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1hb7

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quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography.

1hb7, resolution 14.00Å

Structural highlights

1hb7 is a 12 chain structure with sequence from Enterobacteria phage PRD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 14Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPPRD Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.

Publication Abstract from PubMed

BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A crystallographic structure of its major coat protein, P3, is available. Cryo-electron microscopy (cryo-EM) and three-dimensional reconstruction have shown the capsid at 20-28 A resolution. Striking architectural similarities between PRD1 and the mammalian adenovirus indicate a common ancestor. RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking the membrane and the vertices. Establishing the absolute EM scale was crucial for an accurate match. The resulting "quasi-atomic" models of the capsid define the residues involved in the major P3 interactions, within the quasi-equivalent interfaces and with the membrane, and show how these are altered upon DNA packaging. CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations limited to those P3 residues involved in membrane contacts. These are restricted to a few of the N termini along the icosahedral edges in the empty particle; DNA packaging leads to a 4-fold increase in the number of contacts, including almost all copies of the N terminus and the loop between the two beta barrels. Analysis of the P3 residues in each quasi-equivalent interface suggests two sites for minor proteins in the capsid edges, analogous to those in adenovirus.

Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions.,Martin CS, Burnett RM, de Haas F, Heinkel R, Rutten T, Fuller SD, Butcher SJ, Bamford DH Structure. 2001 Oct;9(10):917-30. PMID:11591347^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Martin CS, Burnett RM, de Haas F, Heinkel R, Rutten T, Fuller SD, Butcher SJ, Bamford DH. Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure. 2001 Oct;9(10):917-30. PMID:11591347

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1hb7"

@@ Line 3: / Line 3: @@
 <SX load='1hb7' size='340' side='right' viewer='molstar' caption='[[1hb7]], [[Resolution|resolution]] 14.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1hb7]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpprd Bpprd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HB7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1hb7]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_PRD1 Enterobacteria phage PRD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HB7 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cjd|1cjd]], [[1hb5|1hb5]], [[1hb9|1hb9]], [[1hqn|1hqn]], [[1hx6|1hx6]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 14&#8491;</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hb7 OCA], [https://pdbe.org/1hb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hb7 RCSB], [https://www.ebi.ac.uk/pdbsum/1hb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hb7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CAPSD_BPPRD CAPSD_BPPRD]] Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.
+[https://www.uniprot.org/uniprot/CAPSD_BPPRD CAPSD_BPPRD] Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </SX>
-[[Category: Bpprd]]
+[[Category: Enterobacteria phage PRD1]]
 [[Category: Large Structures]]
-[[Category: Bamford, D H]]
+[[Category: Bamford DH]]
-[[Category: Burnett, R M]]
+[[Category: Burnett RM]]
-[[Category: Butcher, S J]]
+[[Category: Butcher SJ]]
-[[Category: Fuller, S D]]
+[[Category: De Haas F]]
-[[Category: Haas, F De]]
+[[Category: Fuller SD]]
-[[Category: Heinkel, R]]
+[[Category: Heinkel R]]
-[[Category: Martin, C San]]
+[[Category: Rutten T]]
-[[Category: Rutten, T]]
+[[Category: San Martin C]]
-[[Category: Icosahedral virus]]
-[[Category: Tectiviridae]]
-[[Category: Virus]]
-[[Category: Virus/viral protein]]

1hb7

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Current revision

quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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