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- EMDB-51105: Dissociated FMDV SAT2 Pentamer in complex with ultralong Fab117 -

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Basic information

Entry
Database: EMDB / ID: EMD-51105
TitleDissociated FMDV SAT2 Pentamer in complex with ultralong Fab117
Map dataMap of SAT2 Foot and Mouth Disease pentamer unit with Fab117.
Sample
  • Complex: Complex of pentamer from Foot and Mouth Disease virus serotype SAT2 VLPs with Fab117.
    • Complex: Pentamer from Foot and Mouth Disease Virus serotype SAT2 VLPs
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
    • Complex: Fab117
      • Protein or peptide: Fab117 Heavy Chain
Keywordsdisrupted / dissociated / VLP / internal epitope / pan-specific / ultralong / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle) / Foot-and-mouth disease virus SAT 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsClarke JD / Duyvesteyn HME / Ren J / Fry EE / Owens RJ / Stuart DI / Hammond JA
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: J Gen Virol / Year: 2024
Title: A broadly reactive ultralong bovine antibody that can determine the integrity of foot-and-mouth disease virus capsids.
Authors: John D Clarke / Helen M E Duyvesteyn / Eva Perez-Martin / Undīne Latišenko / Claudine Porta / Kathleen V Humphreys / Abigail L Hay / Jingshan Ren / Elizabeth E Fry / Erwin van den Born / ...Authors: John D Clarke / Helen M E Duyvesteyn / Eva Perez-Martin / Undīne Latišenko / Claudine Porta / Kathleen V Humphreys / Abigail L Hay / Jingshan Ren / Elizabeth E Fry / Erwin van den Born / Bryan Charleston / Marie Bonnet-Di Placido / Raymond J Owens / David I Stuart / John A Hammond /
Abstract: Foot-and-mouth disease vaccination using inactivated virus is suboptimal, as the icosahedral viral capsids often disassemble into antigenically distinct pentameric units during long-term storage, or ...Foot-and-mouth disease vaccination using inactivated virus is suboptimal, as the icosahedral viral capsids often disassemble into antigenically distinct pentameric units during long-term storage, or exposure to elevated temperature or lowered pH, and thus raise a response that is no longer protective. Furthermore, as foot-and-mouth disease virus (FMDV)'s seven serotypes are antigenically diverse, cross-protection from a single serotype vaccine is limited, and most existing mouse and bovine antibodies and camelid single-domain heavy chain-only antibodies are serotype-specific. For quality control purposes, there is a real need for pan-serotype antibodies that clearly distinguish between pentamer (12S) and protective intact FMDV capsid. To date, few cross-serotype bovine-derived antibodies have been reported in the literature. We identify a bovine antibody with an ultralong CDR-H3, Ab117, whose structural analysis reveals that it binds to a deep, hydrophobic pocket on the interior surface of the capsid via the CDR-H3. Main-chain and hydrophobic interactions provide broad serotype specificity. ELISA analysis confirms that Ab117 is a novel pan-serotype and conformational epitope-specific 12S reagent, suitable for assessing capsid integrity.
History
DepositionJul 19, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51105.png

Downloads & links

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Map

FileDownload / File: emd_51105.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of SAT2 Foot and Mouth Disease pentamer unit with Fab117.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 288 pix.
= 303.552 Å		1.05 Å/pix.
x 288 pix.
= 303.552 Å		1.05 Å/pix.
x 288 pix.
= 303.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.344
Minimum - Maximum-3.88694 - 6.992956
Average (Standard dev.)0.0047465707 (±0.14026685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 303.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of SAT2 Foot and Mouth Disease pentamer unit with Fab117.

Fileemd_51105_half_map_1.map
AnnotationHalf map of SAT2 Foot and Mouth Disease pentamer unit with Fab117.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of SAT2 Foot and Mouth Disease pentamer unit with Fab117.

Fileemd_51105_half_map_2.map
AnnotationHalf map of SAT2 Foot and Mouth Disease pentamer unit with Fab117.
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 pentamer from Foot and Mouth Disease virus serotype SA...

EntireName: Complex of pentamer from Foot and Mouth Disease virus serotype SAT2 VLPs with Fab117.
Components
  • Complex: Complex of pentamer from Foot and Mouth Disease virus serotype SAT2 VLPs with Fab117.
    • Complex: Pentamer from Foot and Mouth Disease Virus serotype SAT2 VLPs
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
    • Complex: Fab117
      • Protein or peptide: Fab117 Heavy Chain

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Supramolecule #1: Complex of pentamer from Foot and Mouth Disease virus serotype SA...

SupramoleculeName: Complex of pentamer from Foot and Mouth Disease virus serotype SAT2 VLPs with Fab117.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #2: Pentamer from Foot and Mouth Disease Virus serotype SAT2 VLPs

SupramoleculeName: Pentamer from Foot and Mouth Disease Virus serotype SAT2 VLPs
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Foot-and-mouth disease virus SAT 2 / Strain: SAT2/ZIM/7/83

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Supramolecule #3: Fab117

SupramoleculeName: Fab117 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Bos taurus (domestic cattle) / Tissue: B-Lymphocyte

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus SAT 2 / Strain: SAT2/Zim/7/83
Molecular weightTheoretical: 24.160275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTSSGEGADV VTTDPSTHGG AVTEKKRVHT DVAFVMDRFT HVLTNRTAFA VDLMDTNEKT LVGALLRAAT YYFCDLEIAC LGEHERVWW QPNGAPRTTT LRDNPMVFSH NNVTRFAVPY TAPHRLLSTR YNGECKYTQQ STAIRGDRAV LAAKYANTKH K LPSTFNFG ...String:
TTSSGEGADV VTTDPSTHGG AVTEKKRVHT DVAFVMDRFT HVLTNRTAFA VDLMDTNEKT LVGALLRAAT YYFCDLEIAC LGEHERVWW QPNGAPRTTT LRDNPMVFSH NNVTRFAVPY TAPHRLLSTR YNGECKYTQQ STAIRGDRAV LAAKYANTKH K LPSTFNFG YVTADKPVDV YYRMKRAELY CPRPLLPGYD HADRDRFDSP IGVKKQ

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus SAT 2 / Strain: SAT2/Zim/7/83
Molecular weightTheoretical: 24.631531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKKTEETTLL EDRILTTRHG TTTSTTQSSV GITYGYADAD SFRPGPNTSG LETRVEQAER FFKEKLFDWT SDKPFGTLYV LELPKDHKG IYGYLTDAYT YMRNGWDVQV SATSTQFNGG SLLVAMVPEL CSLKDREEFQ LSLYPHQFIN PRTNTTAHIQ V PYLGVNRH ...String:
DKKTEETTLL EDRILTTRHG TTTSTTQSSV GITYGYADAD SFRPGPNTSG LETRVEQAER FFKEKLFDWT SDKPFGTLYV LELPKDHKG IYGYLTDAYT YMRNGWDVQV SATSTQFNGG SLLVAMVPEL CSLKDREEFQ LSLYPHQFIN PRTNTTAHIQ V PYLGVNRH DQGKRHQAWS LVVMVLTPLT TEAQMQSGTV EVYANIAPTN VFVAGEKPAK Q

UniProtKB: Genome polyprotein

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus SAT 2 / Strain: SAT2/Zim/7/83
Molecular weightTheoretical: 24.620328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIIPVACFDG YGGFQNTDPK TADPIYGYVY NPSRNDCHGR YSNLLDVAEA CPTFLNFDGK PYVVTKNNGD KVMTCFDVAF THKVHKNTF LAGLADYYAQ YQGSLNYHFM YTGPTHHKAK FMVAYIPPGI ETDRLPKTPE DAAHCYHSEW DTGLNSQFTF A VPYVSASD ...String:
GIIPVACFDG YGGFQNTDPK TADPIYGYVY NPSRNDCHGR YSNLLDVAEA CPTFLNFDGK PYVVTKNNGD KVMTCFDVAF THKVHKNTF LAGLADYYAQ YQGSLNYHFM YTGPTHHKAK FMVAYIPPGI ETDRLPKTPE DAAHCYHSEW DTGLNSQFTF A VPYVSASD FSYTHTDTPA MATTNGWVAV FQVTDTHSAE AAVVVSVSAG PDLEFRFPVD PVRQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Fab117 Heavy Chain

MacromoleculeName: Fab117 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Cell: B-Lymphocyte
Molecular weightTheoretical: 32.247385 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAQV QLRESGPSLV KPSQTLSLTC TASGFSLSDK AVGWVRQAPG KALEWLGSVD SGGNTGYNP GLKSRLSITK DNSKSQVSLS VSSVTTEDSA TYYCTTVLQQ TTKKENNCPD GYSCGYRCRS GWGCSGDECC G RRGGGWGS ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAQV QLRESGPSLV KPSQTLSLTC TASGFSLSDK AVGWVRQAPG KALEWLGSVD SGGNTGYNP GLKSRLSITK DNSKSQVSLS VSSVTTEDSA TYYCTTVLQQ TTKKENNCPD GYSCGYRCRS GWGCSGDECC G RRGGGWGS IELIACCSST YIHEFHVDAW GQGLLVTVSS ASTTAPKVYP LSSCCGDKSS STVTLGCLVS SYMPEPVTVT WN SGALKSG VHTFPAVLQS SGLYSLSSMV TVPGSTSGTQ TFTCNVAHPA SSTKVDKAVD PRCGKHHHHH H

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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

BufferpH: 7.55
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
150.0 mMNH2C(CH2OH)3HClTrizma-Hydrochloride
40.0 mMNa3PO4Sodium Phosphate

Details: 150 mM NaCl, 150 mM Tris-HCl, 40 mM Na3PO4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
Details: Grids glow discharged using Harrick Plasma PDC-002-CE on 'High' setting.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in air atmosphere..
DetailsFoot and mouth disease virus SAT2 serotype virus like particle pentamer unit incubated with Fab117.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10965 / Average exposure time: 4.4 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 267890
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5aca

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110210
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g6v:
Dissociated FMDV SAT2 Pentamer in complex with ultralong Fab117

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