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- PDB-6fy3: Crystal structure of a V2-directed, RV144 vaccine-like antibody f... -

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Basic information

Entry
Database: PDB / ID: 6fy3
TitleCrystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-3D, bound to a heterologous V2 peptide
Components
  • CAP228-3D Heavy Chain
  • CAP228-3D Light Chain
  • CAP45 V2 peptide
KeywordsIMMUNE SYSTEM / Fab / HIV-1 Envelope V1V2
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWibmer, C.K. / Moore, P.L. / Morris, L.
Funding support United States, South Africa, 3items
OrganizationGrant numberCountry
National Institutes of HealthAI104387-01 United States
Poliomyelitis Research Foundation15/83 South Africa
NHLS Research Trust South Africa
CitationJournal: Nat Commun / Year: 2018
Title: Common helical V1V2 conformations of HIV-1 Envelope expose the alpha 4 beta 7 binding site on intact virions.
Authors: Wibmer, C.K. / Richardson, S.I. / Yolitz, J. / Cicala, C. / Arthos, J. / Moore, P.L. / Morris, L.
History
DepositionMar 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: CAP228-3D Heavy Chain
Y: CAP228-3D Light Chain
Z: CAP45 V2 peptide
H: CAP228-3D Heavy Chain
L: CAP228-3D Light Chain
P: CAP45 V2 peptide


Theoretical massNumber of molelcules
Total (without water)103,1016
Polymers103,1016
Non-polymers00
Water3,027168
1
X: CAP228-3D Heavy Chain
Y: CAP228-3D Light Chain
Z: CAP45 V2 peptide


Theoretical massNumber of molelcules
Total (without water)51,5513
Polymers51,5513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-22 kcal/mol
Surface area19560 Å2
MethodPISA
2
H: CAP228-3D Heavy Chain
L: CAP228-3D Light Chain
P: CAP45 V2 peptide


Theoretical massNumber of molelcules
Total (without water)51,5513
Polymers51,5513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-28 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.360, 43.808, 119.910
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody CAP228-3D Heavy Chain


Mass: 25697.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGHV5-51 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#2: Antibody CAP228-3D Light Chain


Mass: 23508.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGLV6-57 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#3: Protein/peptide CAP45 V2 peptide


Mass: 2344.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: CAP45 / Gene: Env / Variant: 2.00.G3 / Production host: synthetic construct (others) / References: UniProt: C6FX86*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.65 Å3/Da / Density % sol: 53.55 % / Description: Rods
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M imidazole HCl (pH6.5), 0.05M HEPES NaOH (pH7.5), 20% PEG8000, 5% 2-methyl-2,4-pentanediol (MPD), 0.1 M ammonium sulphate, 5% isopropanol, supplemented up to 25% MPD as a cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33817 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13.2998refinement
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQQ

4hqq


Resolution: 2.6→42.867 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.2503 1697 5.02 %
Rwork0.2201 --
obs0.2217 33796 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 0 168 6694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026702
X-RAY DIFFRACTIONf_angle_d0.5969122
X-RAY DIFFRACTIONf_dihedral_angle_d11.3173993
X-RAY DIFFRACTIONf_chiral_restr0.0441003
X-RAY DIFFRACTIONf_plane_restr0.0031150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.67550.27811190.28062452X-RAY DIFFRACTION93
2.6755-2.76180.29711480.26152653X-RAY DIFFRACTION100
2.7618-2.86050.33051430.25732668X-RAY DIFFRACTION100
2.8605-2.9750.27751460.2482668X-RAY DIFFRACTION100
2.975-3.11040.26641320.22692668X-RAY DIFFRACTION100
3.1104-3.27430.27111420.22142647X-RAY DIFFRACTION100
3.2743-3.47940.24851450.222670X-RAY DIFFRACTION100
3.4794-3.74790.22551400.20512699X-RAY DIFFRACTION100
3.7479-4.12470.25811390.19362702X-RAY DIFFRACTION100
4.1247-4.7210.19151420.1732707X-RAY DIFFRACTION100
4.721-5.94540.20321490.20482740X-RAY DIFFRACTION100
5.9454-42.87260.29171520.25632825X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -34.9625 Å / Origin y: -1.214 Å / Origin z: 15.8981 Å
111213212223313233
T0.3198 Å2-0.0474 Å2-0.0559 Å2--0.0006 Å20.1277 Å2--0.0969 Å2
L2.1356 °20.3437 °2-1.0011 °2-0.573 °20.1404 °2--2.5414 °2
S0.0395 Å °-0.3938 Å °-0.1035 Å °0.0717 Å °-0.0535 Å °-0.1752 Å °-0.3128 Å °0.6789 Å °-0.0195 Å °
Refinement TLS groupSelection details: all

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