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- PDB-1ggi: CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1ggi
TitleCRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN
Components
  • HIV-1 V3 LOOP PEPTIDE ANTIGEN
  • IGG2A 50.1 FAB (HEAVY CHAIN)
  • IGG2A 50.1 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin receptor binding / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...immunoglobulin receptor binding / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
: / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
: / Ig gamma-2A chain C region, A allele / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStanfield, R.L. / Rini, J.M. / Wilson, I.A.
Citation
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.
#1: 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. / Rogusca, M. / Hincapie, L.M. / Simmerman, H.K.B. / Profy, A.T. / Wilson, I.A.
#2: Journal: To be Published
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.
History
DepositionApr 2, 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_sheet
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 / _struct_sheet.number_strands
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

Downloads & links

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Assembly

Deposited unit
L: IGG2A 50.1 FAB (LIGHT CHAIN)
H: IGG2A 50.1 FAB (HEAVY CHAIN)
P: HIV-1 V3 LOOP PEPTIDE ANTIGEN
M: IGG2A 50.1 FAB (LIGHT CHAIN)
J: IGG2A 50.1 FAB (HEAVY CHAIN)
Q: HIV-1 V3 LOOP PEPTIDE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)99,3016
Polymers99,3016
Non-polymers00
Water00
1
L: IGG2A 50.1 FAB (LIGHT CHAIN)
H: IGG2A 50.1 FAB (HEAVY CHAIN)
P: HIV-1 V3 LOOP PEPTIDE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)49,6503
Polymers49,6503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-32 kcal/mol
Surface area19550 Å2
MethodPISA
2
M: IGG2A 50.1 FAB (LIGHT CHAIN)
J: IGG2A 50.1 FAB (HEAVY CHAIN)
Q: HIV-1 V3 LOOP PEPTIDE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)49,6503
Polymers49,6503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-32 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.330, 52.570, 82.040
Angle α, β, γ (deg.)90.00, 97.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 8, 77, 95, 141, 204 OF THE L AND M CHAINS, AND RESIDUES 149, 151, 200 OF THE H AND J CHAINS ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9517, -0.0014, 0.3069), (-0.0158, -0.9989, 0.0442), (0.3065, -0.0469, -0.9507)-57.56, 21.61, -39.18
2given(0.951, -0.0002, 0.3093), (-0.01, -0.9995, 0.03), (0.3092, -0.0316, -0.9505)-57.79, 21.27, -39.59
3given(0.9792, 0.1445, 0.1425), (0.132, -0.9868, 0.0935), (0.1541, -0.0728, -0.9854)-62.58, 19.45, -36.65
4given(0.9785, 0.1548, 0.1361), (0.1415, -0.9846, 0.1025), (0.1499, -0.081, -0.9854)-62.54, 19.34, -36.41
DetailsTHERE ARE TWO FAB MOLECULES IN THE ASYMMETRIC UNIT. THE TRANSFORMATIONS GIVEN ON *MTRIX* RECORDS BELOW YIELD APPROXIMATE COORDINATES FOR CHAINS *L* AND *H* WHEN APPLIED TO CHAINS *M* AND *J*. THESE TRANSFORMATIONS HAVE BEEN PROVIDED SEPARATELY FOR THE VH AND CH DOMAINS OF THE HEAVY CHAIN AND THE VL AND CL DOMAINS OF THE LIGHT CHAIN. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE VL DOMAIN OF CHAIN *L* WHEN APPLIED TO THE VL DOMAIN OF CHAIN *M*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE CL DOMAIN OF CHAIN *L* WHEN APPLIED TO THE CL DOMAIN OF CHAIN *M*. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE VH DOMAIN OF CHAIN *H* WHEN APPLIED TO THE VH DOMAIN OF CHAIN *J*. THE TRANSFORMATION PRESENTED ON *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE CH DOMAIN OF CHAIN *H* WHEN APPLIED TO THE CH DOMAIN OF CHAIN *J*.

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Components

#1: Antibody IGG2A 50.1 FAB (LIGHT CHAIN)


Mass: 23994.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: ASW / References: EMBL: AJ131289
#2: Antibody IGG2A 50.1 FAB (HEAVY CHAIN)


Mass: 23828.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P01863
#3: Protein/peptide HIV-1 V3 LOOP PEPTIDE ANTIGEN


Mass: 1827.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P05877*PLUS
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. ...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. THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE SEQUENCE (L. RATNER, W. HASELTINE, R. PATARCA, K.J. LIVAK, B. STARCICH, S.F. JOSEPHS, E.R. DORAN, J.A. RAFALSKI, E.A. WHITEHORN, K. BAUMEISTER, L. IVANOFF, S.R. PETTEWAY JR., M. L. PEARSON, J.A. LAUTENBERGER, T.S. PAPAS, J. GHRAYEB, N.T. CHANG, R.C. GALLO, F. WONG-STAAL (1985) NATURE V. 313, 277-284.) (*CKRIHIGPG;311-316, 319-321) (*C IS AN ACETAMIDOMETHYLATED CYSTEINE IN THE REAL PEPTIDE; HOWEVER IN THE DEPOSITED MODEL THIS IS A CYS)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlFab1drop
22.5 mg/mlMP1 peptide1drop
30.2 Mimidazole malate1reservoir
414 %PEG100001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 81 % / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.188 / Rfactor obs: 0.188 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 0 0 6718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.79
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
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.79

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