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- PDB-1vge: TR1.9 FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1vge
TitleTR1.9 FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY
Components(TR1.9 FAB) x 2
KeywordsIMMUNOGLOBULIN / TR1.9 / ANTI-THYROID PEROXIDASE / AUTOANTIBODY
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsChacko, S. / Padlan, E.A.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: Structural studies of human autoantibodies. Crystal structure of a thyroid peroxidase autoantibody Fab.
Authors: Chacko, S. / Padlan, E.A. / Portolano, S. / McLachlan, S.M. / Rapoport, B.
History
DepositionJan 4, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: TR1.9 FAB
H: TR1.9 FAB


Theoretical massNumber of molelcules
Total (without water)47,1842
Polymers47,1842
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.926, 62.776, 84.790
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody TR1.9 FAB


Mass: 23216.770 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: XL1-BLUE / Gene: CDNA DERIVED FROM / Plasmid: PBP101
Gene (production host): CDNA DERIVED FROM THYROID-INFILTRATING B CELLS
Production host: XL1-BLUE CELLS / Strain (production host): XL1-BLUE / References: EMBL: X95747
#2: Antibody TR1.9 FAB


Mass: 23966.906 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: XL1-BLUE / Gene: CDNA DERIVED FROM / Plasmid: PBP101
Gene (production host): CDNA DERIVED FROM THYROID-INFILTRATING B CELLS
Production host: XL1-BLUE CELLS / Strain (production host): XL1-BLUE / References: UniProt: P01857
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FRAGMENT HAS TWO POLYPEPTIDE CHAINS: THE LIGHT CHAIN (THE RESIDUES NUMBERED 1 THROUGH 214) AND ...THE FRAGMENT HAS TWO POLYPEPTIDE CHAINS: THE LIGHT CHAIN (THE RESIDUES NUMBERED 1 THROUGH 214) AND THE HEAVY CHAIN (THE RESIDUES NUMBERED 1 THROUGH 225). THE ELECTRON DENSITY IS WEAK FOR RESIDUES 212 THROUGH 214 IN THE LIGHT CHAIN AND FOR RESIDUES 1 AND 2, 136 THROUGH 143, AND 223 THROUGH 225 IN THE HEAVY CHAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1drop
30.02 %sodium azide1drop
58 %(w/v)PEG80001reservoir
60.1 MTris-HCl1reservoir
4reservoir solution1drop0.002 ml

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 11, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 28718 / % possible obs: 92.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.084
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Redundancy: 3.5 % / Num. unique obs: 3364 / Num. measured obs: 9884 / Rmerge(I) obs: 0.807

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Processing

Software
NameClassification
XDSdata scaling
X-PLORrefinement
XDSdata reduction
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.18 -
obs0.18 20274
Displacement parametersBiso mean: 31.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 216 3534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d1.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19
X-RAY DIFFRACTION2
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.37

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