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- EMDB-20818: Cryo-EM structure of HIV-1 neutralizing antibody DH270.6 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-20818
TitleCryo-EM structure of HIV-1 neutralizing antibody DH270.6 in complex with CH848 10.17DT Env
Map data
Sample
  • Complex: Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT
    • Protein or peptide: CH848 10.17DT gp41
    • Protein or peptide: DH270.6 Heavy chain
    • Protein or peptide: DH270.6 Light chain
    • Protein or peptide: CH848 10.17DT gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


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 / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...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 / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAcharya P / Henderson RC / Saunder KO / Haynes BF
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)UM1-AI100645 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)UM1-AI144371 United States
CitationJournal: Science / Year: 2019
Title: Targeted selection of HIV-specific antibody mutations by engineering B cell maturation.
Authors: Kevin O Saunders / Kevin Wiehe / Ming Tian / Priyamvada Acharya / Todd Bradley / S Munir Alam / Eden P Go / Richard Scearce / Laura Sutherland / Rory Henderson / Allen L Hsu / Mario J ...Authors: Kevin O Saunders / Kevin Wiehe / Ming Tian / Priyamvada Acharya / Todd Bradley / S Munir Alam / Eden P Go / Richard Scearce / Laura Sutherland / Rory Henderson / Allen L Hsu / Mario J Borgnia / Haiyan Chen / Xiaozhi Lu / Nelson R Wu / Brian Watts / Chuancang Jiang / David Easterhoff / Hwei-Ling Cheng / Kelly McGovern / Peyton Waddicor / Aimee Chapdelaine-Williams / Amanda Eaton / Jinsong Zhang / Wes Rountree / Laurent Verkoczy / Mark Tomai / Mark G Lewis / Heather R Desaire / Robert J Edwards / Derek W Cain / Mattia Bonsignori / David Montefiori / Frederick W Alt / Barton F Haynes /
Abstract: INTRODUCTION: A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the ...INTRODUCTION: A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the induction of affinity-matured and potent HIV-1 bnAbs. To devise effective vaccine strategies, we previously determined the maturation pathway of select HIV-1 bnAbs from acute infection through neutralizing antibody development. During their evolution, bnAbs acquire an abundance of improbable amino acid substitutions as a result of nucleotide mutations at variable region sequences rarely targeted by activation-induced cytidine deaminase, the enzyme responsible for antibody mutation. A subset of improbable mutations is essential for broad neutralization activity, and their acquisition represents a key roadblock to bnAb development.
RATIONALE: Current bnAb lineage-based vaccine strategies can initiate bnAb lineage development in animal models but have not specifically elicited the improbable mutations required for neutralization ...RATIONALE: Current bnAb lineage-based vaccine strategies can initiate bnAb lineage development in animal models but have not specifically elicited the improbable mutations required for neutralization breadth. Induction of bnAbs requires vaccine strategies that specifically engage bnAb precursors and subsequently select for improbable mutations required for broadly neutralizing activity. We hypothesized that vaccination with immunogens that bind with moderate to high affinity to bnAb B cell precursors, and with higher affinity to precursors that have acquired improbable mutations, could initiate bnAb B cell lineages and select for key improbable mutations required for bnAb development.
RESULTS: We elicited serum neutralizing HIV-1 antibodies in human bnAb precursor knock-in mice and wild-type macaques vaccinated with immunogens designed to select for improbable mutations. We ...RESULTS: We elicited serum neutralizing HIV-1 antibodies in human bnAb precursor knock-in mice and wild-type macaques vaccinated with immunogens designed to select for improbable mutations. We designed two HIV-1 envelope immunogens that bound precursor B cells of either a CD4 binding site or V3-glycan bnAb lineage. In vitro, these immunogens bound more strongly to bnAb precursors once the precursor acquired the desired improbable mutations. Vaccination of macaques with the CD4 binding site–targeting immunogen induced CD4 binding site serum neutralizing antibodies. Antibody sequences elicited in human bnAb precursor knock-in mice encoded functional improbable mutations critical for bnAb development. In bnAb precursor knock-in mice, we isolated a vaccine-elicited monoclonal antibody bearing functional improbable mutations that was capable of neutralizing multiple HIV-1 global isolates. Structures of a bnAb precursor, a bnAb, and the vaccine-elicited antibody revealed the precise roles that acquired improbable mutations played in recognizing the HIV-1 envelope. Thus, our immunogens elicited antibody responses in macaques and knock-in mice that exhibited the mutational patterns, structural characteristics, or neutralization profiles of nascent broadly neutralizing antibodies.
CONCLUSION: Our study represents a proof of concept for targeted selection of improbable mutations to guide antibody affinity maturation. Moreover, this study demonstrates a rational strategy for ...CONCLUSION: Our study represents a proof of concept for targeted selection of improbable mutations to guide antibody affinity maturation. Moreover, this study demonstrates a rational strategy for sequential immunogen design to circumvent the difficult roadblocks in HIV-1 bnAb induction by vaccination. We show that immunogens should exhibit differences in affinity across antibody maturation stages where improbable mutations are necessary for the desired antibody function. This strategy of selection of specific antibody nucleotides by immunogen design can be applied to B cell lineages targeting other pathogens where guided affinity maturation is needed for a protective antibody response.
History
DepositionOct 9, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 18, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6um6
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20818.png

Downloads & links

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Map

FileDownload / File: emd_20818.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.0919611 - 2.0576556
Average (Standard dev.)0.004777402 (±0.08303499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.0922.0580.005

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Supplemental data

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Sample components

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Entire : Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT

EntireName: Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT
Components
  • Complex: Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT
    • Protein or peptide: CH848 10.17DT gp41
    • Protein or peptide: DH270.6 Heavy chain
    • Protein or peptide: DH270.6 Light chain
    • Protein or peptide: CH848 10.17DT gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT

SupramoleculeName: Complex of antibody DH270.6 with HIV-1 Env CH848 10.17DT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4, #1
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightExperimental: 360 KDa

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Macromolecule #1: CH848 10.17DT gp120

MacromoleculeName: CH848 10.17DT gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.736535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDATVKTG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDATVKTG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP KVTFEPIPIH YCAPAGYAIL KCNDETFNGT GPCSNVSTVQ CTHGIRPVVS TQLLLNGSLA EKEIVIRSEN LT NNAKIII VHLHTPVEIV CTRPNNNTRK SVRIGPGQTF YATGDIIGDI KQAHCNISEE KWNDTLQKVG IELQKHFPNK TIK YNQSAG GDMEITTHSF NCGGEFFYCN TSNLFNGTYN GTYISTNSSA NSTSTITLQC RIKQIINMWQ GVGRCMYAPP IAGN ITCRS NITGLLLTRD GGTNSNETET FRPAGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRV

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Macromolecule #2: CH848 10.17DT gp41

MacromoleculeName: CH848 10.17DT gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.24583 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VGRRRRRRAV GIGAVFLGFL GAAGSTMGAA SMTLTVQARN LLSGIVQQQS NLLRAPEAQQ HLLKLTVWGI KQLQARVLAV ERYLRDQQL LGIWGCSGKL ICCTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA L D

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Macromolecule #3: DH270.6 Heavy chain

MacromoleculeName: DH270.6 Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.895893 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAQ MKNPGASVKV SCAPSGYTFT DFYIHWLRQA PGQGLQWMGW MNPQTGRTNT ARNFQGRVTM TRDTSIGTAY MELRSLTSD DTAIYYCTTG GWISLYYDSS YYPNFDHWGQ GTLLTVSGAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAQ MKNPGASVKV SCAPSGYTFT DFYIHWLRQA PGQGLQWMGW MNPQTGRTNT ARNFQGRVTM TRDTSIGTAY MELRSLTSD DTAIYYCTTG GWISLYYDSS YYPNFDHWGQ GTLLTVSGAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK SCDKHHHHHH

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Macromolecule #4: DH270.6 Light chain

MacromoleculeName: DH270.6 Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.783273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTKYDVG SHDLVSWYQQ YPGKVPKYMI YEVNKRPSGV SNRFSGSKSG NTASLTISGL RAEDEADYY CCSFGGSATV VCGGGTKVTV LGQPKGAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPASV SGSPGQSITI SCTGTKYDVG SHDLVSWYQQ YPGKVPKYMI YEVNKRPSGV SNRFSGSKSG NTASLTISGL RAEDEADYY CCSFGGSATV VCGGGTKVTV LGQPKGAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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