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PDBsum entry 1pdm

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Structural protein PDB id
1pdm
Jmol
Contents
Protein chains
(+ 6 more) 328 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1pdm
Name: Structural protein
Title: Fitting of gp8 structure into the cryoem reconstruction of the bacteriophage t4 baseplate
Structure: Baseplate structural protein gp8. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: baseplate wedge protein 8
Source: Enterobacteria phage t4. Organism_taxid: 10665
Authors: V.A.Kostyuchenko,P.G.Leiman,P.R.Chipman,S.Kanamaru,M.J.Van Raaij,F.Arisaka,V.V.Mesyanzhinov,M.G.Rossmann
Key ref:
V.A.Kostyuchenko et al. (2003). Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Biol, 10, 688-693. PubMed id: 12923574 DOI: 10.1038/nsb970
Date:
19-May-03     Release date:   09-Sep-03    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19062  (VG08_BPT4) -  Base plate structural protein gp8
Seq:
Struc:
334 a.a.
328 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     virion   1 term 

 

 
    Key reference    
 
 
DOI no: 10.1038/nsb970 Nat Struct Biol 10:688-693 (2003)
PubMed id: 12923574  
 
 
Three-dimensional structure of bacteriophage T4 baseplate.
V.A.Kostyuchenko, P.G.Leiman, P.R.Chipman, S.Kanamaru, M.J.van Raaij, F.Arisaka, V.V.Mesyanzhinov, M.G.Rossmann.
 
  ABSTRACT  
 
The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Fit of the crystal structures, shown as C traces, into the cryoEM density. (a) The short tail fiber gp12 (magenta) and a part of gp11 (cyan) are viewed as area A in Figure 1. (b) gp9 (green), viewed as area B in Figure 1. An intermediate and two extreme directions of the long tail fiber, as suggested by the orientations of the gp9 trimer, are shown as green, red and blue lines, respectively. The orientation of the tail axis is vertical and is situated behind the display.
Figure 3.
Figure 3. Details of the baseplate structure. Proteins are labeled with their respective gene numbers. (a) The garland of short tail fibers gp12 (magenta) with gp11 structures (cyan C -trace) at the kinks of the gp12 fibers. Black line, six-fold axis of the baseplate. (b) The baseplate 'pins,' composed of gp7 (red), gp8 (dark blue C -trace), gp10 (yellow) and gp11 (cyan C -trace). Shown also is gp9 (green C -trace), the long tail fiber attachment protein, with a green line along its three-fold axis representing the direction of the long tail fibers. (c) Unassigned density around the center of the baseplate representing gp6, gp25 and gp53.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 688-693) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20888470 C.L.Lawson (2010).
Unified data resource for cryo-EM.
  Methods Enzymol, 483, 73-90.  
20660769 L.Cardarelli, L.G.Pell, P.Neudecker, N.Pirani, A.Liu, L.A.Baker, J.L.Rubinstein, K.L.Maxwell, and A.R.Davidson (2010).
Phages have adapted the same protein fold to fulfill multiple functions in virion assembly.
  Proc Natl Acad Sci U S A, 107, 14384-14389.
PDB code: 2kx4
20593364 M.L.Yap, K.Mio, S.Ali, A.Minton, S.Kanamaru, and F.Arisaka (2010).
Sequential assembly of the wedge of the baseplate of phage T4 in the presence and absence of gp11 as monitored by analytical ultracentrifugation.
  Macromol Biosci, 10, 808-813.  
  21129200 P.G.Leiman, F.Arisaka, M.J.van Raaij, V.A.Kostyuchenko, A.A.Aksyuk, S.Kanamaru, and M.G.Rossmann (2010).
Morphogenesis of the T4 tail and tail fibers.
  Virol J, 7, 355.  
21041684 S.G.Bartual, J.M.Otero, C.Garcia-Doval, A.L.Llamas-Saiz, R.Kahn, G.C.Fox, and M.J.van Raaij (2010).
Structure of the bacteriophage T4 long tail fiber receptor-binding tip.
  Proc Natl Acad Sci U S A, 107, 20287-20292.
PDB code: 2xgf
19523898 A.A.Aksyuk, P.G.Leiman, M.M.Shneider, V.V.Mesyanzhinov, and M.G.Rossmann (2009).
The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
  Structure, 17, 800-808.
PDB codes: 3h2t 3h3w 3h3y
19284603 F.Boyer, G.Fichant, J.Berthod, Y.Vandenbrouck, and I.Attree (2009).
Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?
  BMC Genomics, 10, 104.  
19251641 P.G.Leiman, M.Basler, U.A.Ramagopal, J.B.Bonanno, J.M.Sauder, S.Pukatzki, S.K.Burley, S.C.Almo, and J.J.Mekalanos (2009).
Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.
  Proc Natl Acad Sci U S A, 106, 4154-4159.
PDB code: 2p5z
18976216 L.P.Kurochkina, A.Y.Vishnevskiy, and V.V.Mesyanzhinov (2008).
Role of the C-terminus in folding and oligomerization of bacteriophage T4 gene product 9.
  Biochemistry (Mosc), 73, 995-999.  
18326574 M.Nemoto, K.Mio, S.Kanamaru, and F.Arisaka (2008).
ORF334 in Vibrio phage KVP40 plays the role of gp27 in T4 phage to form a heterohexameric complex.
  J Bacteriol, 190, 3606-3612.  
18524932 M.R.Clokie, K.Thalassinos, P.Boulanger, S.E.Slade, S.Stoilova-McPhie, M.Cane, J.H.Scrivens, and N.H.Mann (2008).
A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2.
  Microbiology, 154, 1775-1782.  
17395453 J.E.Johnson, and W.Chiu (2007).
DNA packaging and delivery machines in tailed bacteriophages.
  Curr Opin Struct Biol, 17, 237-243.  
17164521 M.G.Rossmann, F.Arisaka, A.J.Battisti, V.D.Bowman, P.R.Chipman, A.Fokine, S.Hafenstein, S.Kanamaru, V.A.Kostyuchenko, V.V.Mesyanzhinov, M.M.Shneider, M.C.Morais, P.G.Leiman, L.M.Palermo, C.R.Parrish, and C.Xiao (2007).
From structure of the complex to understanding of the biology.
  Acta Crystallogr D Biol Crystallogr, 63, 9.  
  17919320 S.C.Hardies, J.A.Thomas, and P.Serwer (2007).
Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.
  Virol J, 4, 97.  
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
16496021 P.Aloy, and R.B.Russell (2006).
Structural systems biology: modelling protein interactions.
  Nat Rev Mol Cell Biol, 7, 188-197.  
17053784 Y.Xiang, M.C.Morais, A.J.Battisti, S.Grimes, P.J.Jardine, D.L.Anderson, and M.G.Rossmann (2006).
Structural changes of bacteriophage phi29 upon DNA packaging and release.
  EMBO J, 25, 5229-5239.  
16271026 A.Y.Vishnevskiy, L.P.Kurochkina, N.N.Sykilinda, N.V.Solov'eva, M.M.Shneider, P.G.Leiman, and V.V.Mesyanzhinov (2005).
Functional role of the N-terminal domain of bacteriophage T4 gene product 11.
  Biochemistry (Mosc), 70, 1111-1118.  
16142226 B.A.Fane (2005).
A four-dimensional structure of T4 infection.
  Nat Struct Mol Biol, 12, 739-740.
PDB code: 1zku
16396595 F.Arisaka (2005).
Assembly and infection process of bacteriophage T4.
  Chaos, 15, 047502.  
15933718 L.Tang, W.R.Marion, G.Cingolani, P.E.Prevelige, and J.E.Johnson (2005).
Three-dimensional structure of the bacteriophage P22 tail machine.
  EMBO J, 24, 2087-2095.  
15828858 M.B.Sullivan, M.L.Coleman, P.Weigele, F.Rohwer, and S.W.Chisholm (2005).
Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations.
  PLoS Biol, 3, e144.  
15766536 M.G.Rossmann, M.C.Morais, P.G.Leiman, and W.Zhang (2005).
Combining X-ray crystallography and electron microscopy.
  Structure, 13, 355-362.  
15766539 S.Dutta, and H.M.Berman (2005).
Large macromolecular complexes in the Protein Data Bank: a status report.
  Structure, 13, 381-388.  
16116440 V.A.Kostyuchenko, P.R.Chipman, P.G.Leiman, F.Arisaka, V.V.Mesyanzhinov, and M.G.Rossmann (2005).
The tail structure of bacteriophage T4 and its mechanism of contraction.
  Nat Struct Mol Biol, 12, 810-813.
PDB codes: 1zku 2bsg
15315751 A.C.Steven (2004).
Signal transduction at a protein synapse.
  Cell, 118, 403-404.  
15093831 M.G.Rossmann, V.V.Mesyanzhinov, F.Arisaka, and P.G.Leiman (2004).
The bacteriophage T4 DNA injection machine.
  Curr Opin Struct Biol, 14, 171-180.  
15315755 P.G.Leiman, P.R.Chipman, V.A.Kostyuchenko, V.V.Mesyanzhinov, and M.G.Rossmann (2004).
Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.
  Cell, 118, 419-429.
PDB code: 1tja
15193311 R.B.Russell, F.Alber, P.Aloy, F.P.Davis, D.Korkin, M.Pichaud, M.Topf, and A.Sali (2004).
A structural perspective on protein-protein interactions.
  Curr Opin Struct Biol, 14, 313-324.  
15576776 S.Chibani-Chennoufi, C.Canchaya, A.Bruttin, and H.Brüssow (2004).
Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages.
  J Bacteriol, 186, 8276-8286.  
15627372 V.V.Mesyanzhinov, P.G.Leiman, V.A.Kostyuchenko, L.P.Kurochkina, K.A.Miroshnikov, N.N.Sykilinda, and M.M.Shneider (2004).
Molecular architecture of bacteriophage T4.
  Biochemistry (Mosc), 69, 1190-1202.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.