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- EMDB-36372: CryoEM structure of sNS1 complexed with Fab 4B8 -

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Basic information

Entry
Database: EMDB / ID: EMD-36372
TitleCryoEM structure of sNS1 complexed with Fab 4B8
Map data
Sample
  • Complex: the complex of ZIKV NS1 with antibody 4B8
    • Complex: ZIKV NS1
      • Protein or peptide: NS1
    • Complex: antibody 4B8
      • Protein or peptide: the heavy chain of antibody 4B8
      • Protein or peptide: the light chain of antibody 4B8
KeywordsZIKV virus / Non-structural protein 1 / antibody / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsChen Q / Pan Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100963 China
CitationJournal: Hlife / Year: 2024
Title: Structural insights into the distinct protective mechanisms of human antibodies targeting ZIKV NS1
Authors: Pan Q / Xing X / Yu J / Chen Q / Jiao H / Zhang W / Wen Y / Gao M / Zhao W / Yu L / Hu H
History
DepositionJun 1, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36372.png

Downloads & links

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Map

FileDownload / File: emd_36372.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017589411 - 2.030139
Average (Standard dev.)0.0010462482 (±0.024252327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36372_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_36372_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 : the complex of ZIKV NS1 with antibody 4B8

EntireName: the complex of ZIKV NS1 with antibody 4B8
Components
  • Complex: the complex of ZIKV NS1 with antibody 4B8
    • Complex: ZIKV NS1
      • Protein or peptide: NS1
    • Complex: antibody 4B8
      • Protein or peptide: the heavy chain of antibody 4B8
      • Protein or peptide: the light chain of antibody 4B8

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Supramolecule #1: the complex of ZIKV NS1 with antibody 4B8

SupramoleculeName: the complex of ZIKV NS1 with antibody 4B8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: ZIKV NS1

SupramoleculeName: ZIKV NS1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Zika virus

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Supramolecule #3: antibody 4B8

SupramoleculeName: antibody 4B8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NS1

MacromoleculeName: NS1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 40.915293 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHGCSV DFSKKETRCG TGVFVYNDVE AWRDRYKYHP DSPRRLAAAV KQAWEDGICG ISSVSRMENI MWRSVEGELN AILEENGVQ LTVVVGSVKN PMWRGPQRLP VPVNELPHGW KAWGKSYFVR AAKTNNSFVV DGDTLKECPL KHRAWNSFLV E DHGFGVFH ...String:
HHHHHHGCSV DFSKKETRCG TGVFVYNDVE AWRDRYKYHP DSPRRLAAAV KQAWEDGICG ISSVSRMENI MWRSVEGELN AILEENGVQ LTVVVGSVKN PMWRGPQRLP VPVNELPHGW KAWGKSYFVR AAKTNNSFVV DGDTLKECPL KHRAWNSFLV E DHGFGVFH TSVWLKVRED YSLECDPAVI GTAVKGKEAV HSDLGYWIES EKNDTWRLKR AHLIEMKTCE WPKSHTLWTD GI EESDLII PKSLAGPLSH HNTREGYRTQ MKGPWHSEEL EIRFEECPGT KVHVEETCGT RGPSLRSTTA SGRVIEEWCC REC TMPPLS FRAKDGCWYG MEIRPRKEPE SNLVRSMVTA GS

UniProtKB: Genome polyprotein

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Macromolecule #2: the heavy chain of antibody 4B8

MacromoleculeName: the heavy chain of antibody 4B8 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.496972 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LIQPGGSLRL SCAASGFTIS SKYMSWVRQA PGKGLEWVSI IYSSGSTYYA DSVKGRFTIS RDISKNTLYL QMNSLRAED TAVYYCASLG SGSAFGYWGQ GTLVTVSS

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Macromolecule #3: the light chain of antibody 4B8

MacromoleculeName: the light chain of antibody 4B8 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.47279 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPSS VSASVGDRVT ITCRASQGIS TWLAWYQQKP GKAPRLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QANSFPFTFG PGTKVEIK

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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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126116
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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