+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16649 | |||||||||
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Title | HK97 DNA packaging complex | |||||||||
Map data | HK97 bacteriophage packaging complex including Prohead II, portal protein, large terminase and a short DNA substrate | |||||||||
Sample |
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Keywords | HK97 / bacteriophage / packaging motor / DNA complex / VIRAL PROTEIN | |||||||||
Biological species | Hendrixvirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.29 Å | |||||||||
Authors | Hawkins DEDP / Antson AA | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Insights into a viral motor: the structure of the HK97 packaging termination assembly. Authors: Dorothy E D P Hawkins / Oliver W Bayfield / Herman K H Fung / Daniel N Grba / Alexis Huet / James F Conway / Alfred A Antson / Abstract: Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each ...Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16649.map.gz | 767.8 MB | EMDB map data format | |
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Header (meta data) | emd-16649-v30.xml emd-16649.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16649_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_16649.png | 169.5 KB | ||
Masks | emd_16649_msk_1.map | 824 MB | Mask map | |
Others | emd_16649_half_map_1.map.gz emd_16649_half_map_2.map.gz | 665.3 MB 665 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16649 | HTTPS FTP |
-Validation report
Summary document | emd_16649_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_16649_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_16649_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | emd_16649_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16649 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16649 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16649.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | HK97 bacteriophage packaging complex including Prohead II, portal protein, large terminase and a short DNA substrate | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16649_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: HK97 bacteriophage packaging complex including Prohead II, portal...
File | emd_16649_half_map_1.map | ||||||||||||
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Annotation | HK97 bacteriophage packaging complex including Prohead II, portal protein, large terminase and a short DNA substrate | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HK97 bacteriophage packaging complex including Prohead II, portal...
File | emd_16649_half_map_2.map | ||||||||||||
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Annotation | HK97 bacteriophage packaging complex including Prohead II, portal protein, large terminase and a short DNA substrate | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hendrixvirus
Entire | Name: Hendrixvirus |
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Components |
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-Supramolecule #1: Hendrixvirus
Supramolecule | Name: Hendrixvirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Proheads were produced by infection of E. coli 594 cells with HK97 amber mutant amC2, propagated using Escherichia LE392 cells NCBI-ID: 2169654 / Sci species name: Hendrixvirus / Sci species strain: HK97 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Escherichia phage EcSzw-2 (virus) / Strain: 594 |
Molecular weight | Theoretical: 560 KDa |
-Macromolecule #1: HK97 DNA packaging complex (portal)
Macromolecule | Name: HK97 DNA packaging complex (portal) / type: protein_or_peptide / ID: 1 / Details: portal protein / Enantiomer: LEVO |
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Source (natural) | Organism: Hendrixvirus |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDNR KKVDLSNPLA RLLRYSPNQY MTAQEFREAM TMQLCFYGNA YALVDRNSAG DVISLLPLQS ANMDVKLVGK KVVYRYQRDS ...String: MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDNR KKVDLSNPLA RLLRYSPNQY MTAQEFREAM TMQLCFYGNA YALVDRNSAG DVISLLPLQS ANMDVKLVGK KVVYRYQRDS EYADFSQKEI FHLKGFGFTG LVGLSPIAFA CKSAGVAVAM EDQQRDFFAN GAKSPQILST GEKVLTEQQR SQVEENFKEI AGGPVKKRLW ILEAGFSTSA IGVTPQDAEM MASRKFQVSE LARFFGVPPH LVGDVEKSTS WGSGIEQQNL GFLQYTLQPY ISRWENSIQR WLIPSKDVGR LHAEHNLDGL LRGDSASRAA FMKAMGESGL RTINEMRRTD NMPPLPGGDV AMRQAQYVPI TDLGTNKEPR NNGA |
-Macromolecule #2: HK97 prohead II from packaging complex
Macromolecule | Name: HK97 prohead II from packaging complex / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Hendrixvirus |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: SLGSDADSAG SLIQPMQIPG IIMPGLRRLT IRDLLAQGRT SSNALEYVRE EVFTNNADVV AEKALKPESD ITFSKQTANV KTIAHWVQAS RQVMDDAPML QSYINNRLMY GLALKEEGQL LNGDGTGDNL EGLNKVATAY DTSLNATGDT RADIIAHAIY QVTESEFSAS ...String: SLGSDADSAG SLIQPMQIPG IIMPGLRRLT IRDLLAQGRT SSNALEYVRE EVFTNNADVV AEKALKPESD ITFSKQTANV KTIAHWVQAS RQVMDDAPML QSYINNRLMY GLALKEEGQL LNGDGTGDNL EGLNKVATAY DTSLNATGDT RADIIAHAIY QVTESEFSAS GIVLNPRDWH NIALLKDNEG RYIFGGPQAF TSNIMWGLPV VPTKAQAAGT FTVGGFDMAS QVWDRMDATV EVSREDRDNF VKNMLTILCE ERLALAHYRP TAIIKGTFSS GS |
-Macromolecule #3: HK97 packaging complex large terminase
Macromolecule | Name: HK97 packaging complex large terminase / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Hendrixvirus |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MTRGERVIAF IERFCIVPEG KLIGQPMRLD PFQKDFILAV YDNPAGTDMA ILSIARKNGK TGLIAGILLA HLVGPEAVQN TQIVSGALSR EQAAIVFNLA VKMVNLNPKL QEIVHITPSG KKLIGLPCNV EYKALSAEGK TTHGLSPILA ILDETGQVRG PQDDFIDAIT ...String: MTRGERVIAF IERFCIVPEG KLIGQPMRLD PFQKDFILAV YDNPAGTDMA ILSIARKNGK TGLIAGILLA HLVGPEAVQN TQIVSGALSR EQAAIVFNLA VKMVNLNPKL QEIVHITPSG KKLIGLPCNV EYKALSAEGK TTHGLSPILA ILDETGQVRG PQDDFIDAIT TAQGAHENPL LIVISTQAAN DADLLSIWID DAVKSKDPHI VCHVYEAPKD ADISKRESWL AANPALGTFR SEKDMARQAE KAGRMPSFEN TFRNLNLNQR VSTVSPFISR SVWELCGEMP INTPRKWYAG LDLSARNDLT ALVIAGEADD GVWDVFPFFW TPQKTLEERT KTDRAPYDVW VREGLLRTTP GASVDYSFVV ADIAEIIGDF DLTSMAFDRW RIDQFRKDAD AIGLSLPLVE FGQGFKDMGP AVDTLESLML NGRVRHGMHP VLTMCAVNAV VVKDAAGNRK LDKSKATGRI DGMVAMTMSV GAANGEVTEQ GGDFDDFIFR PLSM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: final buffer = 20 mM Tris pH 7.5, 10 mM MgCl2, 50 mM KGlu, 5 mM ATP-gamma-S |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
Details | Packaging reactions 30 nM hk97 proheads, 2.5 micromolar large terminase, 5 micromolar small terminase and 30 nM DNA, 75 micromolar ATP were incubated for 2 mins then 5 micromolar ATP-gamma-S was added. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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