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- EMDB-70320: SIPV3-2E1 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70320
TitleSIPV3-2E1 Complex
Map dataSIPV3-2E1 Complex map
Sample
  • Complex: SIPV3-2E1 Complex
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: 2E1 Heavy Chain
    • Protein or peptide: 2E1 Light Chain
  • Ligand: PALMITIC ACID
KeywordsVirus / Antibody / Complex
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / ribonucleoside triphosphate phosphatase activity ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / 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 / membrane
Similarity search - Function
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 ...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. / 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 speciesPoliovirus 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWaddey BT / Hafenstein SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI10721-01 United States
CitationJournal: Nat Commun / Year: 2026
Title: Neutralizing human monoclonal antibodies to poliovirus map to the receptor binding site.
Authors: Benjamin T Waddey / Andrew J Charnesky / Julia E Faust / Nadia M DiNunno / Rama Devudu Puligedda / Sung Hyun Cho / Carol M Bator / Steven D Dong / Kutub Mahmood / Konstantin M Chumakov / ...Authors: Benjamin T Waddey / Andrew J Charnesky / Julia E Faust / Nadia M DiNunno / Rama Devudu Puligedda / Sung Hyun Cho / Carol M Bator / Steven D Dong / Kutub Mahmood / Konstantin M Chumakov / Scott K Dessain / Susan L Hafenstein /
Abstract: Poliovirus remains a serious threat to human health. Complete eradication of wild-type poliovirus has not yet succeeded, making the development of successful antivirals critical. Microneutralization ...Poliovirus remains a serious threat to human health. Complete eradication of wild-type poliovirus has not yet succeeded, making the development of successful antivirals critical. Microneutralization assays against all three poliovirus serotypes identified a panel of human monoclonal IgGs, which are either serotype-specific or cross-neutralizing. Here, through cryoEM single particle analysis, we solved high resolution structures of four distinct poliovirus-FAb complexes. These antibodies bind to capsids at the circular depression (canyon) surrounding the icosahedral five-fold symmetry axis, which is also the binding site of the poliovirus receptor (PVR). Analysis of these structures confirms overlap of FAb contacts on the viral capsid with those of PVR. For three of the FAbs, the capsid residues are identified that dictate serotype-specific recognition. Contacts for the cross-neutralizing mAb 10D2 are located deep in the capsid canyon. These structural analyses indicate that antibody competition with the receptor likely leads to neutralization of virus particles and inhibition of poliovirus entry into host cells. Thus, the human IgGs studied here may facilitate development of therapeutics for the ongoing efforts in global eradication of poliovirus.
History
DepositionApr 24, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70320.png

Downloads & links

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Map

FileDownload / File: emd_70320.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSIPV3-2E1 Complex map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66
Minimum - Maximum-1.5357052 - 3.126316
Average (Standard dev.)0.0057414114 (±0.15487382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_70320_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_70320_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SIPV3-2E1 Complex

EntireName: SIPV3-2E1 Complex
Components
  • Complex: SIPV3-2E1 Complex
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: 2E1 Heavy Chain
    • Protein or peptide: 2E1 Light Chain
  • Ligand: PALMITIC ACID

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Supramolecule #1: SIPV3-2E1 Complex

SupramoleculeName: SIPV3-2E1 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 8 MDa

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 33.523672 KDa
SequenceString: GIEDLISEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLAPSDTVQ TRHVVQRRSR SESTIESFFA RGACVAIIE VDNEQPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MEFTFVVTAN FTNANNGHAL NQVYQIMYIP P GAPTPKSW ...String:
GIEDLISEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLAPSDTVQ TRHVVQRRSR SESTIESFFA RGACVAIIE VDNEQPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MEFTFVVTAN FTNANNGHAL NQVYQIMYIP P GAPTPKSW DDYTWQTSSN PSIFYTYGAA PARISVPYVG LANAYSHFYD GFAKVPLKTD ANDQIGDSLY SAMTVDDFGV LA VRVVNDH NPTKVTSKVR IYMKPKHVRV WCPRPPRAVP YYGPGVDYRN NLDPLSEKGL TTY

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 30.16992 KDa
SequenceString: SPNVEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GERGGKFYSQ F NKDNAVTS ...String:
SPNVEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GERGGKFYSQ F NKDNAVTS PKREFCPVDY LLGCGVLLGN AFVYPHQIIN LRTNNSATIV LPYVNALAID SMVKHNNWGI AILPLSPLDF AQ DSSVEIP ITVTIAPMCS EFNGLRNVTA PKFQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 26.289127 KDa
SequenceString: GLPVLNTPGS NQYLTSDNHQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLEST KRNTMDMYRV TLSDSADLSQ PILCLSLSP AFDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTSDNHQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLEST KRNTMDMYRV TLSDSADLSQ PILCLSLSP AFDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV PWISNVTYRQ TTQDSFTEGG YISMFYQTRI VVPLSTPKSM SMLGFVSACN DFSVRLLRDT THISQSALPQ

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 7.320917 KDa
SequenceString:
GAQVSSQKVG AHENSNRAYG GSTINYTTIN YYKDSASNAA SKQDYSQDPS KFTEPLKDVL IKTAPALN

UniProtKB: Genome polyprotein

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Macromolecule #5: 2E1 Heavy Chain

MacromoleculeName: 2E1 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.006592 KDa
SequenceString:
EVQLVQSGAE VKKSGESLKI SCKASGYHFT SYWIGWVRQM PGKGLEWMGF IYPGDSDTRY GPSFQGQVSI SADKSSSTAY LQWSRLKAS DTAMYFCARH GGFASSLYSS SFRPPDYWGQ GTLVTVSS

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Macromolecule #6: 2E1 Light Chain

MacromoleculeName: 2E1 Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.837788 KDa
SequenceString:
NFMLTQPHSV SESPGKTVTI SCTRSSGSIA SSYVQWYQQR PGSSPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLIISG LKTEDEADY YCQSYDSSNQ VFGGGTKLTV L

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Macromolecule #7: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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:

8e8x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237897
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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