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- PDB-8g8a: Crystal structure of DH1317.8 Fab in complex with HIV proximal MP... -

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Basic information

Entry
Database: PDB / ID: 8g8a
TitleCrystal structure of DH1317.8 Fab in complex with HIV proximal MPER peptide
Components
  • DH1317.8 heavy chain
  • DH1317.8 light chain
  • Env polyprotein
KeywordsIMMUNE SYSTEM / HIV / Neutralizing Antibody / MPER / gp41
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsJanus, B.M. / Astavans, A. / Ofek, G.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Cell / Year: 2024
Title: Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans.
Authors: Wilton B Williams / S Munir Alam / Gilad Ofek / Nathaniel Erdmann / David C Montefiori / Michael S Seaman / Kshitij Wagh / Bette Korber / Robert J Edwards / Katayoun Mansouri / Amanda Eaton ...Authors: Wilton B Williams / S Munir Alam / Gilad Ofek / Nathaniel Erdmann / David C Montefiori / Michael S Seaman / Kshitij Wagh / Bette Korber / Robert J Edwards / Katayoun Mansouri / Amanda Eaton / Derek W Cain / Mitchell Martin / JongIn Hwang / Aria Arus-Altuz / Xiaozhi Lu / Fangping Cai / Nolan Jamieson / Robert Parks / Maggie Barr / Andrew Foulger / Kara Anasti / Parth Patel / Salam Sammour / Ruth J Parsons / Xiao Huang / Jared Lindenberger / Susan Fetics / Katarzyna Janowska / Aurelie Niyongabo / Benjamin M Janus / Anagh Astavans / Christopher B Fox / Ipsita Mohanty / Tyler Evangelous / Yue Chen / Madison Berry / Helene Kirshner / Elizabeth Van Itallie / Kevin O Saunders / Kevin Wiehe / Kristen W Cohen / M Juliana McElrath / Lawrence Corey / Priyamvada Acharya / Stephen R Walsh / Lindsey R Baden / Barton F Haynes /
Abstract: A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to ...A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to develop. The HVTN 133 clinical trial studied a peptide/liposome immunogen targeting B cell lineages of HIV-1 envelope (Env) membrane-proximal external region (MPER) bnAbs (NCT03934541). Here, we report MPER peptide-liposome induction of polyclonal HIV-1 B cell lineages of mature bnAbs and their precursors, the most potent of which neutralized 15% of global tier 2 HIV-1 strains and 35% of clade B strains with lineage initiation after the second immunization. Neutralization was enhanced by vaccine selection of improbable mutations that increased antibody binding to gp41 and lipids. This study demonstrates proof of concept for rapid vaccine induction of human B cell lineages with heterologous neutralizing activity and selection of antibody improbable mutations and outlines a path for successful HIV-1 vaccine development.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: 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
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 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
A: DH1317.8 heavy chain
B: DH1317.8 light chain
H: DH1317.8 heavy chain
L: DH1317.8 light chain
C: Env polyprotein
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,76012
Polymers100,2266
Non-polymers5346
Water77543
1
A: DH1317.8 heavy chain
B: DH1317.8 light chain
C: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3344
Polymers50,1133
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: DH1317.8 heavy chain
L: DH1317.8 light chain
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4268
Polymers50,1133
Non-polymers3135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.976, 63.840, 111.971
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 8 molecules AHBLCP

#1: Protein DH1317.8 heavy chain


Mass: 24009.912 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 DH1317.8 light chain


Mass: 23599.211 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: Protein/peptide Env polyprotein


Mass: 2503.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q69910
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 47 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20.1% Isopropanol, 10.05% PEG 8000, and 0.1M Imidazole/Hydrochloric acid pH 6.5

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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: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 40649 / % possible obs: 94.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.8
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.61 / Num. unique obs: 3324 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NRX

4nrx


Resolution: 2.44→41.89 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2000 4.93 %
Rwork0.2221 --
obs0.2238 40608 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6823 0 32 43 6898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.848
X-RAY DIFFRACTIONf_dihedral_angle_d12.5882480
X-RAY DIFFRACTIONf_chiral_restr0.0761085
X-RAY DIFFRACTIONf_plane_restr0.0051216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.44591100.43912126X-RAY DIFFRACTION74
2.5-2.570.43311300.39512511X-RAY DIFFRACTION86
2.57-2.650.38341390.3492679X-RAY DIFFRACTION93
2.65-2.730.37361450.32972794X-RAY DIFFRACTION97
2.73-2.830.34991440.30752780X-RAY DIFFRACTION96
2.83-2.940.3191460.29582811X-RAY DIFFRACTION96
2.94-3.080.31971470.30482840X-RAY DIFFRACTION99
3.08-3.240.33281470.2822849X-RAY DIFFRACTION98
3.24-3.440.28821460.24432823X-RAY DIFFRACTION97
3.44-3.710.26521460.23052825X-RAY DIFFRACTION97
3.71-4.080.26511490.2192854X-RAY DIFFRACTION98
4.08-4.670.20061480.17832856X-RAY DIFFRACTION97
4.67-5.880.19921500.1722924X-RAY DIFFRACTION100
5.88-41.890.20741530.17382936X-RAY DIFFRACTION97
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)
18.23142.6127-7.96847.0879-1.50668.4927-0.8787-1.1758-1.36291.4892-0.0394-0.38720.78081.37140.72870.7760.1655-0.15550.71580.1110.600868.094613.43529.6066
29.3763.93631.50429.1433-0.56396.61570.3306-0.68980.07350.7538-0.187-0.969-0.15341.0375-0.14610.5472-0.02270.0890.6245-0.06550.585275.315618.189621.7761
35.98431.4984-1.76575.229-0.26219.18040.5543-0.63061.23660.4995-0.24790.0227-1.69510.7194-0.27481.0166-0.12840.26130.54060.01380.661569.630324.507522.9931
49.05663.4453-1.46377.3337-0.68334.35410.6247-0.07981.18170.4405-0.14070.6729-1.26230.1197-0.47170.7552-0.03480.06970.35980.07380.599565.682719.422822.0671
59.25144.2429-4.50459.1732-4.55245.7032-0.48590.3233-0.3218-1.2187-0.1212-1.02080.69550.6230.50590.6081-0.01590.15140.4077-0.04010.533270.535218.007914.6428
61.36430.5806-0.45066.21910.36822.516-0.36560.0491-0.8113-0.2445-0.0676-0.98321.30860.38960.40381.03350.11320.35730.54420.03760.909360.9057-8.835728.0741
78.66957.24231.32188.14250.73844.5160.342-0.8866-2.34060.5318-0.7102-2.52870.8160.20450.39521.42680.25870.21810.76040.28571.128664.7479-13.497834.7047
86.946-1.3778-1.00188.97141.86787.6304-0.04781.15320.3922-1.4737-0.12560.25720.0042-1.58720.14470.7149-0.1138-0.05640.89820.17360.452958.097212.2588-0.4498
96.90970.8935-1.66476.64750.246510.5497-0.08570.5601-0.1503-1.3476-0.0219-0.61570.53060.10130.08670.69310.03180.14850.44630.00980.477768.945914.20361.7105
105.32983.1478-0.07322.24930.723510.0521-0.01350.1764-0.0886-0.6075-0.19460.16830.064-0.53520.17860.50550.04110.14270.55220.10240.489764.525514.91376.0087
113.96334.279-0.32844.3713-0.1867-0.0278-0.80942.3809-0.4457-1.2068-0.00850.822.0029-1.8490.39611.825-0.6660.34850.857-0.44750.852255.8483-5.81783.4714
123.28640.16380.69181.05161.72433.6614-0.22340.1916-0.53810.03150.39630.12230.2136-0.1635-0.17621.4168-0.20940.38270.5854-0.07851.014949.3517-14.10222.7146
134.2756-0.4377-1.85962.93310.87936.6246-0.6770.3956-0.8091-0.62010.30370.38341.182-0.78190.36261.0564-0.19650.24530.5731-0.14150.927446.0284-14.651821.0429
143.1801-0.267-1.17762.51010.705110.43290.16250.43040.1489-0.2687-0.17660.6472-0.3275-1.41090.00620.56020.0579-0.03110.5988-0.14170.65819.84617.470624.872
156.8698-0.3095-0.75453.40050.44012.41730.09050.06550.3840.2376-0.1011-0.0781-0.0175-0.08840.00740.73360.02480.16380.3847-0.01590.412131.478525.694946.466
168.40260.63261.72131.1746-0.04072.4631-0.27510.9863-1.481-0.32640.2371-0.03480.6262-0.14160.04961.0028-0.08250.18310.5492-0.17380.626626.68842.811516.4101
177.9588-0.73882.23650.6012-0.56997.4366-0.32720.38510.7055-0.0064-0.1339-0.0146-0.9770.23290.46830.8853-0.03540.06560.3635-0.00880.511228.286716.009815.0433
186.3199-1.02250.23161.6690.03431.9874-0.22741.0738-0.6638-0.72360.0810.03120.0362-0.19540.16650.8479-0.10580.08880.5419-0.13470.450125.45196.699715.7169
196.45113.71046.44813.67472.20746.03220.05560.4985-0.8496-0.22680.3881-0.647-0.13260.3939-0.34380.6583-0.00210.17380.4291-0.06870.544842.24147.891230.7723
202.09970.1908-1.20621.8114-0.22348.21160.3125-0.1160.2623-0.0688-0.0828-0.0943-0.56250.0705-0.21810.5899-0.07790.1270.36260.01310.433937.228112.933652.3665
212.2538-0.6367-2.15942.15590.6866.07090.0144-0.2150.104-0.0924-0.0707-0.1983-0.41440.42330.03190.495-0.10150.05470.35820.00750.497740.5312.971651.9375
226.8689-4.46422.42366.06984.00849.87870.4407-1.43982.5724-0.9903-0.0863-1.0130.50590.1354-0.30661.6197-0.30380.44520.7943-0.23851.146578.381532.952210.9983
237.22851.05671.76986.06590.99577.2371-1.5077-1.18430.92990.10561.77830.84860.7560.7106-0.4380.78670.2393-0.08591.62210.00810.77854.636211.64814.8325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 213 )
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 119 )
15X-RAY DIFFRACTION15chain 'H' and (resid 120 through 216 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 38 )
17X-RAY DIFFRACTION17chain 'L' and (resid 39 through 61 )
18X-RAY DIFFRACTION18chain 'L' and (resid 62 through 101 )
19X-RAY DIFFRACTION19chain 'L' and (resid 102 through 113 )
20X-RAY DIFFRACTION20chain 'L' and (resid 114 through 163 )
21X-RAY DIFFRACTION21chain 'L' and (resid 164 through 214 )
22X-RAY DIFFRACTION22chain 'C' and (resid 655 through 668 )
23X-RAY DIFFRACTION23chain 'P' and (resid 656 through 670 )

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