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- EMDB-44423: Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9 -

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Basic information

Entry
Database: EMDB / ID: EMD-44423
TitleCryo-EM structure of Chikungunya virus asymmetric unit with Fab C9
Map datahalf1 map
Sample
  • Virus: Chikungunya virus
    • Protein or peptide: E3 glycoprotein
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Heavy chain of C9
    • Protein or peptide: Light chain of C9
    • Protein or peptide: Capsid protein
KeywordsCHIKV asymmetric unit with Fab C9 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / membrane
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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSu GC / Galaz-Montoya JG / Pintilie G / Jin J / Chiu W / Auguste A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103832 United States
CitationJournal: To Be Published
Title: Cryogenic Electron Microscopy Reveals Dual-Inhibition Mechanisms and Explains the Differential Neutralization Potency of Two anti-CHIKV Antibodies
Authors: Su GC / Galaz-Montoya JG / Pintilie G / Jin J / Chiu W
History
DepositionApr 6, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44423.png

Downloads & links

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Map

FileDownload / File: emd_44423.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf1 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405.6 Å		1.35 Å/pix.
x 300 pix.
= 405.6 Å		1.35 Å/pix.
x 300 pix.
= 405.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.352 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07565571 - 0.16413678
Average (Standard dev.)0.00020345121 (±0.0031305302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin257246400
Dimensions300300300
Spacing300300300
CellA=B=C: 405.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2 map

Fileemd_44423_half_map_1.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: chikv c9 map

Fileemd_44423_half_map_2.map
Annotationchikv_c9_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 : Chikungunya virus

EntireName: Chikungunya virus
Components
  • Virus: Chikungunya virus
    • Protein or peptide: E3 glycoprotein
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Heavy chain of C9
    • Protein or peptide: Light chain of C9
    • Protein or peptide: Capsid protein

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: vaccine strain 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 500 KDa
Virus shellShell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4

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Macromolecule #1: E3 glycoprotein

MacromoleculeName: E3 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: vaccine strain 181/clone
Molecular weightTheoretical: 6.95507 KDa
SequenceString:
PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSPHRQRR

UniProtKB: Structural polyprotein

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Macromolecule #2: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: vaccine strain 181/clone
Molecular weightTheoretical: 47.497906 KDa
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESEDVYANTQ LVLQRPSAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AMNCAVGNMP ISIDIPDAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVAI IKY AASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHPPKDH IVNYPASHTT LGVQ DISVT AMSWVQKITG GVGLVVAVAA LILIVVLCVS FSRH

UniProtKB: Structural polyprotein

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Macromolecule #3: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25
Molecular weightTheoretical: 47.077719 KDa
SequenceString: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP ...String:
NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP PDTPDRTLMS QQSGNVKITV NSQTVRYKCN CGDSNEGLTT TDKVINNCKV DQCHAAVTNH KKWQYNSPLV PR NAELGDR KGKVHIPFPL ANVTCRVPKA RNPTVTYGKN QVIMLLYPDH PTLLSYRNMG EEPNYQEEWV THKKEIRLTV PTE GLEVTW GNNEPYKYWP QLSTNGTAHG HPHEIILYYY ELYPTMTVVV VSVASFVLLS MVGVAVGMCM CARRRCITPY ELTP GATVP FLLSLICCIR TAKA

UniProtKB: Structural polyprotein

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Macromolecule #4: Heavy chain of C9

MacromoleculeName: Heavy chain of C9 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.747697 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGSSVKV SCKAFGGTFS SYAITWVRQA PGQGLEWMGG IIPILGTTDY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCARD PPTHGGDFNY YYYGVAVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVQSGAE VKKPGSSVKV SCKAFGGTFS SYAITWVRQA PGQGLEWMGG IIPILGTTDY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCARD PPTHGGDFNY YYYGVAVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTH

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Macromolecule #5: Light chain of C9

MacromoleculeName: Light chain of C9 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.061602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSNN YLAWYQQKPG QAPRLLIYGA SIRATGIPDR FSGSGSGTDF TLTISRLAPE DFAVYYCQQ YGSSPLTFGP GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSNN YLAWYQQKPG QAPRLLIYGA SIRATGIPDR FSGSGSGTDF TLTISRLAPE DFAVYYCQQ YGSSPLTFGP GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGE

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Macromolecule #6: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25
Molecular weightTheoretical: 16.428607 KDa
SequenceString:
NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

UniProtKB: Structural polyprotein

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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:
ConcentrationName
20.0 mMTris
120.0 mMSodium chloride
1.0 mMEDTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 106000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 192895
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fcg

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 1151475
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8fcg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bbn:
Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9

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