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- PDB-1ai1: HIV-1 V3 LOOP MIMIC -

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Basic information

Entry
Database: PDB / ID: 1ai1
TitleHIV-1 V3 LOOP MIMIC
Components
  • AIB142
  • IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
KeywordsCOMPLEX (ANTIBODY/PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) / ANTIBODY / CONSTRAINED HIV-1 V3 LOOP PEPTIDE / IMMUNOGLOBULIN / COMPLEX (ANTIBODY-PEPTIDE) complex
Function / homology
Function and homology information


phagocytosis, recognition / 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 / Dectin-2 family / immunoglobulin mediated immune response / complement activation, classical pathway ...phagocytosis, recognition / 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 / Dectin-2 family / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of phagocytosis / host cell endosome membrane / B cell differentiation / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / defense response to bacterium / viral protein processing / fusion of virus membrane with host plasma membrane / external side of 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 / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
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
: / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGhiara, J.B. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site.
Authors: Ghiara, J.B. / Ferguson, D.C. / Satterthwait, A.C. / Dyson, H.J. / Wilson, I.A.
History
DepositionNov 6, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
P: AIB142


Theoretical massNumber of molelcules
Total (without water)50,7123
Polymers50,7123
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.930, 154.430, 121.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)


Mass: 23675.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: EMBL: AJ272393, UniProt: P01837*PLUS
#2: Antibody IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)


Mass: 24208.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01868
#3: Protein/peptide AIB142


Mass: 2828.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE
References: UniProt: P05877
Compound detailsTHE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE SEQUENCE (L.RATNER ET AL., NATURE 313:277-284 (1985)).

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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: 4.16 Å3/Da / Density % sol: 70.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.75 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4-1.8 Msodium potassium phosphate1drop
215 mg/mlFab1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 19192 / % possible obs: 92 % / Rsym value: 0.08
Reflection shellResolution: 2.8→2.9 Å / % possible all: 90
Reflection
*PLUS
Num. measured all: 50028 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ACY

1acy


Resolution: 2.8→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.22 --
obs0.22 18955 91 %
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 0 0 3443
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2

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