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- EMDB-9574: Cryo-EM structure of zika virus complexed with Fab C10 at pH 5.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-9574
TitleCryo-EM structure of zika virus complexed with Fab C10 at pH 5.0
Map data
Sample
  • Complex: zika virus complexed with Fab C10 at pH 5.0
    • Complex: zika virus
      • Protein or peptide: structural protein E
    • Complex: Fab C10
      • Protein or peptide: C10 IgG heavy chain variable region
      • Protein or peptide: C10 IgG light chain variable region
KeywordsAntibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding
Similarity search - Function
Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem q(B) protein
Similarity search - Component
Biological speciesZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsZhang S / Kostyuchenko V
Funding support Singapore, United States, 3 items
OrganizationGrant numberCountry
Ministry of Education Tier 3 grantMOE2012-T3-1-008 Singapore
National Research Foundation Investigatorship awardNRF-NRFI2016-01 Singapore
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100625 and AI 107731 United States
CitationJournal: Nat Commun / Year: 2016
Title: Neutralization mechanism of a highly potent antibody against Zika virus.
Authors: Shuijun Zhang / Victor A Kostyuchenko / Thiam-Seng Ng / Xin-Ni Lim / Justin S G Ooi / Sebastian Lambert / Ter Yong Tan / Douglas G Widman / Jian Shi / Ralph S Baric / Shee-Mei Lok /
Abstract: The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies ...The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4.0 Å resolution pH8.0 complex structure shows that the antibody binds to E proteins residues at the intra-dimer interface, and the virus quaternary structure-dependent inter-dimer and inter-raft interfaces. At pH6.5, antibody C10 locks all virus surface E proteins, and at pH5.0, it locks the E protein raft structure, suggesting that it prevents the structural rearrangement of the E proteins during the fusion event-a vital step for infection. This suggests antibody C10 could be a good therapeutic candidate.
History
DepositionOct 20, 2016-
Header (metadata) releaseNov 2, 2016-
Map releaseNov 30, 2016-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h32
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5h32
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9574.png

Downloads & links

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Map

FileDownload / File: emd_9574.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 256 pix.
= 880.64 Å		3.44 Å/pix.
x 256 pix.
= 880.64 Å		3.44 Å/pix.
x 256 pix.
= 880.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-2.1472998 - 6.983688
Average (Standard dev.)-0.000000004648475 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 880.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.443.443.44
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z880.640880.640880.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-2.1476.984-0.000

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Supplemental data

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Sample components

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Entire : zika virus complexed with Fab C10 at pH 5.0

EntireName: zika virus complexed with Fab C10 at pH 5.0
Components
  • Complex: zika virus complexed with Fab C10 at pH 5.0
    • Complex: zika virus
      • Protein or peptide: structural protein E
    • Complex: Fab C10
      • Protein or peptide: C10 IgG heavy chain variable region
      • Protein or peptide: C10 IgG light chain variable region

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Supramolecule #1: zika virus complexed with Fab C10 at pH 5.0

SupramoleculeName: zika virus complexed with Fab C10 at pH 5.0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: zika virus

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

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Supramolecule #3: Fab C10

SupramoleculeName: Fab C10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: structural protein E

MacromoleculeName: structural protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus / Strain: Mr 766
Molecular weightTheoretical: 44.06993 KDa
SequenceString: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGHE T DENRAKVE ...String:
IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGHE T DENRAKVE ITPNSPRAEA TLGGFGSLGL DCEPRTGLDF SDLYYLTMNN KHWLVHKEWF HDIPLPWHAG ADTGTPHWNN KE ALVEFKD AHAKRQTVVV LGSQEGAVHT ALAGALEAEM DGAKGRLSSG HLKCRLKMDK LRLKGVSYSL CTAAFTFTKI PAE TLHGTV TVEVQYAGTD GPCKVPAQMA VDMQTLTPVG RLITANPVIT ESTENSKMML ELDPPFGDSY IVIGVGEKKI THHW HRS

UniProtKB: Photosystem q(B) protein

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Macromolecule #2: C10 IgG heavy chain variable region

MacromoleculeName: C10 IgG heavy chain variable region / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.487058 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKKPGASVKV SCKASGYTFT SYAMHWVRQA PGQRLEWMGW INAGNGNTKY SQKFQDRVTI TRDTSASTAY MELSSLRSE DTAIYYCARD KVDDYGDYWF PTLWYFDYWG QGTLVTVS

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Macromolecule #3: C10 IgG light chain variable region

MacromoleculeName: C10 IgG light chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.298362 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SALTQPASVS GSPGQSITIS CTGTSSDVGG FNYVSWFQQH PGKAPKLMLY DVTSRPSGVS SRFSGSKSGN TASLTISGLQ AEDEADYYC SSHTSRGTWV FGGGTKLTVL

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 23810
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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