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- PDB-5it2: Structure of a transglutaminase 2-specific autoantibody 693-10-B0... -

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Basic information

Entry
Database: PDB / ID: 5it2
TitleStructure of a transglutaminase 2-specific autoantibody 693-10-B06 Fab fragment
Components
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / Transglutaminase 2 / autoantibody / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, X. / Dalhus, B. / Hnida, K. / Iversen, R. / Sollid, L.M.
CitationJournal: Nat. Med. / Year: 2012
Title: High abundance of plasma cells secreting transglutaminase 2-specific IgA autoantibodies with limited somatic hypermutation in celiac disease intestinal lesions
Authors: Di Niro, R. / Mesin, L. / Zheng, N.Y. / Stamnaes, J. / Morrissey, M. / Lee, J.H. / Huang, M. / Iversen, R. / du Pre, M.F. / Qiao, S.W. / Lundin, K.E. / Wilson, P.C. / Sollid, L.M.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)47,8902
Polymers47,8902
Non-polymers00
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-24 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.592, 63.383, 104.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody heavy chain


Mass: 24363.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 23526.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris, pH=8.5, 20%v/v Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→54.24 Å / Num. obs: 54158 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 25.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZD3

4zd3


Resolution: 1.7→43.867 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 --2740
Rwork0.1852 ---
obs0.1861 54088 97.65 %-
Refinement stepCycle: LAST / Resolution: 1.7→43.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 0 637 3941
LS refinement shellResolution: 1.7→1.7293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3083 128 -
Rwork0.2716 2574 -
obs--99 %

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