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- PDB-1iai: IDIOTYPE-ANTI-IDIOTYPE FAB COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1iai
TitleIDIOTYPE-ANTI-IDIOTYPE FAB COMPLEX
Components
  • (ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)) x 2
  • (IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY) x 2
KeywordsCOMPLEX (IMMUNOGLOBULIN IGG1/IGG2A) / COMPLEX (IMMUNOGLOBULIN IGG1-IGG2A) / COMPLEX (IMMUNOGLOBULIN IGG1-IGG2A) complex
Function / homology
Function and homology information


alpha-beta T cell receptor complex / IgG immunoglobulin complex / B cell differentiation / adaptive immune response / 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 kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsBan, N. / Escobar, C. / Garcia, R. / Hasel, K. / Day, J. / Greenwood, A. / McPherson, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of an idiotype-anti-idiotype Fab complex.
Authors: Ban, N. / Escobar, C. / Garcia, R. / Hasel, K. / Day, J. / Greenwood, A. / McPherson, A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Study of a Complex between an Fab of a Monoclonal Feline Peritonitis Virus Neutralizing Antibody and its Anti-Idiotype Fab
Authors: Ban, N. / Escobar, C. / Day, J. / Greenwood, A. / McPherson, A.
History
DepositionDec 28, 1993Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
H: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
M: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)
I: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)


Theoretical massNumber of molelcules
Total (without water)94,8874
Polymers94,8874
Non-polymers00
Water00
1
L: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
H: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
M: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)
I: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)

L: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
H: IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY
M: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)
I: ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)


Theoretical massNumber of molelcules
Total (without water)189,7758
Polymers189,7758
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)187.582, 80.600, 75.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Atom site foot note1: CIS PROLINE - PRO L 141 / 2: CIS PROLINE - PRO H 155 / 3: CIS PROLINE - PRO M 8 / 4: CIS PROLINE - PRO M 96 / 5: CIS PROLINE - PRO M 142

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Components

#1: Antibody IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY


Mass: 23834.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 10121892
#2: Antibody IDIOTYPIC FAB 730.1.4 (IGG1) OF VIRUS NEUTRALIZING ANTIBODY


Mass: 23679.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)


Mass: 23560.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1042224, UniProt: P01837*PLUS
#4: Antibody ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A)


Mass: 23812.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1042226
Has protein modificationY
Sequence detailsFAB 730.1.4: LIGHT CHAIN VARIABLE REGION. SEQUENTIAL RESIDUE NUMBERS KABAT RESIDUE NUMBERS 1 - 107 ...FAB 730.1.4: LIGHT CHAIN VARIABLE REGION. SEQUENTIAL RESIDUE NUMBERS KABAT RESIDUE NUMBERS 1 - 107 1 - 107 HEAVY CHAIN VARIABLE REGION. SEQUENTIAL RESIDUE NUMBERS KABAT RESIDUE NUMBERS 1 - 52 1 - 52 53 52A 54 - 83 53 - 82 84 - 86 82A- 82C 87 - 104 83 - 100 105 - 108 100H- 100K 109 - 121 101 - 113 FAB 409.5.3: LIGHT CHAIN VARIABLE REGION SEQUENTIAL RESIDUE NUMBERS KABAT RESIDUE NUMBERS 1 - 27 1 - 27 28 27A 29 - 108 28 - 107 HEAVY CHAIN VARIABLE REGION SEQUENTIAL RESIDUE NUMBERS KABAT RESIDUE NUMBERS 1 - 52 1 - 52 53 - 55 52A- 52C 56 - 85 53 - 82 86 - 88 82A- 82C 89 - 106 83 - 100 107 - 108 100A- 100B 109 - 121 101 - 113

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
245 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 23640 / % possible obs: 92 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 89898 / Rmerge(I) obs: 0.112 / Biso Wilson estimate: 13 Å2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→40 Å / σ(I): 3
RfactorNum. reflection% reflection
Rwork0.21 --
obs0.21 21310 83 %
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 0 0 6672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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