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- PDB-1qnz: NMR structure of the 0.5b anti-HIV antibody complex with the gp12... -

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Basic information

Entry
Database: PDB / ID: 1qnz
TitleNMR structure of the 0.5b anti-HIV antibody complex with the gp120 V3 peptide
Components
  • 0.5B ANTIBODY (HEAVY CHAIN)
  • 0.5B ANTIBODY (LIGHT CHAIN)
  • GP120
KeywordsIMMUNE SYSTEM / ANTIBODY / V3 PEPTIDE / BINDING SITE
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / immune response / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane ...membrane fusion involved in viral entry into host cell / immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / immune response / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / extracellular region / plasma membrane
Similarity search - Function
: / : / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...: / : / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 kappa chain V-III region PC 7043 / Ig heavy chain V region 102 / Envelope protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HUMAN IMMUNODEFICIENCY VIRUS 1
MethodSOLUTION NMR
Model type detailsMINIMIZED AVERAGE
AuthorsTugarinov, V. / Zvi, A. / Levy, R. / Hayek, Y. / Matsushita, S. / Anglister, J.
CitationJournal: Structure / Year: 2000
Title: NMR Structure of an Anti-Gp120 Antibody Complex with a V3 Peptide Reveals a Surface Important for Co-Receptor Binding
Authors: Tugarinov, V. / Zvi, A. / Levy, R. / Hayek, Y. / Matsushita, S. / Anglister, J.
History
DepositionOct 26, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 0.5B ANTIBODY (HEAVY CHAIN)
L: 0.5B ANTIBODY (LIGHT CHAIN)
P: GP120


Theoretical massNumber of molelcules
Total (without water)27,6093
Polymers27,6093
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Antibody 0.5B ANTIBODY (HEAVY CHAIN)


Mass: 13323.770 Da / Num. of mol.: 1 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01750*PLUS
#2: Antibody 0.5B ANTIBODY (LIGHT CHAIN)


Mass: 12267.469 Da / Num. of mol.: 1 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01665
#3: Protein/peptide GP120


Mass: 2017.406 Da / Num. of mol.: 1 / Fragment: V3 PEPTIDE / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: Q79416
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE OF THE COMPLEX WAS DETERMINED BY ALLOWING THE CDRS OF THE 0.5B ANTIBODY AND THE V3 PEPTIDE RESIDUES TO MOVE WHILE THE FRAMEWORK OF THE ANTIBODY WAS MODELED AS DESCRIBED.

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Sample preparation

Sample conditionsIonic strength: 10 mM sodium phosphate buffer mM / pH: 7.15 / Pressure: 1 atm / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
NMRDrawstructure solution
NMRViewstructure solution
X-PLOR3.8structure solution
RefinementSoftware ordinal: 1
Details: THE STRUCTURE OF THE COMPLEX WAS DETERMINED ALLOWING THE ANTIBODY CDR RESIDUES AND THE COMPLEXED V3 PEPTIDE RESIDUES TO MOVE, WHILE THE ANTIBODY FRAMEWORK WAS HELD FIXED DURING REFINEMENT ...Details: THE STRUCTURE OF THE COMPLEX WAS DETERMINED ALLOWING THE ANTIBODY CDR RESIDUES AND THE COMPLEXED V3 PEPTIDE RESIDUES TO MOVE, WHILE THE ANTIBODY FRAMEWORK WAS HELD FIXED DURING REFINEMENT AND MODELED AS DESCRIBED PREVIOUSLY
NMR ensembleConformers submitted total number: 1

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