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- EMDB-40273: CryoEM structure of VRC01-CH848.0358.80 -

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Basic information

Entry
Database: EMDB / ID: EMD-40273
TitleCryoEM structure of VRC01-CH848.0358.80
Map data
Sample
  • Complex: VRC01-CH848.0358.80
    • Protein or peptide: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp120
    • Protein or peptide: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp41
    • Protein or peptide: VCR01 variable heavy chain
    • Protein or peptide: VCR01 variable light chain
KeywordsHIV-1 / antibody / VRC01 / CH848.0358.80 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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: 4.9 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-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40273.png

Downloads & links

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Map

FileDownload / File: emd_40273.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.)
1.07 Å/pix.
x 320 pix.
= 341.12 Å		1.07 Å/pix.
x 320 pix.
= 341.12 Å		1.07 Å/pix.
x 320 pix.
= 341.12 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: 0.03
Minimum - Maximum-0.05368934 - 0.13912594
Average (Standard dev.)0.00031178814 (±0.005996231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 341.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40273_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40273_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40273_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : VRC01-CH848.0358.80

EntireName: VRC01-CH848.0358.80
Components
  • Complex: VRC01-CH848.0358.80
    • Protein or peptide: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp120
    • Protein or peptide: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp41
    • Protein or peptide: VCR01 variable heavy chain
    • Protein or peptide: VCR01 variable light chain

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Supramolecule #1: VRC01-CH848.0358.80

SupramoleculeName: VRC01-CH848.0358.80 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp120

MacromoleculeName: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Molecular weightTheoretical: 53.415699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLKNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL NCSNARSNVN VTSINNTIMG EMKNCSFNTT TEIRDKEKKE YALFYKPDVV PLNETSNTSE Y RLINCNTS ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLKNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL NCSNARSNVN VTSINNTIMG EMKNCSFNTT TEIRDKEKKE YALFYKPDVV PLNETSNTSE Y RLINCNTS ACTQACPKVT FEPIPIHYCA PAGYAILKCN NKTFNGTGPC SNVSTVQCTH GIRPVVSTQL LLNGSLAEKE IV IRSENLT NNAKIIIVHL NTSVEIVCTR PGNNTRKSVR IGPGQTFYAT GDIIGDIRQA HCNISEGQWN KTLHEVSKEL QKH FPNKTI KYERSAGGDM EIATHSFNCG GEFFYCNTSN LFNGTYNGTY INTSSTSYIT LQCRIKQIIN MWQGVGRCMY APPI AGNIT CKSNITGLLL TRDGGTKNNS NEETFRPAGG DMRDNWRSEL YKYKVVKIEP LGVAPTRCKR RVVGRRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp41

MacromoleculeName: CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP 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: VCR01 variable heavy chain

MacromoleculeName: VCR01 variable heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.801701 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVD DTAVYFCTRG KNCDYNWDFE HWGRGTPVIV SS

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Macromolecule #4: VCR01 variable light chain

MacromoleculeName: VCR01 variable light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.270421 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGETAI ISCRTSQYGS (UNK)(UNK)LAWYQQRP GQAPRLVIYS GSTRAAGIPD RFSGSRWGPD YN LTISNLE SGDFGVYYCQ QYEFFGQGTK VQVD

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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
DetailsVRC01-CH848.0358.80

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46336
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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