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- PDB-7uce: Structure of the anti-HIV-1 neutralizing antibody BG24 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7uce
TitleStructure of the anti-HIV-1 neutralizing antibody BG24 Fab fragment
Components
  • BG24 Fab heavy chain
  • BG24 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / broadly neutralizing antibody / bNAb / HIV-1 / CD4 binding site / VH1-2 / VRC01-class / antiviral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBarnes, C.O. / Bjorkman, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464 United States
Bill & Melinda Gates FoundationOPP1124068 United States
CitationJournal: Sci Adv / Year: 2022
Title: A naturally arising broad and potent CD4-binding site antibody with low somatic mutation.
Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C ...Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C Cetrulo Lorenzi / Alicja Piechocka-Trocha / Johannes F Scheid / Anthony P West / Bruce D Walker / Michael S Seaman / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, ...The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
History
DepositionMar 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 5, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: BG24 Fab light chain
H: BG24 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6763
Polymers47,2522
Non-polymers4241
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-18 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.603, 118.424, 119.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody BG24 Fab light chain


Mass: 21897.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody BG24 Fab heavy chain


Mass: 25354.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293 / Production host: Homo sapiens (human)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.25 M potassium chloride, 18% polyethylene glycol PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→33.3 Å / Num. obs: 28013 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 54.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.063 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 9.2 % / Rmerge(I) obs: 3.82 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2270 / CC1/2: 0.61 / Rpim(I) all: 1.34 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LSU

4lsu


Resolution: 2.25→33.3 Å / SU ML: 0.2893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1088 4.78 %
Rwork0.2038 21667 -
obs0.2059 22755 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.43 Å2
Refinement stepCycle: LAST / Resolution: 2.25→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 28 35 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543316
X-RAY DIFFRACTIONf_angle_d0.86524519
X-RAY DIFFRACTIONf_chiral_restr0.0478512
X-RAY DIFFRACTIONf_plane_restr0.0053578
X-RAY DIFFRACTIONf_dihedral_angle_d6.2393469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.40681490.34432636X-RAY DIFFRACTION98.86
2.35-2.480.39331520.32182635X-RAY DIFFRACTION99.22
2.48-2.630.35981460.30612681X-RAY DIFFRACTION99.65
2.63-2.830.3885970.28972712X-RAY DIFFRACTION99.33
2.83-3.120.36311130.26592721X-RAY DIFFRACTION99.86
3.12-3.570.25961630.22872680X-RAY DIFFRACTION99.79
3.57-4.50.24211260.17752749X-RAY DIFFRACTION99.86
4.5-33.30.16311420.14472853X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.728659203441.65963039412-1.521958202976.513842079731.35509753123.023253405930.3526978310050.789605921394-0.0689474838894-0.0893331042538-0.2974324713170.0848771446162-0.00266352766126-0.7355678518450.005298547499970.602122416546-0.0762925159907-0.06684967855160.839662865689-0.02426682177340.5318402652420.7183930967339.66302015462.2966544502
24.797797615130.07258870296622.286149491584.09705999246-0.9828715490013.816215679890.06451770058120.104651710449-0.1299677381830.1204475963950.4076874120840.271817877321-0.039641341227-0.295076546131-0.5022506292620.4589103303740.0385978778793-0.006687857325870.575418598837-0.006254286898260.529627574287.6311466780841.892842942870.1103009157
37.89281602713-3.275726892443.512078764228.82169099492-5.80882610624.34048704051-0.801759681831-1.164739552870.4413006382441.694257922230.8832313897540.13100893394-1.05900333236-1.56095634117-0.2819133998070.7579598184930.1285379997740.09853430242210.842973649002-0.006943944802050.6812305483573.3818087549748.333154234777.6847390198
46.065222272810.774196659321-0.1827964416222.50735986893-1.708788481075.94659450812-0.0214536029476-0.300873935603-0.310091980273-0.0005570058790280.2383106788040.4526577190830.0305105965933-0.933581463094-0.2105786185830.452505382604-0.02881969537330.03246416624530.7012468285930.03416626301580.5284357564414.3179849351941.269815923768.8234748036
50.358696500819-0.24283314177-2.054609458931.05020447056-0.212449024878.337851747580.230807886210.4318715450490.092916815334-0.4559457728790.09418398803940.498229168453-1.06803681956-1.90084345958-0.3132267588180.6179350877280.139991391067-0.1152117529570.751310959589-0.003362383598120.635975173632.6015064527546.997184377245.6514499406
65.10902406405-0.45477692936-1.15632025462.837926080480.07343126212166.1526262327-0.239280450782-0.0781124756082-0.1450031509410.07170270880470.255132488121-0.1567430763760.511892836472-0.00701905233983-0.0680296434260.5286049529470.0259551687486-0.1429756964870.45110264681-0.01079417572120.38791468585313.96356140139.230065781135.1359867235
78.25296113245-0.116541222695-5.624718836853.388532818930.6480882583048.02275274094-0.1237738251430.232727811767-0.7028856447340.0328909944407-0.2000971306390.285233735767-0.0735345779872-1.34331234570.217062593510.8372346145850.0503531762033-0.1849431715380.722660466171-0.0326556980910.5607389835035.1800211781937.735701091833.2480916211
84.16574903095-2.33656945263-1.293416722443.416097998141.724784719056.330010473980.242677299544-0.5871276787440.2615421910640.02051477205010.0944057624092-0.35118404651-0.6366445232620.491781048538-0.2343291445730.480282400621-0.0616131018951-0.0477011949070.4746277832670.002230279076890.50520211865629.618326911447.121533425771.5182055068
96.16720590865-0.374417713139-1.081593698074.299180646391.790129360257.004373963130.3092824912780.076462658407-0.5362109981490.07090496979210.1152090367530.2101738768310.486906316352-0.229744160152-0.3977519063890.488402818070.0519837731416-0.01082024085450.314652654710.04788115420950.50352703070123.835568371837.98908803771.8923180323
106.38040984811-2.656742807840.1045165081735.305140927361.002827754066.316473617140.154352629156-0.0612369063701-0.9229558814-0.141632308362-0.265278788070.02817254330870.7761687940080.4546153694380.1949921549450.5860940298260.123595980030.03491162775730.4878836802130.126756057610.59319542688331.12449801833.470652529272.8077787966
115.44032830491-0.617919668708-2.34538413953.769954075230.7441960704145.710497822480.084779397325-0.305180108854-0.02662360115110.243812825039-0.150517825070.0576169639164-0.1721862962720.38787526270.04732201122670.433294727772-0.00014732574029-0.03408285406490.3554811304320.0694635662160.43465770489625.132358731142.672929331270.9418991063
123.070918533170.392439606016-0.5833393165143.336249046971.261632705824.93404873477-0.08734389886880.71078664911-0.339290719799-0.3957813268620.1628969408940.407039637216-0.1127952755650.0871971912677-0.08252745229060.6770096735-0.0392935440504-0.1093714513860.354151739681-0.04026744898190.54442134935220.790432735447.295577944631.6670095781
137.125390187110.6004403425311.703106539230.7265193819941.829935311214.75888599529-0.328981677987-0.2569837931960.4302640823050.2728710544140.113990791503-0.104122391061-0.5442423122970.01447147616990.1939143730310.7222084503260.0607998955374-0.1538137205670.477700897027-0.04727769425760.4974383353720.643649048652.03534705137.3529910762
145.05109678874-0.1171139361882.281183134721.827228819130.3546652500033.1097493772-0.5863271956670.7119283675151.05560053898-0.55911328274-0.167210438210.14934253999-0.2670346780950.2059903975720.620819832681.09551860366-0.0669129267628-0.2004764462640.6539526074470.05487987105130.68837815224820.085391595257.877409241625.5087956411
158.563977008610.06862755179394.828467814563.010906966440.9338402079799.570009134630.01338153415661.5142398430.696411660558-0.680213485802-0.1497494104390.21092172722-0.3377925016690.5804052915360.01025286092180.939451203101-0.114740309693-0.05134200188260.8031262483880.03106020801460.53319773537227.484385804953.101359555329.0467742597
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 2 through 17 )LA2 - 171 - 16
22chain 'L' and (resid 18 through 45 )LA18 - 4517 - 44
33chain 'L' and (resid 46 through 57 )LA46 - 5745 - 56
44chain 'L' and (resid 58 through 93 )LA58 - 9357 - 92
55chain 'L' and (resid 94 through 111 )LA94 - 11193 - 110
66chain 'L' and (resid 112 through 183 )LA112 - 183111 - 182
77chain 'L' and (resid 184 through 202 )LA184 - 202183 - 201
88chain 'H' and (resid 1 through 33 )HD1 - 331 - 33
99chain 'H' and (resid 34 through 57 )HD34 - 5734 - 57
1010chain 'H' and (resid 58 through 73 )HD58 - 7358 - 73
1111chain 'H' and (resid 74 through 121 )HD74 - 12174 - 121
1212chain 'H' and (resid 122 through 155 )HD122 - 155122 - 155
1313chain 'H' and (resid 156 through 195 )HD156 - 195156 - 195
1414chain 'H' and (resid 196 through 210 )HD196 - 210196 - 210
1515chain 'H' and (resid 211 through 225 )HD211 - 225211 - 225

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