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- EMDB-40275: CryoEM structure of DH270.6-CH848.0526.25 -

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Basic information

Entry
Database: EMDB / ID: EMD-40275
TitleCryoEM structure of DH270.6-CH848.0526.25
Map data
Sample
  • Complex: DH270.6-CH848.0526.25
    • Protein or peptide: CH848.0526.25 gp120
    • Protein or peptide: CH848.0526.25 gp41
    • Protein or peptide: DH270.6 variable heavy chain
    • Protein or peptide: DH270.6 variable light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / antibody / DH270.6 / CH848.0526.25 / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / : / 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 / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / HIV-1 06TG.HT008 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHenderson R / Zhou Y / Stalls V / Bartesaghi B / Acharya P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)ECCS-2025064 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
Citation
Journal: Nat Commun / Year: 2023
Title: Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage.
Authors: Rory Henderson / Ye Zhou / Victoria Stalls / Kevin Wiehe / Kevin O Saunders / Kshitij Wagh / Kara Anasti / Maggie Barr / Robert Parks / S Munir Alam / Bette Korber / Barton F Haynes / ...Authors: Rory Henderson / Ye Zhou / Victoria Stalls / Kevin Wiehe / Kevin O Saunders / Kshitij Wagh / Kara Anasti / Maggie Barr / Robert Parks / S Munir Alam / Bette Korber / Barton F Haynes / Alberto Bartesaghi / Priyamvada Acharya /
Abstract: Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with ...Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis for breadth development in a HIV-1 neutralizing antibody
Authors: Henderson R / Zhou Y / Stalls V / Wiehe K / Saunders KO / Wagh K / Anasti K / Barr M / Parks R / Alam SM / Korber B / Haynes BF / Bartesaghi A / Acharya P
History
DepositionApr 1, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40275.png

Downloads & links

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Map

FileDownload / File: emd_40275.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 192 pix.
= 204.672 Å		1.07 Å/pix.
x 192 pix.
= 204.672 Å		1.07 Å/pix.
x 192 pix.
= 204.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.24950822 - 0.44598097
Average (Standard dev.)0.0023872498 (±0.019635318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 204.672 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40275_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40275_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40275_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : DH270.6-CH848.0526.25

EntireName: DH270.6-CH848.0526.25
Components
  • Complex: DH270.6-CH848.0526.25
    • Protein or peptide: CH848.0526.25 gp120
    • Protein or peptide: CH848.0526.25 gp41
    • Protein or peptide: DH270.6 variable heavy chain
    • Protein or peptide: DH270.6 variable light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: DH270.6-CH848.0526.25

SupramoleculeName: DH270.6-CH848.0526.25 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CH848.0526.25 gp120

MacromoleculeName: CH848.0526.25 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Molecular weightTheoretical: 54.806148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELFLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSNATVNNR TAYDTRSNVN VTSINNTIMG EMKNCSFNTT TEIRDKEKKE YALFYKPDIV P LNETSNTS ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELFLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSNATVNNR TAYDTRSNVN VTSINNTIMG EMKNCSFNTT TEIRDKEKKE YALFYKPDIV P LNETSNTS EYRLINCNTS ACTQACPKVT FEPIPIHYCA PAGYAILKCN NETFNGTGPC SNVSTVQCTH GIRPVVSTQL LL NGSLAEK EIVIRSENLT NNAKIIIVHL NTSVEIVCTR PGNNTRKSVR IGPGQTFYAT GDIIGDIRQA HCNISEKQWN ETL QKVGKE LQKHFPNKTI KYERSAGGDM EIATHSFNCG GEFFYCNTSK LFNGTYNGTD INISTNSNST ITLQCRIKQI INMW QGVGR CMYAPPIAGN ITCKSNITGL LLTRDGGTNS NKTEETFRPA GGDMRDNWRS ELYKYKVVKI EPLGVAPTRC KRRVV GRRR RRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: CH848.0526.25 gp41

MacromoleculeName: CH848.0526.25 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #3: DH270.6 variable heavy chain

MacromoleculeName: DH270.6 variable heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.25681 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAQ MKNPGASVKV SCAPSGYTFT DFYIHWLRQA PGQGLQWMGW MNPQTGRTNT ARNFQGRVTM TRDTSIGTAY MELRSLTSD DTAIYYCTTG GWISLYYDSS YYPNFDHWGQ GTLLTVSS

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Macromolecule #4: DH270.6 variable light chain

MacromoleculeName: DH270.6 variable light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.510762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTKYDVG SHDLVSWYQQ YPGKVPKYMI YEVNKRPSGV SNRFSGSKSG NTASLTISGL RAEDEADYY CCSFGGSATV VCGGGTKVTV L

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 6 / 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

Concentration1.5 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.1 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119542
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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