFP91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsPederson, K. / Shastry, R. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of Hr7784A
Authors: Pederson, K. / Montelione, G.T. / Prestegard, J.H.
History
DepositionJun 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ZFP91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6964
Polymers11,5001
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein E3 ubiquitin-protein ligase ZFP91 / Zinc finger protein 757 / Zinc finger protein 91 homolog / Zfp-91


Mass: 11500.263 Da / Num. of mol.: 1 / Fragment: UNP residues 370-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKSG11, ZFP91, ZNF757 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The NESG target Hr7784A contains three C2H2 zinc finger motifs between residues 370 and 456 of the Homo sapiens E3 ubiquitin-protein ligase ZFP91. Correlation time measurements using cross- ...Details: The NESG target Hr7784A contains three C2H2 zinc finger motifs between residues 370 and 456 of the Homo sapiens E3 ubiquitin-protein ligase ZFP91. Correlation time measurements using cross-correlation based NMR spin relaxation experiments suggest that the three zinc finger motifs are connected by flexible loops and not restricted with respect to one another. Residual dipolar couplings also indicate that the three domains are oriented independently. Therefore the positions of domains with respect to one another in the structures reported are not significant.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aromatic
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11112D CB(CGCD)HD
11212D CB(CGCDCE)HE
11322D 1H-15N J-modulation HSQC
11432D 1H-15N J-modulation HSQC
11512D 1H-15N J-modulation HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.17 mM [U-100% 13C; U-100% 15N] HR7784A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.66 mM [U-100% 15N] HR7784A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 4.2 % C12E5, 0.02 % sodium azide, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.66 mM [U-100% 13C; U-100% 15N] HR7784A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 5 % positively charged polyacrylamide gel, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.17 mMHR7784A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
50 uMDSS-71
0.66 mMHR7784A-8[U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
4.2 %C12E5-132
0.02 %sodium azide-142
50 uMDSS-152
0.66 mMHR7784A-16[U-100% 13C; U-100% 15N]3
20 mMMES-173
100 mMsodium chloride-183
5 mMcalcium chloride-193
10 mMDTT-203
0.02 %sodium azide-213
50 uMDSS-223
5 %positively charged polyacrylamide gel-233
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.4Bhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 579 / NOE intraresidue total count: 140 / NOE long range total count: 85 / NOE medium range total count: 131 / NOE sequential total count: 223 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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