6QYD image
Deposition Date 2019-03-08
Release Date 2019-06-12
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6QYD
Keywords:
VIRUS
Title:
Cryo-EM structure of the head in mature bacteriophage phi29
Biological Source:
Source Organism:
Bacillus phage phi29 (Taxon ID: 10756)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6QYD validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Major capsid protein
Gene (Uniprot):8
Chain IDs:A (auth: 1A), B (auth: 1B), C (auth: 1C), D (auth: 1D), E (auth: 1E), F (auth: 1F), G (auth: 2A), H (auth: 2B), I (auth: 2C), J (auth: 2D), K (auth: 2E), L (auth: 3A), M (auth: 3B), N (auth: 3C), O (auth: 3D), P (auth: 3E), Q (auth: 3F), R (auth: 4A), S (auth: 4B), T (auth: 4C), U (auth: 4D), V (auth: 4E), W (auth: 4F), X (auth: 5A), Y (auth: 5B), Z (auth: 5C), AA (auth: 5D), BA (auth: 5E), CA (auth: 5F), DA (auth: 6A), EA (auth: 6B), FA (auth: 6C), GA (auth: 6D), HA (auth: 6E), IA (auth: 6F), JA (auth: 7A), KA (auth: 7B), LA (auth: 7C), MA (auth: 7D), NA (auth: 7E), OA (auth: 8A), PA (auth: 8B), QA (auth: 8C), RA (auth: 8D), SA (auth: 8E), TA (auth: 8F), UA (auth: 9A), VA (auth: 1G), WA (auth: 1H), XA (auth: 1I), YA (auth: 1J), ZA (auth: 1K), AB (auth: 1L), BB (auth: 2F), CB (auth: 2G), DB (auth: 2H), EB (auth: 2I), FB (auth: 2J), GB (auth: 3G), HB (auth: 3H), IB (auth: 3I), JB (auth: 3J), KB (auth: 3K), LB (auth: 3L), MB (auth: 4G), NB (auth: 4H), OB (auth: 4I), PB (auth: 4J), QB (auth: 4K), RB (auth: 4L), SB (auth: 5G), TB (auth: 5H), UB (auth: 5I), VB (auth: 5J), WB (auth: 5K), XB (auth: 5L), YB (auth: 6G), ZB (auth: 6H), AC (auth: 6I), BC (auth: 6J), CC (auth: 6K), DC (auth: 6L), EC (auth: 7F), FC (auth: 7G), GC (auth: 7H), HC (auth: 7I), IC (auth: 7J), JC (auth: 8G), KC (auth: 8H), LC (auth: 8I), MC (auth: 8J), NC (auth: 8K), OC (auth: 8L), PC (auth: 9B), QC (auth: 1M), RC (auth: 1N), SC (auth: 1O), TC (auth: 1P), UC (auth: 1Q), VC (auth: 1R), WC (auth: 2K), XC (auth: 2L), YC (auth: 2M), ZC (auth: 2N), AD (auth: 2O), BD (auth: 3M), CD (auth: 3N), DD (auth: 3O), ED (auth: 3P), FD (auth: 3Q), GD (auth: 3R), HD (auth: 4M), ID (auth: 4N), JD (auth: 4O), KD (auth: 4P), LD (auth: 4Q), MD (auth: 4R), ND (auth: 5M), OD (auth: 5N), PD (auth: 5O), QD (auth: 5P), RD (auth: 5Q), SD (auth: 5R), TD (auth: 6M), UD (auth: 6N), VD (auth: 6O), WD (auth: 6P), XD (auth: 6Q), YD (auth: 6R), ZD (auth: 7K), AE (auth: 7L), BE (auth: 7M), CE (auth: 7N), DE (auth: 7O), EE (auth: 8M), FE (auth: 8N), GE (auth: 8O), HE (auth: 8P), IE (auth: 8Q), JE (auth: 8R), KE (auth: 9C), LE (auth: 1S), ME (auth: 1T), NE (auth: 1U), OE (auth: 1V), PE (auth: 1W), QE (auth: 1X), RE (auth: 2P), SE (auth: 2Q), TE (auth: 2R), UE (auth: 2S), VE (auth: 2T), WE (auth: 3S), XE (auth: 3T), YE (auth: 3U), ZE (auth: 3V), AF (auth: 3W), BF (auth: 3X), CF (auth: 4S), DF (auth: 4T), EF (auth: 4U), FF (auth: 4V), GF (auth: 4W), HF (auth: 4X), IF (auth: 5S), JF (auth: 5T), KF (auth: 5U), LF (auth: 5V), MF (auth: 5W), NF (auth: 5X), OF (auth: 6S), PF (auth: 6T), QF (auth: 6U), RF (auth: 6V), SF (auth: 6W), TF (auth: 6X), UF (auth: 7P), VF (auth: 7Q), WF (auth: 7R), XF (auth: 7S), YF (auth: 7T), ZF (auth: 8S), AG (auth: 8T), BG (auth: 8U), CG (auth: 8V), DG (auth: 8W), EG (auth: 8X), FG (auth: 9D), GG (auth: 1Y), HG (auth: 1Z), IG (auth: 1a), JG (auth: 1b), KG (auth: 1c), LG (auth: 1d), MG (auth: 2U), NG (auth: 2V), OG (auth: 2W), PG (auth: 2X), QG (auth: 2Y), RG (auth: 3Y), SG (auth: 3Z), TG (auth: 3a), UG (auth: 3b), VG (auth: 3c), WG (auth: 3d), XG (auth: 4Y), YG (auth: 4Z), ZG (auth: 4a), AH (auth: 4b), BH (auth: 4c), CH (auth: 4d), DH (auth: 5Y), EH (auth: 5Z), FH (auth: 5a), GH (auth: 5b), HH (auth: 5c), IH (auth: 5d), JH (auth: 6Y), KH (auth: 6Z), LH (auth: 6a), MH (auth: 6b), NH (auth: 6c), OH (auth: 6d), PH (auth: 7U), QH (auth: 7V), RH (auth: 7W), SH (auth: 7X), TH (auth: 7Y), UH (auth: 8Y), VH (auth: 8Z), WH (auth: 8a), XH (auth: 8b), YH (auth: 8c), ZH (auth: 8d), AI (auth: 9E)
Chain Length:448
Number of Molecules:235
Biological Source:Bacillus phage phi29
UniProt ID:P13849 Pfam ID:PF02368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Capsid fiber protein
Gene (Uniprot):8.5
Chain IDs:BI (auth: 1e), CI (auth: 1f), DI (auth: 1g), EI (auth: 1h), FI (auth: 2Z), GI (auth: 2a), HI (auth: 2b), II (auth: 2c), JI (auth: 2d), KI (auth: 3e), LI (auth: 3f), MI (auth: 3g), NI (auth: 3h), OI (auth: 4e), PI (auth: 4f), QI (auth: 5e), RI (auth: 5f), SI (auth: 6e), TI (auth: 6f), UI (auth: 6g), VI (auth: 6h), WI (auth: 7Z), XI (auth: 7a), YI (auth: 7b), ZI (auth: 7c), AJ (auth: 7d), BJ (auth: 8e), CJ (auth: 8f), DJ (auth: 8g), EJ (auth: 8h), FJ (auth: 8i), GJ (auth: 8j), HJ (auth: 9F), IJ (auth: 1i), JJ (auth: 1j), KJ (auth: 1k), LJ (auth: 1l), MJ (auth: 2e), NJ (auth: 2f), OJ (auth: 2g), PJ (auth: 2h), QJ (auth: 2i), RJ (auth: 3i), SJ (auth: 3j), TJ (auth: 3k), UJ (auth: 3l), VJ (auth: 4g), WJ (auth: 4h), XJ (auth: 5g), YJ (auth: 5h), ZJ (auth: 6i), AK (auth: 6j), BK (auth: 6k), CK (auth: 6l), DK (auth: 7e), EK (auth: 7f), FK (auth: 7g), GK (auth: 7h), HK (auth: 7i), IK (auth: 8k), JK (auth: 8l), KK (auth: 8m), LK (auth: 8n), MK (auth: 8o), NK (auth: 8p), OK (auth: 9G), PK (auth: 1m), QK (auth: 1n), RK (auth: 1o), SK (auth: 1p), TK (auth: 2j), UK (auth: 2k), VK (auth: 2l), WK (auth: 2m), XK (auth: 2n), YK (auth: 3m), ZK (auth: 3n), AL (auth: 3o), BL (auth: 3p), CL (auth: 4i), DL (auth: 4j), EL (auth: 5i), FL (auth: 5j), GL (auth: 6m), HL (auth: 6n), IL (auth: 6o), JL (auth: 6p), KL (auth: 7j), LL (auth: 7k), ML (auth: 7l), NL (auth: 7m), OL (auth: 7n), PL (auth: 8q), QL (auth: 8r), RL (auth: 8s), SL (auth: 8t), TL (auth: 8u), UL (auth: 8v), VL (auth: 9H), WL (auth: 1q), XL (auth: 1r), YL (auth: 1s), ZL (auth: 1t), AM (auth: 2o), BM (auth: 2p), CM (auth: 2q), DM (auth: 2r), EM (auth: 2s), FM (auth: 3q), GM (auth: 3r), HM (auth: 3s), IM (auth: 3t), JM (auth: 4k), KM (auth: 4l), LM (auth: 5k), MM (auth: 5l), NM (auth: 6q), OM (auth: 6r), PM (auth: 6s), QM (auth: 6t), RM (auth: 7o), SM (auth: 7p), TM (auth: 7q), UM (auth: 7r), VM (auth: 7s), WM (auth: 8w), XM (auth: 8x), YM (auth: 8y), ZM (auth: 8z), AN (auth: 9K), BN (auth: 9L), CN (auth: 9I), DN (auth: 1u), EN (auth: 1v), FN (auth: 1w), GN (auth: 1x), HN (auth: 2t), IN (auth: 2u), JN (auth: 2v), KN (auth: 2w), LN (auth: 2x), MN (auth: 3u), NN (auth: 3v), ON (auth: 3w), PN (auth: 3x), QN (auth: 4m), RN (auth: 4n), SN (auth: 5m), TN (auth: 5n), UN (auth: 6u), VN (auth: 6v), WN (auth: 6w), XN (auth: 6x), YN (auth: 7t), ZN (auth: 7u), AO (auth: 7v), BO (auth: 7w), CO (auth: 7x), DO (auth: 9M), EO (auth: 9N), FO (auth: 9O), GO (auth: 9P), HO (auth: 9Q), IO (auth: 9R), JO (auth: 9J)
Chain Length:281
Number of Molecules:165
Biological Source:Bacillus phage phi29
UniProt ID:B3VMP4 Pfam ID:PF11133
Ligand Molecules
NA
Primary Citation
Structural assembly of the tailed bacteriophage φ29.
Nat Commun 10 2366 2366 (2019)
PMID: 31147544 DOI: 10.1038/s41467-019-10272-3

Abstact

The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.

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Disease

Primary Citation of related structures
6QYD