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- PDB-8vvb: Influenza antibody L5A7 Fab -

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Basic information

Entry
Database: PDB / ID: 8vvb
TitleInfluenza antibody L5A7 Fab
Components
  • L5A7 Heavy Chain
  • L5A7 Light Chain
KeywordsANTIVIRAL PROTEIN / antibody / influenza
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHarris, D.R. / Olia, A.S. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2024
Title: Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody.
Authors: Adam S Olia / Madhu Prabhakaran / Darcy R Harris / Crystal Sao-Fong Cheung / Rebecca A Gillespie / Jason Gorman / Abigayle Hoover / Nicholas C Morano / Amine Ourahmane / Abhinaya Srikanth / ...Authors: Adam S Olia / Madhu Prabhakaran / Darcy R Harris / Crystal Sao-Fong Cheung / Rebecca A Gillespie / Jason Gorman / Abigayle Hoover / Nicholas C Morano / Amine Ourahmane / Abhinaya Srikanth / Shuishu Wang / Weiwei Wu / Tongqing Zhou / Sarah F Andrews / Masaru Kanekiyo / Lawrence Shapiro / Adrian B McDermott / Peter D Kwong /
Abstract: The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline ...The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen.
History
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L5A7 Heavy Chain
B: L5A7 Light Chain
C: L5A7 Heavy Chain
D: L5A7 Light Chain


Theoretical massNumber of molelcules
Total (without water)94,7184
Polymers94,7184
Non-polymers00
Water21,4921193
1
A: L5A7 Heavy Chain
B: L5A7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,3592
Polymers47,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21 kcal/mol
Surface area20080 Å2
MethodPISA
2
C: L5A7 Heavy Chain
D: L5A7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,3592
Polymers47,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-18 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.760, 109.190, 140.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody L5A7 Heavy Chain


Mass: 24642.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody L5A7 Light Chain


Mass: 22716.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1193 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17.5% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→60 Å / Num. obs: 141507 / % possible obs: 94.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.47 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Net I/σ(I): 18.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.919 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3715 / Rpim(I) all: 1.485 / Rrim(I) all: 2.451 / % possible all: 50.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→48.02 Å / SU ML: 0.1414 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 19.4602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 1999 2.11 %
Rwork0.1738 92911 -
obs0.1746 94910 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.87 Å2
Refinement stepCycle: LAST / Resolution: 1.78→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 0 1193 7722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00536675
X-RAY DIFFRACTIONf_angle_d0.8439093
X-RAY DIFFRACTIONf_chiral_restr0.05921052
X-RAY DIFFRACTIONf_plane_restr0.00641155
X-RAY DIFFRACTIONf_dihedral_angle_d6.2702915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.22481330.18546197X-RAY DIFFRACTION91.98
1.82-1.870.23711360.18666301X-RAY DIFFRACTION93.36
1.87-1.930.25151370.19496378X-RAY DIFFRACTION94.72
1.93-1.990.22171390.17796474X-RAY DIFFRACTION95.85
1.99-2.060.21391400.17486519X-RAY DIFFRACTION96.33
2.06-2.150.21241420.17446557X-RAY DIFFRACTION97.31
2.15-2.240.21451420.17746613X-RAY DIFFRACTION97.76
2.24-2.360.23021440.18256689X-RAY DIFFRACTION98.42
2.36-2.510.2471440.18816739X-RAY DIFFRACTION98.82
2.51-2.70.19631450.196718X-RAY DIFFRACTION98.88
2.7-2.970.21081460.18536794X-RAY DIFFRACTION99.03
2.97-3.40.20141470.17396821X-RAY DIFFRACTION99.47
3.4-4.290.19061500.15316923X-RAY DIFFRACTION99.75
4.29-48.020.19721540.1647188X-RAY DIFFRACTION99.86

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