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- PDB-6fy0: Crystal structure of a V2-directed, RV144 vaccine-like antibody f... -

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Basic information

Entry
Database: PDB / ID: 6fy0
TitleCrystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-16H, bound to a heterologous V2 peptide
Components
  • CAP228-16H Heavy Chain
  • CAP228-16H Light Chain
  • CAP45 V2 peptide
KeywordsIMMUNE SYSTEM / Fab / HIV V2 peptide
Function / homology
Function and homology information


: / positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / apoptotic process ...: / positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / apoptotic process / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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: 2.57 Å
AuthorsWibmer, C.K. / Fernandes, M. / Vijayakumar, B. / Dirr, H.W. / Sayed, Y. / Moore, P.L. / Morris, L.
CitationJournal: Cell Rep / Year: 2018
Title: V2-Directed Vaccine-like Antibodies from HIV-1 Infection Identify an Additional K169-Binding Light Chain Motif with Broad ADCC Activity.
Authors: van Eeden, C. / Wibmer, C.K. / Scheepers, C. / Richardson, S.I. / Nonyane, M. / Lambson, B. / Mkhize, N.N. / Vijayakumar, B. / Sheng, Z. / Stanfield-Oakley, S. / Bhiman, J.N. / Bekker, V. / ...Authors: van Eeden, C. / Wibmer, C.K. / Scheepers, C. / Richardson, S.I. / Nonyane, M. / Lambson, B. / Mkhize, N.N. / Vijayakumar, B. / Sheng, Z. / Stanfield-Oakley, S. / Bhiman, J.N. / Bekker, V. / Hermanus, T. / Mabvakure, B. / Ismail, A. / Moody, M.A. / Wiehe, K. / Garrett, N. / Karim, S.A. / Dirr, H. / Fernandes, M.A. / Sayed, Y. / Shapiro, L. / Ferrari, G. / Haynes, B.F. / Moore, P.L. / Morris, L.
History
DepositionMar 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CAP228-16H Heavy Chain
L: CAP228-16H Light Chain
M: CAP228-16H Light Chain
I: CAP228-16H Heavy Chain
A: CAP45 V2 peptide
P: CAP45 V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4668
Polymers100,2746
Non-polymers1922
Water2,072115
1
H: CAP228-16H Heavy Chain
L: CAP228-16H Light Chain
P: CAP45 V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2334
Polymers50,1373
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-44 kcal/mol
Surface area20710 Å2
MethodPISA
2
M: CAP228-16H Light Chain
I: CAP228-16H Heavy Chain
A: CAP45 V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2334
Polymers50,1373
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-40 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.299, 104.265, 212.218
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 CAP228-16H Heavy Chain


Mass: 25145.332 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 / Cell line (production host): FreeStyle 293-F Cells / Production host: Homo sapiens (human)
#2: Antibody CAP228-16H Light Chain


Mass: 22647.047 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 / Cell line (production host): FreeStyle 293-F Cells / 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 / Production host: synthetic construct (others) / References: UniProt: L7TQU8*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.67 % / Description: Large diamond shaped crystals (0.3-0.5mm)
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG8000, 200mM sodium chloride, 100mM sodium phosphate-citrate (pH4.2), 160mM ammonium sulphate, 8% 2-Methyl-2,4-pentanediol (25% 2-Methyl-2,4-pentanediol for cryoprotection)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28958 / % possible obs: 91.3 % / Redundancy: 5.1 % / CC1/2: 0.987 / Rpim(I) all: 0.068 / Rsym value: 0.158 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1701 / CC1/2: 0.873 / Rpim(I) all: 0.263 / Rsym value: 0.373 / % possible all: 60.8

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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: 2.57→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.21 --
obs-26375 90.11 %
Refinement stepCycle: LAST / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6760 0 10 115 6885

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