+Open data
-Basic information
Entry | Database: PDB / ID: 1if0 | ||||||
---|---|---|---|---|---|---|---|
Title | PSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II) | ||||||
Components | PROTEIN (MAJOR CAPSID PROTEIN GP5) | ||||||
Keywords | VIRUS / Bacteriophage / Capsid / cryoEM / Pseudo-atomic model. / Icosahedral virus | ||||||
Function / homology | Phage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein Function and homology information | ||||||
Biological species | Enterobacteria phage HK97 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
Authors | Conway, J.F. / Wikoff, W.R. / Cheng, N. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Steven, A.C. | ||||||
Citation | Journal: Science / Year: 2001 Title: Virus maturation involving large subunit rotations and local refolding. Authors: J F Conway / W R Wikoff / N Cheng / R L Duda / R W Hendrix / J E Johnson / A C Steven / Abstract: Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a ...Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging. #1: Journal: Science / Year: 2000 Title: Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid Authors: Wikoff, W.R. / Liljas, L. / Duda, R.L. / Tsuruta, H. / Hendrix, R.W. / Johnson, J.E. #2: Journal: Science / Year: 1995 Title: Proteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System Authors: Conway, J.F. / Duda, R.L. / Cheng, N. / Hendrix, R.W. / Steven, A.C. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1if0.cif.gz | 62 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1if0.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 1if0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1if0_validation.pdf.gz | 325.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1if0_full_validation.pdf.gz | 326.1 KB | Display | |
Data in XML | 1if0_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 1if0_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1if0 ftp://data.pdbj.org/pub/pdb/validation_reports/if/1if0 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 28279.750 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Genus: Lambda-like viruses / Plasmid: PT7-5 / Production host: Escherichia coli (E. coli) / Strain (production host): PT7-HD2.9B / References: UniProt: P49861 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II) / Type: VIRUS |
---|---|
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Film or detector model: GENERIC FILM |
Image scans | Scanner model: ZEISS SCAI |
-Processing
Particle selection | Num. of particles selected: 2939 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 12 Å / Resolution method: OTHER / Num. of particles: 981 Details: IMAGE RECONSTRUCTION INCLUDING CONTRAST TRANSFER CORRECTION, WAS DONE AS DESCRIBED IN T.S.Baker & R.H.Cheng, J.Struct.Biol. 116, 120-130 (1996) and J.F.Conway & A.C.Steven, J.Struct.Biol. ...Details: IMAGE RECONSTRUCTION INCLUDING CONTRAST TRANSFER CORRECTION, WAS DONE AS DESCRIBED IN T.S.Baker & R.H.Cheng, J.Struct.Biol. 116, 120-130 (1996) and J.F.Conway & A.C.Steven, J.Struct.Biol. 128, 106 (1999). Nine focal pairs were analyzed, yielding 2939 particles, of which 981 were included in the final map. This map was calculated to 12 Angstroms, its resolution as assessed by Fourier Ring Correlation (cutoff 2 sigma), as calculated between reprojections of two maps from half data sets. Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL | ||||||||||||
Refinement | Highest resolution: 12 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 12 Å
| ||||||||||||
Refinement | *PLUS Highest resolution: 12 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |