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- PDB-1ggc: MAJOR ANTIGEN-INDUCED DOMAIN REARRANGEMENTS IN AN ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1ggc
TitleMAJOR ANTIGEN-INDUCED DOMAIN REARRANGEMENTS IN AN ANTIBODY
Components
  • IGG2A-KAPPA 50.1 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 50.1 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / 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 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTakimoto-Kamimura, M. / Wilson, I.A.
Citation
Journal: Structure / Year: 1993
Title: Major antigen-induced domain rearrangements in an antibody.
Authors: Stanfield, R.L. / Takimoto-Kamimura, M. / Rini, J.M. / Profy, A.T. / Wilson, I.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of a Human Immunodeficiency Virus Type 1 Neutralizing Antibody, 50.1, In Complex with its V3 Loop Peptide Antigen
Authors: Rini, J.M. / Stanfield, R.L. / Stura, E.A. / Salinas, P.A. / Profy, A.T. / Wilson, I.A.
#2: Journal: Proteins / Year: 1992
Title: Crystallization, Sequence, and Preliminary Crystallographic Data for an Antipeptide Fab 50.1 And Peptide Complexes with the Principal Neutralizing Determinant of HIV-1 Gp120
Authors: Stura, E.A. / Stanfield, R.L. / Fieser, G.G. / Silver, S. / Roguska, M. / Hincapie, L.M. / Simmerman, H.K.B. / Profy, A.T. / Wilson, I.A.
History
DepositionJul 19, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 23, 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

Downloads & links

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Assembly

Deposited unit
L: IGG2A-KAPPA 50.1 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 50.1 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,7782
Polymers46,7782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-22 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.700, 110.700, 56.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8
2: GLN L 42 - PRO L 43 OMEGA =146.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO L 77 / 4: CIS PROLINE - PRO L 95 / 5: CIS PROLINE - PRO L 141 / 6: CIS PROLINE - PRO H 149 / 7: CIS PROLINE - PRO H 151 / 8: CIS PROLINE - PRO H 200

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Components

#1: Antibody IGG2A-KAPPA 50.1 FAB (LIGHT CHAIN)


Mass: 23647.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: ASW / References: EMBL: AJ131289
#2: Antibody IGG2A-KAPPA 50.1 FAB (HEAVY CHAIN)


Mass: 23129.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: ASW / References: UniProt: P01865
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT, T.T.WU, M.REID-MILLER, H.M. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT, T.T.WU, M.REID-MILLER, H.M.PERRY, K.S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH, BETHESDA, MD.)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Details: referred to 'Stura, E.A.', (1992) 'Proteins.Struct.,Funct., Genet.', 14, 499-508
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlFab1drop
21.8 M1reservoirNaH2PO4
31reservoirK2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 75 % / Rmerge(I) obs: 0.096

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 0 3291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg4.05
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.19 / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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