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- EMDB-27949: 9H2 Fab-Sabin poliovirus 3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-27949
Title9H2 Fab-Sabin poliovirus 3 complex
Map dataCryosparc sharpened
Sample
  • Virus: Human poliovirus 3 strain Sabin
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: 9H2 Fab heavy chain
    • Protein or peptide: 9H2 Fab light chain
  • Ligand: PALMITIC ACID
KeywordsComplex / Fab / poliovirus / neutralizing / VIRUS-IMMUNE SYSTEM 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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 / 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
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 3 strain Sabin / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCharnesky AJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD026822-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI107121-01 United States
Bill & Melinda Gates FoundationOPP1135787 United States
CitationJournal: Nat Commun / Year: 2023
Title: A human monoclonal antibody binds within the poliovirus receptor-binding site to neutralize all three serotypes.
Authors: Andrew J Charnesky / Julia E Faust / Hyunwook Lee / Rama Devudu Puligedda / Daniel J Goetschius / Nadia M DiNunno / Vaskar Thapa / Carol M Bator / Sung Hyun Joseph Cho / Rahnuma Wahid / ...Authors: Andrew J Charnesky / Julia E Faust / Hyunwook Lee / Rama Devudu Puligedda / Daniel J Goetschius / Nadia M DiNunno / Vaskar Thapa / Carol M Bator / Sung Hyun Joseph Cho / Rahnuma Wahid / Kutub Mahmood / Scott Dessain / Konstantin M Chumakov / Amy Rosenfeld / Susan L Hafenstein /
Abstract: Global eradication of poliovirus remains elusive, and it is critical to develop next generation vaccines and antivirals. In support of this goal, we map the epitope of human monoclonal antibody 9H2 ...Global eradication of poliovirus remains elusive, and it is critical to develop next generation vaccines and antivirals. In support of this goal, we map the epitope of human monoclonal antibody 9H2 which is able to neutralize the three serotypes of poliovirus. Using cryo-EM we solve the near-atomic structures of 9H2 fragments (Fab) bound to capsids of poliovirus serotypes 1, 2, and 3. The Fab-virus complexes show that Fab interacts with the same binding mode for each serotype and at the same angle of interaction relative to the capsid surface. For each of the Fab-virus complexes, we find that the binding site overlaps with the poliovirus receptor (PVR) binding site and maps across and into a depression in the capsid called the canyon. No conformational changes to the capsid are induced by Fab binding for any complex. Competition binding experiments between 9H2 and PVR reveal that 9H2 impedes receptor binding. Thus, 9H2 outcompetes the receptor to neutralize poliovirus. The ability to neutralize all three serotypes, coupled with the critical importance of the conserved receptor binding site make 9H2 an attractive antiviral candidate for future development.
History
DepositionAug 26, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27949.png

Downloads & links

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Map

FileDownload / File: emd_27949.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 560 pix.
= 616. Å		1.1 Å/pix.
x 560 pix.
= 616. Å		1.1 Å/pix.
x 560 pix.
= 616. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.965167 - 8.100712
Average (Standard dev.)0.02155382 (±0.35195467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-280-280-280
Dimensions560560560
Spacing560560560
CellA=B=C: 616.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer sharpened

Fileemd_27949_additional_1.map
AnnotationDeepEMhancer sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_27949_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_27949_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human poliovirus 3 strain Sabin

EntireName: Human poliovirus 3 strain Sabin
Components
  • Virus: Human poliovirus 3 strain Sabin
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: 9H2 Fab heavy chain
    • Protein or peptide: 9H2 Fab light chain
  • Ligand: PALMITIC ACID

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Supramolecule #1: Human poliovirus 3 strain Sabin

SupramoleculeName: Human poliovirus 3 strain Sabin / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / NCBI-ID: 270338 / Sci species name: Human poliovirus 3 strain Sabin / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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: Human poliovirus 3 strain Sabin / Strain: Sabin
Molecular weightTheoretical: 31.358221 KDa
SequenceString: QDSLPDTKAS GPAHSKEVPA LTAVETGATN PLAPSDTVQT RHVVQRRSRS ESTIESFFAR GACVAIIEVD NEQPTTRAQK LFAMWRITY KDTVQLRRKL EFFTYSRFDM EFTFVVTANF TNANNGHALN QVYQIMYIPP GAPTPKSWDD YTWQTSSNPS I FYTYGAAP ...String:
QDSLPDTKAS GPAHSKEVPA LTAVETGATN PLAPSDTVQT RHVVQRRSRS ESTIESFFAR GACVAIIEVD NEQPTTRAQK LFAMWRITY KDTVQLRRKL EFFTYSRFDM EFTFVVTANF TNANNGHALN QVYQIMYIPP GAPTPKSWDD YTWQTSSNPS I FYTYGAAP ARISVPYVGL ANAYSHFYDG FAKVPLKTDA NDQIGDSLYS AMTVDDFGVL AVRVVNDHNP TKVTSKVRIY MK PKHVRVW CPRPPRAVPY YGPGVDYRNN LDPLSEKGLT TY

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: Human poliovirus 3 strain Sabin / Strain: Sabin
Molecular weightTheoretical: 29.412111 KDa
SequenceString: YSDRVLQLTL GNSTITTQEA ANSVVAYGRW PEFIRDDEAN PVDQPTEPDV ATCRFYTLDT VMWGKESKGW WWKLPDALRD MGLFGQNMY YHYLGRSGYT VHVQCNASKF HQGALGVFAI PEYCLAGDSD KQRYTSYANA NPGERGGKFY SQFNKDNAVT S PKREFCPV ...String:
YSDRVLQLTL GNSTITTQEA ANSVVAYGRW PEFIRDDEAN PVDQPTEPDV ATCRFYTLDT VMWGKESKGW WWKLPDALRD MGLFGQNMY YHYLGRSGYT VHVQCNASKF HQGALGVFAI PEYCLAGDSD KQRYTSYANA NPGERGGKFY SQFNKDNAVT S PKREFCPV DYLLGCGVLL GNAFVYPHQI INLRTNNSAT IVLPYVNALA IDSMVKHNNW GIAILPLSPL DFAQDSSVEI PI TVTIAPM CSEFNGLRNV TAPKFQ

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: Human poliovirus 3 strain Sabin / Strain: Sabin
Molecular weightTheoretical: 25.950723 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 THISQSA

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: Human poliovirus 3 strain Sabin / Strain: Sabin
Molecular weightTheoretical: 7.320917 KDa
SequenceString:
GAQVSSQKVG AHENSNRAYG GSTINYTTIN YYKDSASNAA SKQDYSQDPS KFTEPLKDVL IKTAPALN

UniProtKB: Genome polyprotein

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Macromolecule #5: 9H2 Fab heavy chain

MacromoleculeName: 9H2 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.052716 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LVQSGAELKK PGASVKFSCQ ASGFTFTTYD IHWVRQAPGQ GLEWMGMISP SRDSTIYAQK FQGRVTMTSD TSTSTVYMEL TSLRSEDTA LYYCATASRP SAWVFRSLYT YYYMDVWGTG TTVTVSS

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Macromolecule #6: 9H2 Fab light chain

MacromoleculeName: 9H2 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.738903 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTITDIG YYNYVSWYQQ HPGKAPKLII FDVTNRPSGV SDRFSGSKSG NTASLTISGL QAEDEGDYY CFSHRSNNIR 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52115
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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