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- EMDB-65832: HRV14 3C in complex with single chain antibody YDF and cloverleaf... -

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Basic information

Entry
Database: EMDB / ID: EMD-65832
TitleHRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation1-composite-1
Map data
Sample
  • Complex: 3C-YDF-RNA-conformation1
    • Protein or peptide: Protease 3C
    • Protein or peptide: YDF heavy chain
    • Protein or peptide: YDF light chain
    • RNA: RNA (83-MER)
KeywordscloverleafRNA / 3c / ydf / RNA BINDING PROTEIN/RNA/IMMUNE SYSTEM / RNA BINDING PROTEIN-RNA-IMMUNE SYSTEM complex
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase ...lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / 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 / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesrhinovirus B14 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWang Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation1-composite-1
Authors: Wang Q
History
DepositionAug 13, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65832.png

Downloads & links

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Map

FileDownload / File: emd_65832.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0018033006 - 2.1084397
Average (Standard dev.)0.00055069913 (±0.017933872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65832_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 3C-YDF-RNA-conformation1

EntireName: 3C-YDF-RNA-conformation1
Components
  • Complex: 3C-YDF-RNA-conformation1
    • Protein or peptide: Protease 3C
    • Protein or peptide: YDF heavy chain
    • Protein or peptide: YDF light chain
    • RNA: RNA (83-MER)

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Supramolecule #1: 3C-YDF-RNA-conformation1

SupramoleculeName: 3C-YDF-RNA-conformation1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: rhinovirus B14

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Macromolecule #1: Protease 3C

MacromoleculeName: Protease 3C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 3C
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 19.836695 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
PNTEFALSLL RKNIMTITTS KGEFTGLGIH DRVCVIPTHA QPGDDVLVNG QKIRVKDKYK LVDPENINLE LTVLTLDRNE KFRDIRGFI SEDLEGVDAT LVVHSNNFTN TILEVGPVTM AGLINLSSTP TNRMIRYDYA TKTGQCGGVL CATGKIFGIH V GGNGRQGF SAQLKKQYFV EK

UniProtKB: Genome polyprotein

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Macromolecule #2: YDF heavy chain

MacromoleculeName: YDF heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.833439 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLLQSGGG VVQPGRSLRL SCAASGFTFS SYAMHWVRQA PGKGLEWVAV ISYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARV GKGGYDFWSG SGYMDVWGKG TTVTVSSG

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Macromolecule #3: YDF light chain

MacromoleculeName: YDF light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.129237 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
SYVLTQPPSV SVSPGQTASI TCSGDKLGDK YACWYQQKPG QSPVLVIYQD SKRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSSTVVFGG GTKLTV

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Macromolecule #4: RNA (83-MER)

MacromoleculeName: RNA (83-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 26.533643 KDa
SequenceString:
GGGAAACAGC GGAUGGGUAU CCCACCAUUC GACCCAUUGG GUGUAGUACU CUGGUACUAU GUACCUUUGU ACGCCUGUUU CCC

GENBANK: GENBANK: L05355.1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 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: PDB ENTRY
PDB model - PDB ID:

6kyz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 357917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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