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- EMDB-70339: SIPV3-6B5 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70339
TitleSIPV3-6B5 Complex
Map dataSIPV3-6B5 Complex map
Sample
  • Complex: SIPV3-6B5 Complex
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: 6B5 Heavy Chain
    • Protein or peptide: 6B5 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: 2.94 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: To Be Published
Title: Neutralizing human monoclonal antibodies to poliovirus map to the receptor binding site
Authors: Waddey BT / Charnesky AJ / Faust JE / DiNunno NM / Cho SH / Bator CM / Dong S / Mahmood K / Chumakov KM / Dessain SK / Hafenstein SL
History
DepositionApr 25, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70339.png

Downloads & links

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Map

FileDownload / File: emd_70339.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSIPV3-6B5 Complex map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 700 pix.
= 770. Å		1.1 Å/pix.
x 700 pix.
= 770. Å		1.1 Å/pix.
x 700 pix.
= 770. 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: 0.445
Minimum - Maximum-1.0257903 - 2.525595
Average (Standard dev.)-0.011419452 (±0.11446588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-350-350-350
Dimensions700700700
Spacing700700700
CellA=B=C: 770.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70339_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_70339_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 : SIPV3-6B5 Complex

EntireName: SIPV3-6B5 Complex
Components
  • Complex: SIPV3-6B5 Complex
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
    • Protein or peptide: 6B5 Heavy Chain
    • Protein or peptide: 6B5 Light Chain
  • Ligand: PALMITIC ACID

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Supramolecule #1: SIPV3-6B5 Complex

SupramoleculeName: SIPV3-6B5 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: 6B5 Heavy Chain

MacromoleculeName: 6B5 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.395861 KDa
SequenceString:
EVQLVESGGG LVQPGRSLRL SCEASGFNFD DYAMHWVRQA PGKGLEWVSG ISWSSSSRDY ADSVKGRFTI SRDNAKNSLY LHMNSLREE DTALYYCAKD MSYYGSGGVL HYYYYGMDVW GQGTTVTVSS

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Macromolecule #6: 6B5 Light Chain

MacromoleculeName: 6B5 Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.397425 KDa
SequenceString:
SALTQPASVS GSPGQSITIS CTGTSSDVGG YDYVSWYQQH PGKAPKVMIY DVSNRPSGVS NRFSGSKSGN TASLTISGLQ AEDEAEYYC TSYTRSSTLV FGTGTKVTVL

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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: 50.0 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: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459882
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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