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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20956 | |||||||||
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Title | Portal vertex structure of bacteriophage T4 | |||||||||
![]() | low-pass filtered and B-factor sharpened map | |||||||||
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![]() | portal protein assembly / gp20 / gp23 / portal vertex / VIRUS | |||||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope, contractile tail mechanism / T=13 icosahedral viral capsid / viral portal complex / viral genome packaging / viral release from host cell / viral capsid / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Fang Q / Fokine A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural morphing in a symmetry-mismatched viral vertex. Authors: Qianglin Fang / Wei-Chun Tang / Pan Tao / Marthandan Mahalingam / Andrei Fokine / Michael G Rossmann / Venigalla B Rao / ![]() Abstract: Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of ...Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 275.6 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 24.3 MB 916.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uzcMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | low-pass filtered and B-factor sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: unfiltered map
File | emd_20956_additional_1.map | ||||||||||||
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Annotation | unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Supplemental map: emd 20956 additional 2.map
File | emd_20956_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Escherichia virus T4
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Escherichia virus T4
Supramolecule | Name: Escherichia virus T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10665 / Sci species name: Escherichia virus T4 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.074242 KDa |
Sequence | String: MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA ...String: MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA STQTTVGDIY THFFQETGTV YLQASVQVTI DAGATDAAKL DAEIKKQMEA GALVEIAEGM ATSIAELQEG FN GSTDNPW NEMGFRIDKQ VIEAKSRQLK AAYSIELAQD LRAVHGMDAD AELSGILATE IMLEINREVV DWINYSAQVG KSG MTLTPG SKAGVFDFQD PIDIRGARWA GESFKALLFQ IDKEAVEIAR QTGRGEGNFI IASRNVVNVL ASVDTGISYA AQGL ATGFS TDTTKSVFAG VLGGKYRVYI DQYAKQDYFT VGYKGPNEMD AGIYYAPYVA LTPLRGSDPK NFQPVMGFKT RYGIG INPF AESAAQAPAS RIQSGMPSIL NSLGKNAYFR RVYVKGI UniProtKB: Major capsid protein |
-Macromolecule #2: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.117082 KDa |
Sequence | String: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK ...String: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK EGIKELRRLD PRQVQYVREI ITETEAGTKI VKGYKEYFIY DTAHESYACD GRMYEAGTKI KIPKAAVVYA HS GLVDCCG KNIIGYLHRA VKPANQLKLL EDAVVIYRIT RAPDRRVWYV DTGNMPARKA AEHMQHVMNT MKNRVVYDAS TGK IKNQQH NMSMTEDYWL QRRDGKAVTE VDTLPGADNT GNMEDIRWFR QALYMALRVP LSRIPQDQQG GVMFDSGTSI TRDE LTFAK FIRELQHKFE EVFLDPLKTN LLLKGIITED EWNDEINNIK IEFHRDSYFA ELKEAEILER RINMLTMAEP FIGKY ISHR TAMKDILQMT DEEIEQEAKQ IEEESKEARF QDPDQEQEDF UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 23.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53608 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6uzc: |