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- EMDB-0433: AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targe... -

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Basic information

Entry
Database: EMDB / ID: EMD-0433
TitleAMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding
Map datasharpened map
Sample
  • Complex: Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen binding
    • Complex: HIV-1 Env AMC011 v4.2 SOSIP gp120
      • Protein or peptide: AMC011 v4.2 SOSIP gp120
    • Complex: HIV-1 Env AMC011 v4.2 SOSIP gp41
      • Protein or peptide: AMC011 v4.2 SOSIP gp41
    • Complex: VRC34.01
      • Protein or peptide: Monoclonal antibody ACS202 fragment antigen binding heavy chain
      • Protein or peptide: Monoclonal antibody ACS202 fragment antigen binding kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / membrane => GO:0016020 / viral envelope / structural molecule activity / host cell plasma membrane / virion membrane / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsOzorowski G / de Val N / Cottrell CA / Copps J / Ward AB
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
Bill & Melinda Gates FoundationOPP1084519 United States
Bill & Melinda Gates FoundationOPP1115782 United States
Other private109718-63-RKNT United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 Al131873 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies.
Authors: Meng Yuan / Christopher A Cottrell / Gabriel Ozorowski / Marit J van Gils / Sonu Kumar / Nicholas C Wu / Anita Sarkar / Jonathan L Torres / Natalia de Val / Jeffrey Copps / John P Moore / ...Authors: Meng Yuan / Christopher A Cottrell / Gabriel Ozorowski / Marit J van Gils / Sonu Kumar / Nicholas C Wu / Anita Sarkar / Jonathan L Torres / Natalia de Val / Jeffrey Copps / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson /
Abstract: The fusion peptide (FP) of HIV-1 envelope glycoprotein (Env) is essential for mediating viral entry. Detection of broadly neutralizing antibodies (bnAbs) that interact with the FP has revealed it as ...The fusion peptide (FP) of HIV-1 envelope glycoprotein (Env) is essential for mediating viral entry. Detection of broadly neutralizing antibodies (bnAbs) that interact with the FP has revealed it as a site of vulnerability. We delineate X-ray and cryo-electron microscopy (cryo-EM) structures of bnAb ACS202, from an HIV-infected elite neutralizer, with an FP and with a soluble Env trimer (AMC011 SOSIP.v4.2) derived from the same patient. We show that ACS202 CDRH3 forms a "β strand" interaction with the exposed hydrophobic FP and recognizes a continuous region of gp120, including a conserved N-linked glycan at N88. A cryo-EM structure of another previously identified bnAb VRC34.01 with AMC011 SOSIP.v4.2 shows that it also penetrates through glycans to target the FP. We further demonstrate that the FP can twist and present different conformations for recognition by bnAbs, which enables approach to Env from diverse angles. The variable recognition of FP by bnAbs thus provides insights for vaccine design.
History
DepositionDec 10, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJun 19, 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nc2
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0433.png

Downloads & links

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Map

FileDownload / File: emd_0433.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.030829472 - 0.09938333
Average (Standard dev.)0.0015213995 (±0.008293105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0310.0990.002

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Supplemental data

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Mask #1

Fileemd_0433_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_0433_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_0433_half_map_2.map
AnnotationHalf map 1
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 AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen b...

EntireName: Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen binding
Components
  • Complex: Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen binding
    • Complex: HIV-1 Env AMC011 v4.2 SOSIP gp120
      • Protein or peptide: AMC011 v4.2 SOSIP gp120
    • Complex: HIV-1 Env AMC011 v4.2 SOSIP gp41
      • Protein or peptide: AMC011 v4.2 SOSIP gp41
    • Complex: VRC34.01
      • Protein or peptide: Monoclonal antibody ACS202 fragment antigen binding heavy chain
      • Protein or peptide: Monoclonal antibody ACS202 fragment antigen binding kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen b...

SupramoleculeName: Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 570 KDa

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Supramolecule #2: HIV-1 Env AMC011 v4.2 SOSIP gp120

SupramoleculeName: HIV-1 Env AMC011 v4.2 SOSIP gp120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: HIV-1 Env AMC011 v4.2 SOSIP gp41

SupramoleculeName: HIV-1 Env AMC011 v4.2 SOSIP gp41 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: VRC34.01

SupramoleculeName: VRC34.01 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: AMC011 v4.2 SOSIP gp120

MacromoleculeName: AMC011 v4.2 SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.668938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEQLW VTVYYGVPVW KEATTTLFCA SDARAYDTEV RNVWATHACV PTDPNPQEV VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTDL RNATNTNATN TTSSSRGTME G GEIKNCSF ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAEQLW VTVYYGVPVW KEATTTLFCA SDARAYDTEV RNVWATHACV PTDPNPQEV VLENVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCTDL RNATNTNATN TTSSSRGTME G GEIKNCSF NITTSMRDKV QKEYALFYKL DVVPIKNDNT SYRLISCNTS VITQACPKVS FEPIPIHYCA PAGFAILKCN DK KFNGTGP CTNVSTVQCT HGIRPVVSTQ LLLNGSLAEE EVVIRSANFT DNAKIIIVQL NKSVEINCTR PNNNTRKSIH IGP GRWFYT TGEIIGDIRQ AHCNISGTKW NDTLKQIVVK LKEQFGNKTI VFNHSSGGDP EIVMHSFNCG GEFFYCNSTQ LFNS TWNDG SNYTGTIVLP CRIKQIVNMW QEVGKAMYAP PIKGQIRCSS NITGLILIRD GGKNRSENTE IFRPGGGDMR DNWRS ELYK YKVVKIEPLG IAPTKCKRRV VQRRRRRR

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Macromolecule #2: AMC011 v4.2 SOSIP gp41

MacromoleculeName: AMC011 v4.2 SOSIP gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.300666 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RQLLSGIVQQ QNNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICCTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELD

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Macromolecule #3: Monoclonal antibody ACS202 fragment antigen binding heavy chain

MacromoleculeName: Monoclonal antibody ACS202 fragment antigen binding heavy chain
type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.392023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEVHSQV QLVESGGGVV QPGGSLRLSC AASGFAFKDF GMHWVRQAPG KGLEWVAVIG GGHGQHQSYS ESVKGRFAI TRDNEKNKLY LHMDRLRTED TAVYYCAKDR LGRPWNIGGR LVYYYYGMDV WGQGTTVTVS SASTKGPSVF P LAPSSKST ...String:
MELGLRWVFL VAILEVHSQV QLVESGGGVV QPGGSLRLSC AASGFAFKDF GMHWVRQAPG KGLEWVAVIG GGHGQHQSYS ESVKGRFAI TRDNEKNKLY LHMDRLRTED TAVYYCAKDR LGRPWNIGGR LVYYYYGMDV WGQGTTVTVS SASTKGPSVF P LAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PS NTKVDKK VEPKSCD

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Macromolecule #4: Monoclonal antibody ACS202 fragment antigen binding kappa chain

MacromoleculeName: Monoclonal antibody ACS202 fragment antigen binding kappa chain
type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.475658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHCA IRMTQSPSSL SASVGDRVTI TCQASQDIKK SLNWYRQKPG KAPELLIHDA SILQTGVPSA FTASGSGTH FSFVINKLQP EDVGTYFCQE YENLQFTFGP GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHCA IRMTQSPSSL SASVGDRVTI TCQASQDIKK SLNWYRQKPG KAPELLIHDA SILQTGVPSA FTASGSGTH FSFVINKLQP EDVGTYFCQE YENLQFTFGP GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaClSodium chloride
0.06 mMn-dodecyl beta-D-maltoside

Details: Detergent (DDM) added immediately prior to grid preparation
GridModel: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus 950 Plasma system
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsSEC purified sample after overnight incubation of molar excess Fab to trimer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Number real images: 1641 / Average exposure time: 10.0 sec. / Average electron dose: 92.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: PDB coordinates converted to low pass filtered map
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 49878
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6nc2:
AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding

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