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- PDB-2lnb: Solution NMR structure of N-terminal domain (6-74) of human ZBP1 ... -

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Basic information

Entry
Database: PDB / ID: 2lnb
TitleSolution NMR structure of N-terminal domain (6-74) of human ZBP1 protein, Northeast Structural Genomics Consortium Target HR8174A.
ComponentsZ-DNA-binding protein 1
KeywordsIMMUNE SYSTEM / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-BIOLOGY / Protein Structure Initiative
Function / homology
Function and homology information


ZBP1(DAI) mediated induction of type I IFNs / left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / IRF3 mediated activation of type 1 IFN / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response ...ZBP1(DAI) mediated induction of type I IFNs / left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / IRF3 mediated activation of type 1 IFN / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response / defense response to fungus / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / defense response to virus / Potential therapeutics for SARS / positive regulation of apoptotic process / apoptotic process / DNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Z-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Hamilton, K. / Kohan, E. / Wang, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of N-terminal domain (6-74) of human ZBP1 protein, Northeast Structural Genomics Consortium Target HR8174A
Authors: Yang, Y. / Ramelot, T.A. / Hamilton, K. / Kohan, E. / Wang, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Z-DNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)9,0411
Polymers9,0411
Non-polymers00
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Z-DNA-binding protein 1 / Tumor stroma and activated macrophage protein DLM-1


Mass: 9041.406 Da / Num. of mol.: 1 / Fragment: DRADA 1 repeat region, residues 6-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf183, DLM1, ZBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9H171

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1712D 1H-15N HSQC NH2 only
1822D 1H-13C HSQC aliphatic
1912D 1H-13C HSQC aromatic
11013D 1H-15N NOESY
11113D 1H-13C NUS-NOESY aliphatic
11213D HNCA
11313D HN(CO)CA
11413D C(CO)NH
11513D HBHA(CO)NH
11613D (H)CCH-COSY
11713D (H)CCH-TOCSY
11813D CCH-TOCSY
11914D CC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] N-terminal domain (6-74) of human ZBP1 protein, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.00 mM [U-5% 13C; U-100% 15N] N-terminal domain (6-74) of human ZBP1 protein, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMN-terminal domain (6-74) of human ZBP1 protein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
10 mMDTT-41
0.02 %sodium azide-51
5 mMcalcium chloride-61
1.00 mMN-terminal domain (6-74) of human ZBP1 protein-7[U-5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
10 mMDTT-102
0.02 %sodium azide-112
5 mMcalcium chloride-122
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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