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- EMDB-62513: Cryo-EM Structure of Mature Semliki Forest Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-62513
TitleCryo-EM Structure of Mature Semliki Forest Virus
Map datanew main
Sample
  • Virus: Semliki Forest virus
    • Protein or peptide: Envelope glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Spike glycoprotein E1
Keywordsalphavirus / Semliki Forest Virus / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / 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 / Frameshifted structural polyprotein
Similarity search - Component
Biological speciesSemliki Forest virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsJia X / Li S / Zhang Q / He J
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2021B1212040017 China
CitationJournal: Dian Zi Xian Wei Xue Bao / Year: 2025
Title: Structural study of Semliki Forest virus through Cryo-EM
Authors: Jia X / Li S / Yu H / Zhang Q / He J
History
DepositionNov 26, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62513.png

Downloads & links

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Map

FileDownload / File: emd_62513.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnew main
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 700 pix.
= 930.02 Å		1.33 Å/pix.
x 700 pix.
= 930.02 Å		1.33 Å/pix.
x 700 pix.
= 930.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3286 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.80359447 - 1.3485968
Average (Standard dev.)0.0036314314 (±0.025468541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 930.02 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62513_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_62513_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 : Semliki Forest virus

EntireName: Semliki Forest virus
Components
  • Virus: Semliki Forest virus
    • Protein or peptide: Envelope glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Spike glycoprotein E1

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Supramolecule #1: Semliki Forest virus

SupramoleculeName: Semliki Forest virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Mature Semliki Forest Virus Voron isolated from infected Vero cell
NCBI-ID: 11033 / Sci species name: Semliki Forest virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope glycoprotein E2

MacromoleculeName: Envelope glycoprotein E2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 46.870211 KDa
SequenceString: SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AETVEEID ...String:
SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AETVEEID MHMPPDTPDR TLLSQQSGNV KITVGGKKVK YNCTCGTGNV GTTNSDMTIN TCLIEQCHVS VTDHKKWQFN SP FVPRADE PARKGKVHIP FPLDNITCRV PMAREPTVIH GKREVTLHLH PDHPTLFSYR TLGEDPQYHE EWVTAAVERT IPV PVDGME YHWGNNDPVR LWSQLTTEGK PHGWPHQIVQ YYYGLYPAAT VSAVVGMSLL ALISIFASCY MLVAARSKCL TPYA LTPGA AVPWTLGILC CAPRAHA

UniProtKB: Frameshifted structural polyprotein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 29.920711 KDa
SequenceString: MNYIPTQTFY GRRWRPRPAA RPWPLQATPV APVVPDFQAQ QMQQLISAVN ALTMRQNAIA PARPPKPKKK KTTKPKPKTQ PKKINGKTQ QQKKKDKQAD KKKKKPGKRE RMCMKIENDC IFEVKHEGKV TGYACLVGDK VMKPAHVKGV IDNADLAKLA F KKSSKYDL ...String:
MNYIPTQTFY GRRWRPRPAA RPWPLQATPV APVVPDFQAQ QMQQLISAVN ALTMRQNAIA PARPPKPKKK KTTKPKPKTQ PKKINGKTQ QQKKKDKQAD KKKKKPGKRE RMCMKIENDC IFEVKHEGKV TGYACLVGDK VMKPAHVKGV IDNADLAKLA F KKSSKYDL ECAQIPVHMR SDASKYTHEK PEGHYNWHHG AVQYSGGRFT IPTGAGKPGD SGRPIFDNKG RVVAIVLGGA NE GSRTALS VVTWNKDMVT RVTPEGSEEW

UniProtKB: Frameshifted structural polyprotein

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Macromolecule #3: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 47.488781 KDa
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTNKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYAASHSN VVFP DMSGT ALSWVQKISG GLGAFAIGAI LVLVVVTCIG LRR

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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 739620
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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