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- PDB-2mkl: Solution structure of the fourth constant immunoglobulin domain o... -

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Basic information

Entry
Database: PDB / ID: 2mkl
TitleSolution structure of the fourth constant immunoglobulin domain of nurse shark IgNAR
ComponentsNovel antigen receptor
KeywordsIMMUNE SYSTEM / Ig domain / IgNAR
Function / homology
Function and homology information


Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Novel antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodSOLUTION NMR / simulated annealing
AuthorsHennig, J. / Sattler, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins.
Authors: Feige, M.J. / Grawert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslander, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionFeb 10, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: 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_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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Novel antigen receptor


Theoretical massNumber of molelcules
Total (without water)11,8321
Polymers11,8321
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)10 / 20structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein Novel antigen receptor


Mass: 11832.433 Da / Num. of mol.: 1
Fragment: the fourth constant immunoglobulin domain (UNP residues 454-556)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q90544

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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
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11322D 1H-13C HSQC aliphatic
11432D 1H-15N HSQC
11533D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
1300-500 uM [U-100% 13C; U-100% 15N] protein, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 2 mM potassium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
2300-500 uM [U-10% 13C] protein, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 2 mM potassium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
3300-500 uM [U-100% 13C; U-100% 15N] protein, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 2 mM potassium phosphate, 0.02 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMentity-1[U-100% 13C; U-100% 15N]300-5001
137 mMsodium chloride-21
2.7 mMpotassium chloride-31
10 mMsodium phosphate-41
2 mMpotassium phosphate-51
0.02 %sodium azide-61
uMentity-7[U-10% 13C]300-5002
137 mMsodium chloride-82
2.7 mMpotassium chloride-92
10 mMsodium phosphate-102
2 mMpotassium phosphate-112
0.02 %sodium azide-122
uMentity-13[U-100% 13C; U-100% 15N]300-5003
137 mMsodium chloride-143
2.7 mMpotassium chloride-153
10 mMsodium phosphate-163
2 mMpotassium phosphate-173
0.02 %sodium azide-183
10 mg/mLPf1 phage-193
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
ARIALinge, O'Donoghue and Nilgeswater refinement
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1265 / NOE intraresidue total count: 756 / NOE long range total count: 429 / NOE medium range total count: 80
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.007 Å / Distance rms dev error: 0.002 Å

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