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- PDB-1acy: CRYSTAL STRUCTURE OF THE PRINCIPAL NEUTRALIZING SITE OF HIV-1 -

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Basic information

Entry
Database: PDB / ID: 1acy
TitleCRYSTAL STRUCTURE OF THE PRINCIPAL NEUTRALIZING SITE OF HIV-1
Components
  • HIV-1 GP120 (MN ISOLATE)
  • IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
KeywordsCOMPLEX(ANTIBODY/HIV-1 FRAGMENT) / COMPLEX(ANTIBODY-HIV-1 FRAGMENT) / COMPLEX(ANTIBODY-HIV-1 FRAGMENT) complex
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 / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / Dectin-2 family / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / antigen binding / B cell differentiation / host cell endosome membrane / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / viral protein processing / defense response to bacterium / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / identical protein binding / 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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig gamma-1 chain C region, membrane-bound form / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
HIV-1 M:B_MN (virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsGhiara, J.B. / Wilson, I.A.
CitationJournal: Science / Year: 1994
Title: Crystal structure of the principal neutralization site of HIV-1.
Authors: Ghiara, J.B. / Stura, E.A. / Stanfield, R.L. / Profy, A.T. / Wilson, I.A.
History
DepositionFeb 10, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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_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_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

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Assembly

Deposited unit
L: IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
P: HIV-1 GP120 (MN ISOLATE)


Theoretical massNumber of molelcules
Total (without water)50,6983
Polymers50,6983
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-30 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.700, 154.000, 121.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 77 / 3: CIS PROLINE - PRO L 95 / 4: CIS PROLINE - PRO L 141 / 5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151 / 7: CIS PROLINE - PRO H 200

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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 genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)


Mass: 24208.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01869
#3: Protein/peptide HIV-1 GP120 (MN ISOLATE)


Mass: 2814.339 Da / Num. of mol.: 1 / Fragment: FRAGMENT (RESIDUES 308 - 332)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_MN (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / References: UniProt: P05877
Compound detailsTHE PEPTIDE USED WAS A SYNTHETIC HOMOLOGUE OF RESIDUES 308 - 332 OF HIV-1 GP120 (MN STRAIN), WITH ...THE PEPTIDE USED WAS A SYNTHETIC HOMOLOGUE OF RESIDUES 308 - 332 OF HIV-1 GP120 (MN STRAIN), WITH AN ADDITIONAL CYS AT THE C-TERMINAL END.
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID- ...THE FAB FRAGMENT IS NUMBERED ACCORDING TO 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.)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.75 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.65 M1reservoirNaKHPO4
310 mg/mlFab1reservoir
21

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 16265 / % possible obs: 94 % / Num. measured all: 79118 / Rmerge(I) obs: 0.116

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→12 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.21 -
obs0.21 15181
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 0 3442
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_deg3.8
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
Num. reflection all: 15181 / Rfactor all: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.8

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