[English] 日本語
Yorodumi
- EMDB-44290: Envelope protein ASU of YFV-ES504 with YFV-17D DIII in complex wi... -

+
Open data


ID or keywords:

Loading...

-
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: Nat Commun / Year: 2025
Title: A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.
Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli ...Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli Coulibaly / Paul Young / Roy A Hall / Jody Hobson-Peters / Naphak Modhiran / Daniel Watterson /
Abstract: Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. ...Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.
History
DepositionMar 26, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44290.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #2

Fileemd_44290_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44290_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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)

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more