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- EMDB-65728: Chikungunya virus E protein complexed with 8D1-H-10D5 -

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Basic information

Entry
Database: EMDB / ID: EMD-65728
TitleChikungunya virus E protein complexed with 8D1-H-10D5
Map data
Sample
  • Complex: Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5
    • Protein or peptide: 10D5 Light Chain
    • Protein or peptide: 10D5 Heavy Chain
    • Protein or peptide: Spike glycoprotein E2,Spike glycoprotein E1
    • Protein or peptide: 10D5 Heavy Chain
KeywordsChikungunya virus / antibody / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Chikungunya virus (strain 37997) / Camelus bactrianus (Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsYuan HY / Song LY / Li JM
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82202033 China
CitationJournal: To Be Published
Title: Chikungunya virus E protein complexed with 8D1-H-10D5
Authors: Yuan HY / Song LY / Li JM
History
DepositionAug 6, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65728.png

Downloads & links

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Map

FileDownload / File: emd_65728.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 258.56 Å		0.81 Å/pix.
x 320 pix.
= 258.56 Å		0.81 Å/pix.
x 320 pix.
= 258.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.552
Minimum - Maximum-2.595896 - 3.5095103
Average (Standard dev.)0.00066316477 (±0.07183626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 258.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65728_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_65728_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 : Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5

EntireName: Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5
Components
  • Complex: Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5
    • Protein or peptide: 10D5 Light Chain
    • Protein or peptide: 10D5 Heavy Chain
    • Protein or peptide: Spike glycoprotein E2,Spike glycoprotein E1
    • Protein or peptide: 10D5 Heavy Chain

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Supramolecule #1: Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5

SupramoleculeName: Cryo-EM structure of Chikungunya virus E complexed with 8D1-H-10D5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 10D5 Light Chain

MacromoleculeName: 10D5 Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.111393 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPAT LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYFFGPGTK VDIK

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Macromolecule #2: 10D5 Heavy Chain

MacromoleculeName: 10D5 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.885175 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVSA ISGSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCANK EDGDYVPFDY WGQGTLVTVS S

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Macromolecule #3: Spike glycoprotein E2,Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E2,Spike glycoprotein E1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 37997) / Strain: 37997
Molecular weightTheoretical: 71.151945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TKDNFNVYKA TRPYLAHCPD CGEGHSCHSP IALERIRNEA TDGTLKIQVS LQIGIKTDDS HDWTKLRYMD SHTPADAERA GLLVRTSAP CTITGTMGHF ILARCPKGET LTVGFTDSRK ISHTCTHPFH HEPPVIGRER FHSRPQHGKE LPCSTYVQST A ATAEEIEV ...String:
TKDNFNVYKA TRPYLAHCPD CGEGHSCHSP IALERIRNEA TDGTLKIQVS LQIGIKTDDS HDWTKLRYMD SHTPADAERA GLLVRTSAP CTITGTMGHF ILARCPKGET LTVGFTDSRK ISHTCTHPFH HEPPVIGRER FHSRPQHGKE LPCSTYVQST A ATAEEIEV HMPPDTPDRT LMTQQSGNVK ITVNGQTVRY KCNCGGSNEG LTTTDKVINN CKIDQCHAAV TNHKNWQYNS PL VPRNAEL GDRKGKIHIP FPLANVTCRV PKARNPTVTY GKNQVTMLLY PDHPTLLSYR NMGQEPNYHE EWVTHKKEVT LTV PTEGLE VTWGNNEPYK YWPQGGGGSG GGGSGGGGSG GGGSYEHVTV IPNTVGVPYK TLVNRPGYSP MVLEMELQSV TLEP TLSLD YITCEYKTVI PSPYVKCCGT AECKDKSLPD YSCKVFTGVY PFMWGGAYCF CDAENTQLSE AHVEKSESCK TEFAS AYRA HTASASAKLR VLYQGNNITV AAYANGDHAV TVKDAKFVVG PMSSAWTPFD NKIVVYKGDV YNMDYPPFGA GRPGQF GDI QSRTPESKDV YANTQLVLQR PAAGTVHVPY SQAPSGFKYW LKERGASLQH TAPFGCQIAT NPVRAVNCAV GNIPISI DI PDAAFTR

UniProtKB: Structural polyprotein, Structural polyprotein

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Macromolecule #4: 10D5 Heavy Chain

MacromoleculeName: 10D5 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 13.503754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGGG SVQSGGSLRL SCAVSGYTYS SYCRGWFRQA PGKEREGVAG IDSDGSTRYA DSVKGRFTIS QDNAKNTLYL QMNSLKPED TAMYYCAEVF CDSFHQGKYE AFYWGQGTQV TVSS

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 86632
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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