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- EMDB-44290: Envelope protein ASU of YFV-ES504 with YFV-17D DIII in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-44290
TitleEnvelope protein ASU of YFV-ES504 with YFV-17D DIII in complex with 2C9 Fab
Map data
Sample
  • Complex: YFV envelope protein expressed in the backbone of Binjari virus in complex with 2C9 Fab
    • Complex: YFV envelope protein expressed in the genomic backbone of BinJV
      • Protein or peptide: Envelope protein
    • Complex: 2C9 Fab HC
      • Protein or peptide: 2C9 Fab heavy chain
    • Complex: 2C9 Fab LC
      • Protein or peptide: 2C9 Fab light chain
KeywordsFlavivirus / Envelope protein / Yellow fever virus / VIRUS / VIRUS-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 / viral capsid / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2B / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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 NS2B / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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 capsid protein C / Flavivirus capsid protein C / 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 NS3 helicase, C-terminal helical 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 / 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. / Helicase, C-terminal / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesYellow fever virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBibby S / James J / Modhiran N / Watterson D
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1164216 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2004582 Australia
CitationJournal: To Be Published
Title: A single residue in the yellow fever virus envelope protein modulates virion architecture and vaccine potency
Authors: Bibby S / Jung J / Low YS / Amarilla AA / Newton ND / Scott CAP / Balk J / Ting YT / Freney ME / Liang B / Grant T / Coulibaly F / Young P / Hall R / Hobson-Peters J / Modhiran N / Watterson D
History
DepositionMar 26, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44290.png

Downloads & links

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Map

FileDownload / File: emd_44290.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 423.28 Å		0.96 Å/pix.
x 440 pix.
= 423.28 Å		0.96 Å/pix.
x 440 pix.
= 423.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.962 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-5.8419623 - 7.780713
Average (Standard dev.)0.013287454 (±0.22141299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 423.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44290_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44290_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 : YFV envelope protein expressed in the backbone of Binjari virus i...

EntireName: YFV envelope protein expressed in the backbone of Binjari virus in complex with 2C9 Fab
Components
  • Complex: YFV envelope protein expressed in the backbone of Binjari virus in complex with 2C9 Fab
    • Complex: YFV envelope protein expressed in the genomic backbone of BinJV
      • Protein or peptide: Envelope protein
    • Complex: 2C9 Fab HC
      • Protein or peptide: 2C9 Fab heavy chain
    • Complex: 2C9 Fab LC
      • Protein or peptide: 2C9 Fab light chain

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Supramolecule #1: YFV envelope protein expressed in the backbone of Binjari virus i...

SupramoleculeName: YFV envelope protein expressed in the backbone of Binjari virus in complex with 2C9 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: YFV envelope protein expressed in the genomic backbone of BinJV

SupramoleculeName: YFV envelope protein expressed in the genomic backbone of BinJV
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Yellow fever virus

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Supramolecule #3: 2C9 Fab HC

SupramoleculeName: 2C9 Fab HC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: 2C9 Fab LC

SupramoleculeName: 2C9 Fab LC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Envelope protein

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Yellow fever virus
Molecular weightTheoretical: 42.714352 KDa
Recombinant expressionOrganism: Binjari virus
SequenceString: AHCIGITDRD FIEGVHGGTW VSATLEQDKC VTVMAPDKPS LDISLETVAI DGPAEARKVC YSAVLTNVKI NDKCPSTGEA HLEEENEGD NACKRTYSDR GWGNGCGLFG KGSIVACAKF TCAKSMSLFE VDQTKIQYVI RAQLHVGAKQ ENWNTDIKTL K FDALSGSQ ...String:
AHCIGITDRD FIEGVHGGTW VSATLEQDKC VTVMAPDKPS LDISLETVAI DGPAEARKVC YSAVLTNVKI NDKCPSTGEA HLEEENEGD NACKRTYSDR GWGNGCGLFG KGSIVACAKF TCAKSMSLFE VDQTKIQYVI RAQLHVGAKQ ENWNTDIKTL K FDALSGSQ EAEFTGYGRA TLECQVQTAV DFSNSYIAEM EKESWIVDKQ WAQDLTLPWQ SGSGGVWREM HHLVEFEPPH AA TIKVLAL GNQEGSLKTA LTGAMRVTKD TNNSKLYKLH GGHVACRVKL SALTLKGTSY KICTDKMFFV KNPTDTGHGT VVM QVKVSK GAPCRIPVIV ADDLTAAINK GILVTVNPIA STNDDEVLIE VNPPFGDSYI IVGRGDSRLT YQWHK

UniProtKB: Genome polyprotein

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Macromolecule #2: 2C9 Fab heavy chain

MacromoleculeName: 2C9 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.278872 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVKLVESGGG LVKPGGSLKL SCAASGFTFT NYAMSWVRQT PEKRLEWVAS ISSGHTPYYP DSVKGRFTIS RDNARNILFL QMSSLRSED TAMYYCARGD YYGSVYSAMD YWGQGTSLTV S

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Macromolecule #3: 2C9 Fab light chain

MacromoleculeName: 2C9 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.04551 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EIRMTQSPSS MYASLGERVT VTCKASQDIN SYLSWLQQKP GKSPKTLIYR ANRLFDGVPS RFSGSGSGQD YSLTISSLEY EDMGIFYCL QYDEFPFTFG SGTKLELK

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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
Component:
ConcentrationFormulaName
120.0 nMNaClSodium chloride
10.0 mMNH2C(CH2OH)3Tris-base
1.0 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 25.0 µm / Nominal defocus min: 5.0 µm

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 2.0.0) / Number images used: 314100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9b6w:
Envelope protein ASU of YFV-ES504 with YFV-17D DIII in complex with 2C9 Fab

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