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- PDB-4q9b: IgNAR antibody domain C2 -

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Basic information

Entry
Database: PDB / ID: 4q9b
TitleIgNAR antibody domain C2
ComponentsNovel antigen receptor
KeywordsIMMUNE SYSTEM / protein evolution / antibody structure / protein folding
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
Similarity search - Function
Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFeige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. ...Feige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
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
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Novel antigen receptor
B: Novel antigen receptor


Theoretical massNumber of molelcules
Total (without water)22,7222
Polymers22,7222
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.840, 48.450, 47.190
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Novel antigen receptor / IgNAR antibody


Mass: 11360.874 Da / Num. of mol.: 2 / Fragment: C2 domain (UNP residues 243-344)
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 Star (DE3) / References: UniProt: Q90544
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 30% PEG10000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2009
RadiationMonochromator: LN2 cooled fixed-exit double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 28514 / Num. obs: 27506 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.5
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q97

4q97


Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.952 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.105 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21657 1376 5 %RANDOM
Rwork0.17981 ---
all0.184 27506 --
obs0.18169 26130 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.095 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.48 Å2
2--1.94 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 140 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021508
X-RAY DIFFRACTIONr_bond_other_d0.0010.021471
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9522042
X-RAY DIFFRACTIONr_angle_other_deg0.67833391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4465189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84724.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5461510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
X-RAY DIFFRACTIONr_mcbond_it2.3112.225768
X-RAY DIFFRACTIONr_mcbond_other2.3062.223767
X-RAY DIFFRACTIONr_mcangle_it2.7413.326953
X-RAY DIFFRACTIONr_mcangle_other2.743.327954
X-RAY DIFFRACTIONr_scbond_it2.7552.588740
X-RAY DIFFRACTIONr_scbond_other2.7542.588741
X-RAY DIFFRACTIONr_scangle_other2.9733.7111090
X-RAY DIFFRACTIONr_long_range_B_refined3.61318.5751666
X-RAY DIFFRACTIONr_long_range_B_other3.51518.2461624
X-RAY DIFFRACTIONr_rigid_bond_restr3.38832979
X-RAY DIFFRACTIONr_sphericity_free22.013541
X-RAY DIFFRACTIONr_sphericity_bonded7.5153060
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 98 -
Rwork0.23 1849 -
obs--94.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96970.2309-0.9830.0274-0.10342.2654-0.0313-0.11390.0746-0.0048-0.00230.01120.08120.13880.03360.01540.00330.01010.0107-0.00260.0357-7.94165.65815.1636
20.5035-0.2404-0.23080.11750.15051.783-0.0425-0.0043-0.03820.01920.00320.025-0.02130.23210.03930.0213-0.02110.0060.0466-0.00110.0259-2.50763.9786-15.773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 343
2X-RAY DIFFRACTION2B246 - 343

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