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- EMDB-48509: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing mono... -

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Basic information

Entry
Database: EMDB / ID: EMD-48509
TitleComplex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS5
Map data
Sample
  • Complex: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS5
    • Complex: porcine-derived neutralizing monoclonal antibody PAS5
      • Protein or peptide: PAS5 Fv Heavy chain
      • Protein or peptide: PAS5 Fv Light chain
    • Virus: Foot-and-mouth disease virus Asia 1
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
KeywordsFoot-and-mouth disease virus Asia1 / Sus scrofa / VIRUS/IMMUNE SYSTEM / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / 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 / RNA-directed RNA polymerase / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 speciesSus scrofa (pig) / Foot-and-mouth disease virus Asia 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsWu S / Lei D
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32373028 China
National Natural Science Foundation of China (NSFC)32171300 China
National Natural Science Foundation of China (NSFC)32072873 China
Other government2021YFD1800304
Other governmentlzujbky-2021-ct05
CitationJournal: To Be Published
Title: Porcine B cell receptor repertoire uncovers immunodominant properties of antigenic structures on serotype Asia1 foot-and-mouth disease virus
Authors: Huang S / Wu S / Li K / Li F / Li P / Cao Y / Bao H / Dong K / Yang J / Zhao Q / Sun Y / Li D / Sun P / Bai X / Fu Y / Yuan H / Ma X / Zhao Z / Zhang J / Wang J / Liu Z / Hua J / Zhang Q / Lei D / Lu Z
History
DepositionJan 1, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48509.png

Downloads & links

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Map

FileDownload / File: emd_48509.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 480 pix.
= 465.36 Å		0.97 Å/pix.
x 480 pix.
= 465.36 Å		0.97 Å/pix.
x 480 pix.
= 465.36 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9695 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-1.0868374 - 25.456773999999999
Average (Standard dev.)0.25092456 (±1.6266266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 465.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48509_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48509_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48509_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing mono...

EntireName: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS5
Components
  • Complex: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS5
    • Complex: porcine-derived neutralizing monoclonal antibody PAS5
      • Protein or peptide: PAS5 Fv Heavy chain
      • Protein or peptide: PAS5 Fv Light chain
    • Virus: Foot-and-mouth disease virus Asia 1
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4

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Supramolecule #1: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing mono...

SupramoleculeName: Complex of FMDV Asia1/JS/05 and porcine-derived neutralizing monoclonal antibody PAS5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: porcine-derived neutralizing monoclonal antibody PAS5

SupramoleculeName: porcine-derived neutralizing monoclonal antibody PAS5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #2: Foot-and-mouth disease virus Asia 1

SupramoleculeName: Foot-and-mouth disease virus Asia 1 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / NCBI-ID: 110195 / Sci species name: Foot-and-mouth disease virus Asia 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus Asia 1
Molecular weightTheoretical: 23.471611 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: TTTTGESADP VTTTVENYGG ETQTARRLHT DVAFVLDRFV KLTQPKSTQT LDLMQIPSHT LVGALLRSAT YYFSDLEVAL VHTGPVTWV PNGAPKTALN NHTNPTAYQK QPITRLALPY TAPHRVLSTV YNGKTTYGEE SSRRGDLAAL ARRVNNRLPT S FNYGAVKA ...String:
TTTTGESADP VTTTVENYGG ETQTARRLHT DVAFVLDRFV KLTQPKSTQT LDLMQIPSHT LVGALLRSAT YYFSDLEVAL VHTGPVTWV PNGAPKTALN NHTNPTAYQK QPITRLALPY TAPHRVLSTV YNGKTTYGEE SSRRGDLAAL ARRVNNRLPT S FNYGAVKA DTITELLIRM KRAETYCPRP LLALDTTQDR RKQKIIAPEK QTL

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus Asia 1
Molecular weightTheoretical: 24.471596 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYAVAE DAVSGPNTSG LETRVTQAER FFKKHLFDWT PDLSFGHCHY LELPSEHKG VFGSLMSSYA YMRNGWDIEV TAVGNQFNGG CLLVALVPEL KELDTRQKYQ LTLFPHQFIN PRTNMTAHIN V PYVGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYAVAE DAVSGPNTSG LETRVTQAER FFKKHLFDWT PDLSFGHCHY LELPSEHKG VFGSLMSSYA YMRNGWDIEV TAVGNQFNGG CLLVALVPEL KELDTRQKYQ LTLFPHQFIN PRTNMTAHIN V PYVGVNRY DQYELHKPWT LVVMVVAPLT VKTGGSEQIK VYMNAAPTYV HVAGELPSKE

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus Asia 1
Molecular weightTheoretical: 23.845801 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: GIVPVACVDG YGNMVTTDPK TADPVYGKVS NPPRTSFPGR FTNFLDVAEA CPTFLRFGEV PFVKTVNSGD RLLAKFDVSL AAGHMSNTY LAGLAQYYTQ YSGTMNIHFM FTGPTDAKAR YMVAYIPPGM TPPTDPERAA HCIHSEWDTG LNSKFTFSIP Y LSAADYAY ...String:
GIVPVACVDG YGNMVTTDPK TADPVYGKVS NPPRTSFPGR FTNFLDVAEA CPTFLRFGEV PFVKTVNSGD RLLAKFDVSL AAGHMSNTY LAGLAQYYTQ YSGTMNIHFM FTGPTDAKAR YMVAYIPPGM TPPTDPERAA HCIHSEWDTG LNSKFTFSIP Y LSAADYAY TASDVAETTS VQGWVCIYQI THGKAEGDAL VVSVSAGKDF EFRLPVDARQ Q

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus Asia 1
Molecular weightTheoretical: 8.789116 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTN NTQNNDWFSR LASSAFGGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: PAS5 Fv Heavy chain

MacromoleculeName: PAS5 Fv Heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.878345 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEKLVESGGG LVQPGGSLRL SCVGSGFTFS NTYINWVRRA PGKGLEWLAA VSSDGGLKYY TDSVKGRFTI SSDNSQNTAY LQMNSLRTE DTARYYCARG RIGWQMNLWG PGVEVVVSS

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Macromolecule #6: PAS5 Fv Light chain

MacromoleculeName: PAS5 Fv Light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.629072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIQMTQSPAS LAASLGDTVS ITCRASQSIS KNVDWYQQQP GKSPKLLIYY ADSLQSGVPS RFKGSGSGTD FTLTISGLQA EDVATYYCL QYNFIPRSFG AGTKLELKRD YKDDDDKGGH HHHHH

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14129
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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