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- PDB-6db6: Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a ... -

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Entry
Database: PDB / ID: 6db6
TitleCrystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain
Components
  • HIV-1 gp120 V3 peptide from MN strain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / gp120 / V3 / mAb
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / membrane / identical protein binding
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.978 Å
AuthorsChan, K.-W. / Kong, X.-P.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082676 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI087191 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112546 United States
CitationJournal: J. Virol. / Year: 2018
Title: Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection.
Authors: Chan, K.W. / Pan, R. / Costa, M. / Gorny, M.K. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab heavy chain
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab light chain
P: HIV-1 gp120 V3 peptide from MN strain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0824
Polymers50,1873
Non-polymers8951
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-13 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.568, 69.157, 141.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab heavy chain


Mass: 24539.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab light chain


Mass: 22936.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 V3 peptide from MN strain


Mass: 2711.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[DFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-D-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Imidazole pH 6.5, 15% PEG 8000, 30% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.978→28.22 Å / Num. obs: 32451 / % possible obs: 98.74 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.1
Reflection shellResolution: 1.978→2.049 Å / Rmerge(I) obs: 0.784 / Num. measured obs: 2060

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementResolution: 1.978→28.218 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.2164 1999 6.16 %
Rwork0.1735 --
obs0.1761 32441 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.978→28.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 0 348 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073565
X-RAY DIFFRACTIONf_angle_d0.9314866
X-RAY DIFFRACTIONf_dihedral_angle_d14.9572123
X-RAY DIFFRACTIONf_chiral_restr0.057558
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9782-2.02770.33331210.25321851X-RAY DIFFRACTION84
2.0277-2.08250.23861420.22232136X-RAY DIFFRACTION100
2.0825-2.14370.25271420.1992161X-RAY DIFFRACTION100
2.1437-2.21290.27361420.18992174X-RAY DIFFRACTION100
2.2129-2.2920.22741420.19182150X-RAY DIFFRACTION100
2.292-2.38370.25341420.19272175X-RAY DIFFRACTION100
2.3837-2.49210.2121420.19092170X-RAY DIFFRACTION100
2.4921-2.62340.23891430.18942181X-RAY DIFFRACTION100
2.6234-2.78760.26441440.18642202X-RAY DIFFRACTION100
2.7876-3.00260.24371450.18642189X-RAY DIFFRACTION100
3.0026-3.30440.22291450.18022208X-RAY DIFFRACTION100
3.3044-3.78160.19811460.162221X-RAY DIFFRACTION100
3.7816-4.76070.181480.13912252X-RAY DIFFRACTION100
4.7607-28.22070.17061550.15552372X-RAY DIFFRACTION100

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