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- EMDB-44739: HIV Envelope trimer CH505 SOSIP.664 in complex with wild type CH1... -

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Basic information

Entry
Database: EMDB / ID: EMD-44739
TitleHIV Envelope trimer CH505 SOSIP.664 in complex with wild type CH103 antibody
Map dataHIV Envelope trimer CH505 SOSIP.664 in complex with wild type CH103 antibody
Sample
  • Complex: Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs
    • Complex: CH505 SOSIP Trimer
    • Complex: CH103 wildtype Fab
    • Complex: CH103 wildtype Fab
    • Complex: CH103 wildtype Fab
KeywordsHIV Envelope Antibody Complex / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 12.0 Å
AuthorsEdwards RJ / Mansouri K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144371 United States
CitationJournal: Structure / Year: 2025
Title: Acquisition of quaternary trimer interaction as a key step in the lineage maturation of a broad and potent HIV-1 neutralizing antibody.
Authors: Qingbo Liu / Ruth J Parsons / Kevin Wiehe / Robert J Edwards / Kevin O Saunders / Peng Zhang / Huiyi Miao / Kedamawit Tilahun / Julia Jones / Yue Chen / Bhavna Hora / Wilton B Williams / ...Authors: Qingbo Liu / Ruth J Parsons / Kevin Wiehe / Robert J Edwards / Kevin O Saunders / Peng Zhang / Huiyi Miao / Kedamawit Tilahun / Julia Jones / Yue Chen / Bhavna Hora / Wilton B Williams / David Easterhoff / Xiao Huang / Katarzyna Janowska / Katayoun Mansouri / Barton F Haynes / Priyamvada Acharya / Paolo Lusso /
Abstract: Although most broadly neutralizing antibodies (bNAbs) specific for the CD4-binding site (CD4-BS) of HIV-1 interact with a single gp120 protomer, a few mimic the quaternary binding mode of CD4, making ...Although most broadly neutralizing antibodies (bNAbs) specific for the CD4-binding site (CD4-BS) of HIV-1 interact with a single gp120 protomer, a few mimic the quaternary binding mode of CD4, making contact with a second protomer through elongated heavy chain framework 3 (FRH3) or complementarity-determining region 1 (CDRH1) loops. Here, we show that a CDRH3-dominated anti-CD4-BS bNAb, CH103, establishes quaternary interaction despite regular-length FRH3 and CDRH1. This quaternary interaction is critical for neutralization and is primarily mediated by two FRH3 acidic residues that were sequentially acquired and subjected to strong positive selection during CH103 maturation. Cryoelectron microscopy (cryo-EM) structures confirmed the role of the two FRH3 acidic residues in mediating quaternary contact and demonstrated that CH103 reaches the adjacent gp120 protomer by virtue of its unique angle of approach. Thus, the acquisition of quaternary interaction may constitute a key step in the lineage maturation of a broad and potent HIV-1 neutralizing antibody.
History
DepositionMay 3, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44739.png

Downloads & links

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Map

FileDownload / File: emd_44739.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV Envelope trimer CH505 SOSIP.664 in complex with wild type CH103 antibody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 160 pix.
= 336. Å		2.1 Å/pix.
x 160 pix.
= 336. Å		2.1 Å/pix.
x 160 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0206
Minimum - Maximum-0.034393445 - 0.0677065
Average (Standard dev.)0.0005828834 (±0.0054747583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CH505 complex with CH103 wildtype halfmap

Fileemd_44739_half_map_1.map
AnnotationCH505 complex with CH103 wildtype halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CH505 complex with CH103 wildtype halfmap

Fileemd_44739_half_map_2.map
AnnotationCH505 complex with CH103 wildtype halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs

EntireName: Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs
Components
  • Complex: Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs
    • Complex: CH505 SOSIP Trimer
    • Complex: CH103 wildtype Fab
    • Complex: CH103 wildtype Fab
    • Complex: CH103 wildtype Fab

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Supramolecule #1: Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs

SupramoleculeName: Complex of CH505 SOSIP.664 with three CH103 wildtype Fabs
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 46 KDa

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Supramolecule #2: CH505 SOSIP Trimer

SupramoleculeName: CH505 SOSIP Trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: CH505

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Supramolecule #3: CH103 wildtype Fab

SupramoleculeName: CH103 wildtype Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Strain: BG505

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Supramolecule #4: CH103 wildtype Fab

SupramoleculeName: CH103 wildtype Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: CH103 wildtype Fab

SupramoleculeName: CH103 wildtype Fab / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPESHEPES buffer
5.0 mMNaN3sodium azide
StainingType: NEGATIVE / Material: uranyl formate
Details: Quenched sample was applied to a glow-discharged carbon-coated 300 mesh EM grid for 10 seconds, blotted and stained with 2 g/dL uranyl formate for 1 minute, blotted and air dried.
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
DetailsComplex formed by incubating 20 micrograms trimer with 36 micrograms Fab overnight at 4 degrees C, followed by SEC purification over a Superose 6 Increase 10 300 column. Purified complex was concentrated to 1-2 mg/ml with a 100 kDA spin concentrator, then diluted with buffer containing 8 mM glutaraldehyde and incubated for 5 minutes. Excess glutaraldehyde was quenched by adding 1 M Tris buffer to a final Tris concentration of 80 mM.

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Electron microscopy

MicroscopeFEI/PHILIPS EM420
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 8736 pixel / Digitization - Dimensions - Height: 8740 pixel / Number grids imaged: 1 / Number real images: 130 / Average exposure time: 0.25 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Particle selectionNumber selected: 345464
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uda


Details: Low-pass filtered at 60 angstroms
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 39615
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 9 / Avg.num./class: 16667 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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