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Yorodumi- EMDB-32005: Focused refinement of asymmetric unit of bacteriophage lambda pro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32005 | |||||||||
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Title | Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 Angstrom | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacteriophage lambda / capsid / procapsid / capsid maturation / virus structure / cryo-EM / auxiliary protein / conformational expansion / cementing protein / DNA packaging / VIRUS | |||||||||
Function / homology | Major capsid protein GpE / Phage major capsid protein E / T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm / Major capsid protein Function and homology information | |||||||||
Biological species | Escherichia phage lambda (virus) / Escherichia virus Lambda | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | Wang JW | |||||||||
Funding support | China, 2 items
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Citation | Journal: Structure / Year: 2022 Title: Structural basis of bacteriophage lambda capsid maturation. Authors: Chang Wang / Jianwei Zeng / Jiawei Wang / Abstract: Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins ...Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins initially assemble into a precursor capsid (procapsid) and subsequent genome packaging triggers morphological expansion of the shell. An auxiliary protein is required to stabilize the expanded capsid structure. To investigate the capsid maturation mechanism, we determined the cryo-electron microscopy structures of the bacteriophage lambda procapsid and mature capsid at 3.88 Å and 3.76 Å resolution, respectively. Besides primarily rigid body movements of common features of the major capsid protein gpE, large-scale structural rearrangements of other domains occur simultaneously. Assembly of intercapsomers within the procapsid is facilitated by layer-stacking effects at 3-fold vertices. Upon conformational expansion of the capsid shell, the missing top layer is fulfilled by cementing the gpD protein against the internal pressure of DNA packaging. Our structures illuminate the assembly mechanisms of dsDNA viruses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32005.map.gz | 70.4 MB | EMDB map data format | |
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Header (meta data) | emd-32005-v30.xml emd-32005.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32005_fsc.xml | 25.3 KB | Display | FSC data file |
Images | emd_32005.png | 159.6 KB | ||
Filedesc metadata | emd-32005.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32005 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32005 | HTTPS FTP |
-Validation report
Summary document | emd_32005_validation.pdf.gz | 346.6 KB | Display | EMDB validaton report |
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Full document | emd_32005_full_validation.pdf.gz | 346.2 KB | Display | |
Data in XML | emd_32005_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_32005_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32005 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32005 | HTTPS FTP |
-Related structure data
Related structure data | 7viaMC 7vi9C 7viiC 7vikC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32005.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.30654 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Escherichia virus Lambda
Entire | Name: Escherichia virus Lambda |
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Components |
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-Supramolecule #1: Escherichia virus Lambda
Supramolecule | Name: Escherichia virus Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10710 / Sci species name: Escherichia virus Lambda / 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: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage lambda (virus) |
Molecular weight | Theoretical: 38.22916 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT ...String: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT EWSKRDKSTY DPTDDIEAYA LNASGVVNII VFDPKGWALF RSFKAVKEKL DTRRGSNSEL ETAVKDLGKA VS YKGMYGD VAIVVYSGQY VENGVKKNFL PDNTMVLGNT QARGLRTYGC IQDADAQREG INASARYPKN WVTTGDPARE FTM IQSAPL MLLADPDEFV SVQLA UniProtKB: Major capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |