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- EMDB-22804: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-22804
TitleCryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
Map dataSharpened Map
Sample
  • Complex: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
    • Complex: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Fusion protein of Hemagglutinin and Envelope glycoprotein
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light 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 / 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 B / Fibritin C-terminal / Fibritin C-terminal region / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Envelope glycoprotein
Similarity search - Component
Biological speciesInfluenza A virus / Human immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsGorman J / Kwong PD
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSF349247 United States
Other privateAgouron Institute (F00316) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH S10 OD019994-01 United States
CitationJournal: Front Immunol / Year: 2021
Title: Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses.
Authors: Gwo-Yu Chuang / Chen-Hsiang Shen / Crystal Sao-Fong Cheung / Jason Gorman / Adrian Creanga / M Gordon Joyce / Kwanyee Leung / Reda Rawi / Lingshu Wang / Eun Sung Yang / Yongping Yang / ...Authors: Gwo-Yu Chuang / Chen-Hsiang Shen / Crystal Sao-Fong Cheung / Jason Gorman / Adrian Creanga / M Gordon Joyce / Kwanyee Leung / Reda Rawi / Lingshu Wang / Eun Sung Yang / Yongping Yang / Baoshan Zhang / Yi Zhang / Masaru Kanekiyo / Tongqing Zhou / Brandon J DeKosky / Barney S Graham / John R Mascola / Peter D Kwong /
Abstract: Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly ...Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
History
DepositionOct 4, 2020-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kc1
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kc1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22804.png

Downloads & links

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Map

FileDownload / File: emd_22804.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Voxel sizeX=Y=Z: 1.07325 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.9034209 - 2.763516
Average (Standard dev.)0.008714546 (±0.07081852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 377.78403 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z377.784377.784377.784
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.9032.7640.009

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Supplemental data

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Mask #1

Fileemd_22804_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_22804_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_22804_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_22804_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex w...

EntireName: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
Components
  • Complex: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
    • Complex: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Fusion protein of Hemagglutinin and Envelope glycoprotein
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex w...

SupramoleculeName: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex w...

SupramoleculeName: Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 38.515629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN ...String:
MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN WLTQLNFKYP ALNVTMPNNE QFDKLYIWGV HHPVTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGYRPR IR NIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCNSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK QSTLKLATGM RNVPEKQTR

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Macromolecule #2: Fusion protein of Hemagglutinin and Envelope glycoprotein

MacromoleculeName: Fusion protein of Hemagglutinin and Envelope glycoprotein
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 25.259078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN NRFQIKGVSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

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Macromolecule #3: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.292277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIQLQQSGPG LVKPSQTLSL TCSISGDTVT NNYAAWDWIR QSPTRGLEWL GRTFYRSKWY KEYALSVKSR LTISPDTSKN QISLQLSSV TPEDTAVYYC ARAGITIFGL ITGGLDYWGQ GSLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QIQLQQSGPG LVKPSQTLSL TCSISGDTVT NNYAAWDWIR QSPTRGLEWL GRTFYRSKWY KEYALSVKSR LTISPDTSKN QISLQLSSV TPEDTAVYYC ARAGITIFGL ITGGLDYWGQ GSLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEP

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Macromolecule #4: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.450832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTQSPSSLSA SVGDRVTITC RTSQSLSSYT HWYQQKPGKA PKLLIYAASS RGSGVPSRFS GSGSGTDFTL TISSLQPEDF ATYYCQQSR TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ D SKDSTYSL ...String:
MTQSPSSLSA SVGDRVTITC RTSQSLSSYT HWYQQKPGKA PKLLIYAASS RGSGVPSRFS GSGSGTDFTL TISSLQPEDF ATYYCQQSR TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ D SKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGE

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration2.0 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10024 / Average exposure time: 10.0 sec. / Average electron dose: 71.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 29735
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.14)

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Atomic model buiding 1

Initial modelPDB ID:

4o5n

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7kc1:
Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA

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