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- EMDB-21961: Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited,... -

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Basic information

Entry
Database: EMDB / ID: EMD-21961
TitleCryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA trimer
Map dataSharpened map
Sample
  • Complex: 1D12 in complex with an H7 SH13 HA trimer
    • Complex: H7 SH13 HA trimer
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
    • Complex: 1D12 Fab
      • Protein or peptide: 1D12 Light chain
      • Protein or peptide: 1D21 Heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus / Homo sapiens (human) / Influenza A virus (A/Shanghai/JS01/2013(H7N9))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsGorman J / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Structure / Year: 2022
Title: Structure of an influenza group 2-neutralizing antibody targeting the hemagglutinin stem supersite.
Authors: Crystal Sao-Fong Cheung / Jason Gorman / Sarah F Andrews / Reda Rawi / Mateo Reveiz / Chen-Hsiang Shen / Yiran Wang / Darcy R Harris / Alexandra F Nazzari / Adam S Olia / Julie Raab / I-Ting ...Authors: Crystal Sao-Fong Cheung / Jason Gorman / Sarah F Andrews / Reda Rawi / Mateo Reveiz / Chen-Hsiang Shen / Yiran Wang / Darcy R Harris / Alexandra F Nazzari / Adam S Olia / Julie Raab / I-Ting Teng / Raffaello Verardi / Shuishu Wang / Yongping Yang / Gwo-Yu Chuang / Adrian B McDermott / Tongqing Zhou / Peter D Kwong /
Abstract: Several influenza antibodies with broad group 2 neutralization have recently been isolated. Here, we analyze the structure, class, and binding of one of these antibodies from an H7N9 vaccine trial, ...Several influenza antibodies with broad group 2 neutralization have recently been isolated. Here, we analyze the structure, class, and binding of one of these antibodies from an H7N9 vaccine trial, 315-19-1D12. The cryo-EM structure of 315-19-1D12 Fab in complex with the hemagglutinin (HA) trimer revealed the antibody to recognize the helix A region of the HA stem, at the supersite of vulnerability recognized by group 1-specific and by cross-group-neutralizing antibodies. 315-19-1D12 was derived from HV1-2 and KV2-28 genes and appeared to form a new antibody class. Bioinformatic analysis indicated its group 2 neutralization specificity to be a consequence of four key residue positions. We specifically tested the impact of the group 1-specific N33 glycan, which decreased but did not abolish group 2 binding of 315-19-1D12. Overall, this study highlights the recognition of a broad group 2-neutralizing antibody, revealing unexpected diversity in neutralization specificity for antibodies that recognize the HA stem supersite.
History
DepositionMay 11, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wxl
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21961.png

Downloads & links

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Map

FileDownload / File: emd_21961.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.083 Å
Density
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.6
Minimum - Maximum-7.2338057 - 11.215036
Average (Standard dev.)0.0055630556 (±0.21956788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 433.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0831.0831.083
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z433.200433.200433.200
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-7.23411.2150.006

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Supplemental data

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Mask #1

Fileemd_21961_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_21961_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap A

Fileemd_21961_half_map_1.map
AnnotationHalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap B

Fileemd_21961_half_map_2.map
AnnotationHalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 1D12 in complex with an H7 SH13 HA trimer

EntireName: 1D12 in complex with an H7 SH13 HA trimer
Components
  • Complex: 1D12 in complex with an H7 SH13 HA trimer
    • Complex: H7 SH13 HA trimer
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
    • Complex: 1D12 Fab
      • Protein or peptide: 1D12 Light chain
      • Protein or peptide: 1D21 Heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 1D12 in complex with an H7 SH13 HA trimer

SupramoleculeName: 1D12 in complex with an H7 SH13 HA trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: H7 SH13 HA trimer

SupramoleculeName: H7 SH13 HA trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: 1D12 Fab

SupramoleculeName: 1D12 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Shanghai/JS01/2013(H7N9)) / Strain: A/Shanghai/JS01/2013(H7N9)
Molecular weightTheoretical: 35.039473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNIPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KEAMGFTYSG IRTNGATSSC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRKNPAL ...String:
DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNIPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KEAMGFTYSG IRTNGATSSC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRKNPAL IVWGIHHSGS TAEQTKLYGS GNKLVTVGSS NYQQSFVPSP GARTQVNGQS GRIDFHWLML NPNDTVTFSF NG AFIAPDR ASFLRGKSMG IQSGVQVDAD CEGDCYYSGG TIISNLPFQN IDSRAVGKCP RYVKQRSLLL ATGMKNVPEI PKG R

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Shanghai/JS01/2013(H7N9)) / Strain: A/Shanghai/JS01/2013(H7N9)
Molecular weightTheoretical: 25.234352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI ENGWEGLIDG WYGFRHQNAQ GEGTAADYKS TQSAIDQITG KLNRLIEKTN QQFELIDNEF TEVEKQIGNV INWTRDSIT EVWSYNAELL VAMENQHTID LADSEMDKLY ERVKRQLREN AEEDGTGCFE IFHKCDDDCM ASIRNNTYDH S KYREEAMQ ...String:
GLFGAIAGFI ENGWEGLIDG WYGFRHQNAQ GEGTAADYKS TQSAIDQITG KLNRLIEKTN QQFELIDNEF TEVEKQIGNV INWTRDSIT EVWSYNAELL VAMENQHTID LADSEMDKLY ERVKRQLREN AEEDGTGCFE IFHKCDDDCM ASIRNNTYDH S KYREEAMQ NRIQIDPVKL SSGYKDVILW FSFGASCFIL LAIAMGLVFI CVKNGNMRCT ICI

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Macromolecule #3: 1D12 Light chain

MacromoleculeName: 1D12 Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.971762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPLS LSVTPGEPAS ISCRSSHSLL HLNGYNYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG IYYCMQALRT PPGLTFGGGT KVDIKRTVAA PSVFIFPPSE DQVKSGTVSV VCLLNNFYPR EASVKWKVDG A LKTGNSQE ...String:
DIVMTQSPLS LSVTPGEPAS ISCRSSHSLL HLNGYNYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG IYYCMQALRT PPGLTFGGGT KVDIKRTVAA PSVFIFPPSE DQVKSGTVSV VCLLNNFYPR EASVKWKVDG A LKTGNSQE SVTEQDSKDN TYSLSSTLTL SSTEYQSHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #4: 1D21 Heavy chain

MacromoleculeName: 1D21 Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.042229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLVQSGAEVK KPGASVKVSC KASGYTFTGY YLHWVRQAPG QGLEWMGRIN PDTGGTNYAQ KFQGRVSMTR DMSISTHYME LSRLTSDDT AVYYCATKRG AVTAMVYYYF YGMDVWGQGT TVTVSSASTK GPSVFPLAPS SESTAALGCL VKDYFPEPVT V SWNSGSLT ...String:
QLVQSGAEVK KPGASVKVSC KASGYTFTGY YLHWVRQAPG QGLEWMGRIN PDTGGTNYAQ KFQGRVSMTR DMSISTHYME LSRLTSDDT AVYYCATKRG AVTAMVYYYF YGMDVWGQGT TVTVSSASTK GPSVFPLAPS SESTAALGCL VKDYFPEPVT V SWNSGSLT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYVCNVNH KPSNTKVDKR VEIKTCGGLE VLFQ

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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

Concentration2 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsCryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1878 / Average exposure time: 2.0 sec. / Average electron dose: 49.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 142628

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Atomic model buiding 1

Initial model(PDB ID:

4hk0

,

6idd

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6wxl:
Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA trimer

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