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- EMDB-38815: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizi... -

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Basic information

Entry
Database: EMDB / ID: EMD-38815
TitleComplex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
Map data
Sample
  • Complex: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
    • Complex: FMDV A/WH/CHA/09
      • Protein or peptide: VP1 of capsid protein
      • Protein or peptide: VP2 of capsid protein
      • Protein or peptide: VP3 of capsid protein
      • Protein or peptide: VP4 of capsid protein
    • Complex: inter-serotype broadly neutralizing antibodies pOA-2
      • Protein or peptide: pOA2 VH
      • Protein or peptide: pOA2 VL
KeywordsFoot-and-mouth disease virus A / Sus scrofa / VIRUS/IMMUNE SYSTEM / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation ...symbiont-mediated perturbation of host chromatin organization / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methylation / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / cytosol
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 / Thymidylate synthase, active site / Thymidylate synthase active site. ...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 / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Picornavirus coat protein / 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 / Papain-like cysteine peptidase superfamily / 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
thymidylate synthase / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus A / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsWu S / Lei D
Funding support China, 6 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 China
Other governmentlzujbky-2021-ct05 China
Other governmentNCTIP-MY23004 China
CitationJournal: To Be Published
Title: Discovery, evolution and recognizing antigenic structures of cross-serotype broadly neutralizing antibodies from porcine B-cell repertoires against foot-and-mouth disease virus
Authors: Li F / Wu S / Huang S / Zerang Z / Zhang Z / Li P / Cao Y / Bao H / Sun P / Bai X / Fu Y / Yuan H / Ma X / Zhao Z / Zhang J / Wang J / Wang T / Li D / Zhang Q / Liu Z / Lu Z / Lei D / Li K
History
DepositionJan 23, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38815.png

Downloads & links

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Map

FileDownload / File: emd_38815.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.)
1.11 Å/pix.
x 480 pix.
= 531.84 Å		1.11 Å/pix.
x 480 pix.
= 531.84 Å		1.11 Å/pix.
x 480 pix.
= 531.84 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.09846746 - 2.1880133
Average (Standard dev.)0.006801401 (±0.09914311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 531.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38815_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38815_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38815_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizi...

EntireName: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
Components
  • Complex: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
    • Complex: FMDV A/WH/CHA/09
      • Protein or peptide: VP1 of capsid protein
      • Protein or peptide: VP2 of capsid protein
      • Protein or peptide: VP3 of capsid protein
      • Protein or peptide: VP4 of capsid protein
    • Complex: inter-serotype broadly neutralizing antibodies pOA-2
      • Protein or peptide: pOA2 VH
      • Protein or peptide: pOA2 VL

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Supramolecule #1: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizi...

SupramoleculeName: Complex of FMDV A/WH/CHA/09 and inter-serotype broadly neutralizing antibodies pOA-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FMDV A/WH/CHA/09

SupramoleculeName: FMDV A/WH/CHA/09 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Foot-and-mouth disease virus A

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Supramolecule #3: inter-serotype broadly neutralizing antibodies pOA-2

SupramoleculeName: inter-serotype broadly neutralizing antibodies pOA-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: VP1 of capsid protein

MacromoleculeName: VP1 of capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 23.402678 KDa
SequenceString: TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA ...String:
TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA TEIQELLVRM KRAELYCPRP LLAVKVTSQD RHKQKIIAPA KQLL

UniProtKB: thymidylate synthase

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Macromolecule #2: VP2 of capsid protein

MacromoleculeName: VP2 of capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 24.541584 KDa
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYNKHKPWT LVVMVVSPLT TSSIGASQIK VYTNIAPTHV HVAGELPSKE

UniProtKB: thymidylate synthase

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Macromolecule #3: VP3 of capsid protein

MacromoleculeName: VP3 of capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 24.157025 KDa
SequenceString: GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String:
GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVADT TNVQGWVCIY QITHGKAEQD TLVVSVSAGK DFELRLPIDP RAQ

UniProtKB: thymidylate synthase

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Macromolecule #4: VP4 of capsid protein

MacromoleculeName: VP4 of capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 8.778129 KDa
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSSHTT NTQNNDWFSK LASSAFTGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: pOA2 VH

MacromoleculeName: pOA2 VH / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.721396 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEKVVESGGG LVQPGGSLRL SCVGSGFNFK NYEINWVRQA PGKALEWLAY ITQTSDFIYY ADSVKGRFTI SRDNSRNTAY LQMNNLRTE DTARYFCTRA GLTGCKSRHC MYVWGPGAEV VVSS

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Macromolecule #6: pOA2 VL

MacromoleculeName: pOA2 VL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 11.587944 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QTVIQEPAMS VSLGGTVTLT CGFISGSVTG TNYPSWFQQT PGQPPRLLIY YANSRPTEVP SRFSGAISGN KAALTITGAQ AEDEADYFC CLYKTNNNIL FGGGTHLTVL

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7341
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
FSC plot (resolution estimation)

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