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- PDB-1etz: THE THREE-DIMENSIONAL STRUCTURE OF AN ANTI-SWEETENER FAB, NC10.14... -

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Basic information

Entry
Database: PDB / ID: 1etz
TitleTHE THREE-DIMENSIONAL STRUCTURE OF AN ANTI-SWEETENER FAB, NC10.14, SHOWS THE EXTENT OF STRUCTURAL DIVERSITY IN ANTIGEN RECOGNITION BY IMMUNOGLOBULINS
Components
  • FAB NC10.14 - HEAVY CHAIN
  • FAB NC10.14 - LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Anti-sweetener Fab / Antigen-antibody / Complex / Receptor Mimicry / Antigen Recognition
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / positive regulation of immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-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 V-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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GAS / Anti-human Langerin 2G3 lambda chain / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsGuddat, L.W. / Shan, L. / Broomell, C. / Ramsland, P.A. / Fan, Z. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The three-dimensional structure of a complex of a murine Fab (NC10. 14) with a potent sweetener (NC174): an illustration of structural diversity in antigen recognition by immunoglobulins.
Authors: Guddat, L.W. / Shan, L. / Broomell, C. / Ramsland, P.A. / Fan, Z. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Local and Transmitted Conformational Changes on Complexation of an Anti-sweetener Fab
Authors: Guddat, L.W. / Shan, L. / Anchin, J.M. / Linthicum, D.S. / Edmundson, A.B.
History
DepositionApr 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FAB NC10.14 - LIGHT CHAIN
H: FAB NC10.14 - HEAVY CHAIN
A: FAB NC10.14 - LIGHT CHAIN
B: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0376
Polymers95,2684
Non-polymers7692
Water1,38777
1
L: FAB NC10.14 - LIGHT CHAIN
H: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0183
Polymers47,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-33 kcal/mol
Surface area19520 Å2
MethodPISA
2
A: FAB NC10.14 - LIGHT CHAIN
B: FAB NC10.14 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0183
Polymers47,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-27 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.9, 66.3, 75.2
Angle α, β, γ (deg.)106.7, 107.6, 97.3
Int Tables number1
Space group name H-MP1
DetailsA Fab is formed by Light Chain and Heavy Chain. There are two Fab with non-crystallographic symmetry in a unit cell.

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Components

#1: Antibody FAB NC10.14 - LIGHT CHAIN


Mass: 23165.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ASCITES / References: UniProt: G0YP42*PLUS
#2: Antibody FAB NC10.14 - HEAVY CHAIN


Mass: 24468.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ASCITES / References: UniProt: P01867*PLUS
#3: Chemical ChemComp-GAS / N-(P-CYANOPHENYL)-N'-DIPHENYLMETHYL-GUANIDINE-ACETIC ACID


Mass: 384.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NC10.14 Fab with excess molarity NC174, 10%(w/v) PEG 8000, 0.05M NaCl, 0.05%(w/v) Sodium Azide, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal
*PLUS
Density % sol: 50.2 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein11
20.05 M11NaCl
30.05 %sodium azide11
433 %(w/w)PEG800011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 9, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. all: 26144 / Num. obs: 26144 / % possible obs: 90.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.125 / Num. unique all: 2420 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 101821
Reflection shell
*PLUS
% possible obs: 66.8 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
MERLOTphasing
X-PLOR3.851refinement
RefinementResolution: 2.6→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2638 -Random
Rwork0.198 ---
all0.211 26144 --
obs0.211 26144 10 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 58 77 6833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg28
X-RAY DIFFRACTIONx_torsion_impr_deg1.3
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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