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- EMDB-25730: Cryo-EM structure of full-length hepatitis C virus E1E2 glycoprot... -

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Entry
Database: EMDB / ID: EMD-25730
TitleCryo-EM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009, and IGH505 Fabs
Map dataSharpened non-focused map of the full complex
Sample
  • Complex: cryoEM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009 and IGH505 Fabs
    • Protein or peptide: Envelope glycoprotein E2
    • Protein or peptide: AR4A Fab, heavy chain
    • Protein or peptide: AR4A, kappa light chain
    • Protein or peptide: IGH505, heavy chain
    • Protein or peptide: IGH505, lambda light chain
    • Protein or peptide: AT12009 crossMab, light kappa chain
    • Protein or peptide: AT12009 CrossMab, heavy chain
    • Protein or peptide: Envelope glycoprotein E1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / virus-mediated perturbation of host defense response / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / virion membrane ...host cell mitochondrial membrane / host cell lipid droplet / virus-mediated perturbation of host defense response / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / virion membrane / structural molecule activity / membrane / cytoplasm
Similarity search - Function
Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1
Similarity search - Domain/homology
Biological speciesHepacivirus C / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsTorrents de la Pena A / Ward AB / Eshun-Wilson L / Lander GC
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Science / Year: 2022
Title: Structure of the hepatitis C virus E1E2 glycoprotein complex.
Authors: Alba Torrents de la Peña / Kwinten Sliepen / Lisa Eshun-Wilson / Maddy L Newby / Joel D Allen / Ian Zon / Sylvie Koekkoek / Ana Chumbe / Max Crispin / Janke Schinkel / Gabriel C Lander / ...Authors: Alba Torrents de la Peña / Kwinten Sliepen / Lisa Eshun-Wilson / Maddy L Newby / Joel D Allen / Ian Zon / Sylvie Koekkoek / Ana Chumbe / Max Crispin / Janke Schinkel / Gabriel C Lander / Rogier W Sanders / Andrew B Ward /
Abstract: Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope ...Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope E1 and E2 glycoproteins are essential for viral entry and comprise the primary antigenic target for neutralizing antibody responses. The molecular mechanisms of E1E2 assembly, as well as how the E1E2 heterodimer binds broadly neutralizing antibodies, remain elusive. Here, we present the cryo-electron microscopy structure of the membrane-extracted full-length E1E2 heterodimer in complex with three broadly neutralizing antibodies-AR4A, AT1209, and IGH505-at ~3.5-angstrom resolution. We resolve the interface between the E1 and E2 ectodomains and deliver a blueprint for the rational design of vaccine immunogens and antiviral drugs.
History
DepositionDec 14, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25730.png

Downloads & links

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Map

FileDownload / File: emd_25730.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened non-focused map of the full complex
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.60087013 - 1.2189401
Average (Standard dev.)0.0002346476 (±0.024856634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25730_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite sharpened map of the complex generated from...

Fileemd_25730_additional_1.map
AnnotationComposite sharpened map of the complex generated from multiple focused maps of different sub-regions of the complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened non-focused map of the full complex

Fileemd_25730_additional_2.map
AnnotationUnsharpened non-focused map of the full complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of sharpened non-focused map of full complex

Fileemd_25730_half_map_1.map
AnnotationHalf map of sharpened non-focused map of full complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of sharpened non-focused map of full complex

Fileemd_25730_half_map_2.map
AnnotationHalf map of sharpened non-focused map of full complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryoEM structure of full-length hepatitis C virus E1E2 glycoprote...

EntireName: cryoEM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009 and IGH505 Fabs
Components
  • Complex: cryoEM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009 and IGH505 Fabs
    • Protein or peptide: Envelope glycoprotein E2
    • Protein or peptide: AR4A Fab, heavy chain
    • Protein or peptide: AR4A, kappa light chain
    • Protein or peptide: IGH505, heavy chain
    • Protein or peptide: IGH505, lambda light chain
    • Protein or peptide: AT12009 crossMab, light kappa chain
    • Protein or peptide: AT12009 CrossMab, heavy chain
    • Protein or peptide: Envelope glycoprotein E1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: cryoEM structure of full-length hepatitis C virus E1E2 glycoprote...

SupramoleculeName: cryoEM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009 and IGH505 Fabs
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Hepacivirus C / Strain: AMS0232

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Macromolecule #1: Envelope glycoprotein E2

MacromoleculeName: Envelope glycoprotein E2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepacivirus C
Molecular weightTheoretical: 40.156699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTYVTGGTAA RATSGLANFF SPGAKQDVQL INTNGSWHIN RTALNCNTSL ETGWIAGLIY LNKFNSSGCP ERMASCRPLA DFAQGWGPI SYANGSGPDH RPYCWHYPPK PCGIVSAKSV CGPVYCFTPS PVVVGTTNKL GAPTYSWGEN ETDVFVLNNT R PPLGNWFG ...String:
QTYVTGGTAA RATSGLANFF SPGAKQDVQL INTNGSWHIN RTALNCNTSL ETGWIAGLIY LNKFNSSGCP ERMASCRPLA DFAQGWGPI SYANGSGPDH RPYCWHYPPK PCGIVSAKSV CGPVYCFTPS PVVVGTTNKL GAPTYSWGEN ETDVFVLNNT R PPLGNWFG CTWMNSTGFT KVCGAPPCAI GGVGNNTLHC PTDCFRKHPE ATYSRCGSGP WITPRCLVDY PYRLWHYPCT IN YTRFKVR MYIGGVEHRL DAACNWTRGE RCDLEDRDRS ELSPLLLSTT QWQVLPCSFT TLPALSTGLI HLHQNIVDVQ YLY GVGSSI VSWAIKWEYV VLLFLLLADA RVCSCLWMML LISQAEA

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Macromolecule #2: AR4A Fab, heavy chain

MacromoleculeName: AR4A Fab, heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.8085 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHEV QLLEQSGPEV KKPGDSLRIS CKMSGDSLVT TWIGWVRQKP GQGLEWMGII NPGDSSTNIY PGDSATRYG PSFQGQVTIS IDKSTSTAYL QWNNVKASDT GIYYCARHVP VPISGTFLWR EREMHDFGYF DDWGQGTLVI V SSASTKGP ...String:
MGWSCIILFL VATATGVHEV QLLEQSGPEV KKPGDSLRIS CKMSGDSLVT TWIGWVRQKP GQGLEWMGII NPGDSSTNIY PGDSATRYG PSFQGQVTIS IDKSTSTAYL QWNNVKASDT GIYYCARHVP VPISGTFLWR EREMHDFGYF DDWGQGTLVI V SSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GT QTYICNV NHKPSNTKVD KRVEPKSCGG SAWSHPQFEK

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Macromolecule #3: AR4A, kappa light chain

MacromoleculeName: AR4A, kappa light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.290209 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHEL TLTQSPGTLS LSPGERATLS CRASQSVSNN YLAWYQQKPG QAPRLLIYGA SSRATGIPDR FSGSGSGTG FTLIISRLEP EDFAVYYCQQ YGSSSITFGQ GTRLEIKRTA AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHEL TLTQSPGTLS LSPGERATLS CRASQSVSNN YLAWYQQKPG QAPRLLIYGA SSRATGIPDR FSGSGSGTG FTLIISRLEP EDFAVYYCQQ YGSSSITFGQ GTRLEIKRTA AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #4: IGH505, heavy chain

MacromoleculeName: IGH505, heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.277027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLSWLFL VAILAQPAMA QVQFVQSGAE VKKPGASVKV SCKASGYTFT RHAIHWVRQA PGQRLEWMGW INPGNGNAKY SQKFQGRVT ITRDTPASTV YMELSSLRSE DMGVYYCARD GGYSHDYSYF YGLDVWGPGT TVIVSSASTK GPSVFPLAPS S KSTSGGTA ...String:
MELGLSWLFL VAILAQPAMA QVQFVQSGAE VKKPGASVKV SCKASGYTFT RHAIHWVRQA PGQRLEWMGW INPGNGNAKY SQKFQGRVT ITRDTPASTV YMELSSLRSE DMGVYYCARD GGYSHDYSYF YGLDVWGPGT TVIVSSASTK GPSVFPLAPS S KSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VD KRVEPKS CDKTHTCPPC PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPR EEQYNS TYRVVSVLTV LHQDWLNGKE YKCKVSNKAL PAPIEKTISK AKGQPREPQV YTLPPSREEM TKNQVSLTCL VKGF YPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK

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Macromolecule #5: IGH505, lambda light chain

MacromoleculeName: IGH505, lambda light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.974764 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METPAQLLFL LLLWLPGSTQ SVLTQPPSAA SGTPGQRVTI SCSGSSSNIG GNFVDWYQQF PGTAPKLLIY TNDQRPSGVP ARFSGSKSG TSASLAISGL RSEDEADYYC AAWDDIVNGW VFGGGTKLEI KRTAAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
METPAQLLFL LLLWLPGSTQ SVLTQPPSAA SGTPGQRVTI SCSGSSSNIG GNFVDWYQQF PGTAPKLLIY TNDQRPSGVP ARFSGSKSG TSASLAISGL RSEDEADYYC AAWDDIVNGW VFGGGTKLEI KRTAAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #6: AT12009 crossMab, light kappa chain

MacromoleculeName: AT12009 crossMab, light kappa chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.014084 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHEI MLTQSPVTLS VSPGERATLS CRASQSIGTN LAWYQKPGQA PRLLIHGAST RATGVPVSFS GSGSGTEFT LTISSLQSED FAVYYCQQYN NWPLTFGGGT KVEIKSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
MGWSCIILFL VATATGVHEI MLTQSPVTLS VSPGERATLS CRASQSIGTN LAWYQKPGQA PRLLIHGAST RATGVPVSFS GSGSGTEFT LTISSLQSED FAVYYCQQYN NWPLTFGGGT KVEIKSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS C

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Macromolecule #7: AT12009 CrossMab, heavy chain

MacromoleculeName: AT12009 CrossMab, heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.151678 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VLVQSGAEVK KPGSSVRVSC KASGDTFKTH AISWVRQAPG QGLEWVGGTV RQAPGDGLEL LGGFVPILA PANDAQKFQG RVTITADGST GPVYMDLSTL TSEDTAMYYC VTSLSEPIPR SCRGGRCYSG PFDAFGVWGQ G TLVTVSSA ...String:
MGWSCIILFL VATATGVHSQ VLVQSGAEVK KPGSSVRVSC KASGDTFKTH AISWVRQAPG QGLEWVGGTV RQAPGDGLEL LGGFVPILA PANDAQKFQG RVTITADGST GPVYMDLSTL TSEDTAMYYC VTSLSEPIPR SCRGGRCYSG PFDAFGVWGQ G TLVTVSSA SVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LT LSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #8: Envelope glycoprotein E1

MacromoleculeName: Envelope glycoprotein E1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepacivirus C
Molecular weightTheoretical: 20.956279 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YQVRNSTGLY HVTNDCPNSS IVYETADAIL HTPGCVPCVR EGNASRCWVP MTPTVATRDG KLPATQLRRH IDLLVGSATL CSALYVGDL CGSVFLVGQL FTFSPRRHWT TQDCNCSIYP GHVTGHRMAW DMMMNWSPTT ALVVAQLLRI PQAILDMIAG A HWGVLAGL ...String:
YQVRNSTGLY HVTNDCPNSS IVYETADAIL HTPGCVPCVR EGNASRCWVP MTPTVATRDG KLPATQLRRH IDLLVGSATL CSALYVGDL CGSVFLVGQL FTFSPRRHWT TQDCNCSIYP GHVTGHRMAW DMMMNWSPTT ALVVAQLLRI PQAILDMIAG A HWGVLAGL AYFSMVGNWA KVLAVLLLFA GVDA

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 6 / 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

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
25.0 mMTRIS hydrochloride
150.0 mMsodium ChlorideNaClSodium chloride

Details: TBS buffer, pH 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 40 K / Instrument: FEI VITROBOT MARK IV
Details: Blotting time: 5 s; Blotting force: 0; Waiting time: 7 s.
DetailsFull-length hepatitis C virus E1E2 glycoprotein complexed with AR4A, AT12009, and IGH505 Fabs and embedded in peptidiscs is diluted in TBS to a final concentration of 0.8 mg/ml.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.12 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 5121 / Average exposure time: 9.0 sec. / Average electron dose: 50.0 e/Å2
Details: images were collected at 250 ms per frame. 36 frames were collected.
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2017845
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: NONE
Details: None for E1 and E2 and homology model for AR4A, AT12009, and IGH505 Fabs.
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v3.2.0)
Details: We used the Ab initio feature in cryoSPARC to generate an initial model.
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3.2.0)
Details: We used the Non-Uniform Refinement feature in cryoSPARC.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48546
FSC plot (resolution estimation)

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