PDBsum entry 2v9u

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protein Protein-protein interface(s) links
Transport protein PDB id
Protein chains
(+ 2 more) 132 a.a. *
Waters ×30
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Rim domain of main porin from mycobacteria smegmatis
Structure: Mspa. Chain: a, b, c, d, e, f, g, h. Fragment: rim domain, residues 28-96,149-211. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 246196. Strain: mc2 155. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.59Å     R-factor:   0.274     R-free:   0.299
Authors: D.Grueninger,M.O.P.Ziegler,J.W.A.Koetter,N.Treiber,M.-S.Schu G.E.Schulz
Key ref:
D.Grueninger et al. (2008). Designed protein-protein association. Science, 319, 206-209. PubMed id: 18187656 DOI: 10.1126/science.1150421
27-Aug-07     Release date:   15-Jan-08    
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Protein chains
Pfam   ArchSchema ?
A0QR29  (MSPA_MYCS2) -  Porin MspA
211 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     cytolysis in other organism   1 term 


DOI no: 10.1126/science.1150421 Science 319:206-209 (2008)
PubMed id: 18187656  
Designed protein-protein association.
D.Grueninger, N.Treiber, M.O.Ziegler, J.W.Koetter, M.S.Schulze, G.E.Schulz.
The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.
  Selected figure(s)  
Figure 1.
Fig. 1. Design of protein assemblies (24). The proteins in (C) to (H) are depicted as thick-lined C plots at various scales with mutated residues as colored spheres. (A) Sketch of an asymmetric interface between patches a and b, which, in general, gives rise to an infinite helix (top). A C[2]-symmetric interface also between patches a and b doubles the numbers of contacts and forms a globular complex (bottom). Along the same lines, the reported D[2], D[4], and D[8] oligomers have 4-, 8-, and 16-fold contacts, respectively (fig. S4). (B) Side-chain mobility of the C[4]-symmetric Rua, color-coded from 0° (blue) to 90° (red) angular spread in the torsion angles [1] and [2] (24). The C- and N-terminal domains are at the top and bottom, respectively. (C) Pga-A and -B designed in crystal contact a-a(25). (D) Pga-C and-D designed in crystal contact f-f (25). (E) Oas-A and-B planned as a D[2] tetramer at a rotation angle of 86° around a common molecular twofold axis (vertical). (F) Oas-C designed as a D[2] tetramer at an alternative rotation angle of 29°. (G) Designed D[2] tetramer of Uro-A around a common molecular twofold axis (vertical). The designed contact is between the NAD^+-binding domains (residues 142 to 343), which are given in lighter hues. (H) Designed octameric Rua-D with a head-head contact.
Figure 3.
Fig. 3. Established oligomer structures (24). All mutations are marked by purple spheres. (A) Crystal structure of C[2]-symmetric Uro-A showing the twofold molecular symmetry axis (red) and four local twofold axes relating the cores (darker colors) and the NAD^+ domains (light colors) to their counterparts. The interface between core and NAD^+ domains was broken in the lower left and upper right chains. (B) D[4]-symmetric octamer Rua-A. (C) C[2]-symmetric octamer Rua-B. (D) Negatively stained electron micrograph of Rua-E showing the fiber association and a Rua-A octamer (B) at the scale defined by the box edge. (E) Native mycobacterial porin (28). The encircled membrane-immersed part was deleted, giving rise to Myp-A. (F) D[8]-symmetric association of two Myp-A molecules (top and bottom ring). The positions of the 52-residue deletions are marked by red spheres (fig. S1D).
  The above figures are reprinted by permission from the AAAs: Science (2008, 319, 206-209) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315729 G.E.Schulz (2011).
A new classification of membrane protein crystals.
  J Mol Biol, 407, 640-646.  
21082721 G.J.Forse, N.Ram, D.R.Banatao, D.Cascio, M.R.Sawaya, H.E.Klock, S.A.Lesley, and T.O.Yeates (2011).
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.
  Protein Sci, 20, 168-178.
PDB code: 3o7o
21042600 A.Onoda, Y.Ueya, T.Sakamoto, T.Uematsu, and T.Hayashi (2010).
Supramolecular hemoprotein-gold nanoparticle conjugates.
  Chem Commun (Camb), 46, 9107-9109.  
20308536 C.Fan, S.Cheng, Y.Liu, C.M.Escobar, C.S.Crowley, R.E.Jefferson, T.O.Yeates, and T.A.Bobik (2010).
Short N-terminal sequences package proteins into bacterial microcompartments.
  Proc Natl Acad Sci U S A, 107, 7509-7514.  
21048085 K.Hashimoto, and A.R.Panchenko (2010).
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states.
  Proc Natl Acad Sci U S A, 107, 20352-20357.  
20133689 M.Biancalana, K.Makabe, and S.Koide (2010).
Minimalist design of water-soluble cross-beta architecture.
  Proc Natl Acad Sci U S A, 107, 3469-3474.
PDB codes: 3cka 3eex
20662000 N.Mitchell, A.Ebner, P.Hinterdorfer, R.Tampé, and S.Howorka (2010).
Chemical tags mediate the orthogonal self-assembly of DNA duplexes into supramolecular structures.
  Small, 6, 1732-1735.  
20661999 N.Yokoi, H.Inaba, M.Terauchi, A.Z.Stieg, N.J.Sanghamitra, T.Koshiyama, K.Yutani, S.Kanamaru, F.Arisaka, T.Hikage, A.Suzuki, T.Yamane, J.K.Gimzewski, Y.Watanabe, S.Kitagawa, and T.Ueno (2010).
Construction of robust bio-nanotubes using the controlled self-assembly of component proteins of bacteriophage T4.
  Small, 6, 1873-1879.
PDB code: 3a1m
19562111 D.Papapostolou, and S.Howorka (2009).
Engineering and exploiting protein assemblies in synthetic biology.
  Mol Biosyst, 5, 723-732.  
18840610 J.Wang, T.Palzkill, and D.C.Chow (2009).
Structural insight into the kinetics and DeltaCp of interactions between TEM-1 beta-lactamase and beta-lactamase inhibitory protein (BLIP).
  J Biol Chem, 284, 595-609.
PDB codes: 3c7u 3c7v
19243584 M.Bhattacharyya, and S.Vishveshwara (2009).
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks.
  BMC Struct Biol, 9, 8.  
19478874 M.Montal (2009).
Vpu matchmakers as a therapeutic strategy for HIV infection.
  PLoS Pathog, 5, e1000246.  
18798561 N.Jouravel, E.Sablin, M.Togashi, J.D.Baxter, P.Webb, and R.J.Fletterick (2009).
Molecular basis for dimer formation of TRbeta variant D355R.
  Proteins, 75, 111-117.
PDB code: 3d57
19834935 P.B.Crowley, P.M.Matias, A.R.Khan, M.Roessle, and D.I.Svergun (2009).
Metal-mediated self-assembly of a beta-sandwich protein.
  Chemistry, 15, 12672-12680.
PDB codes: 2w88 2w8c
19189379 T.A.Whitehead, E.Je, and D.S.Clark (2009).
Rational shape engineering of the filamentous protein gamma prefoldin through incremental gene truncation.
  Biopolymers, 91, 496-503.  
19575413 Y.Wine, N.Cohen-Hadar, R.Lamed, A.Freeman, and F.Frolow (2009).
Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity.
  Biotechnol Bioeng, 104, 444-457.  
18445293 D.Marsic, R.C.Hughes, M.L.Byrne-Steele, and J.D.Ng (2008).
PCR-based gene synthesis to produce recombinant proteins for crystallization.
  BMC Biotechnol, 8, 44.  
18563089 E.D.Levy, E.Boeri Erba, C.V.Robinson, and S.A.Teichmann (2008).
Assembly reflects evolution of protein complexes.
  Nature, 453, 1262-1265.  
18422313 E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, and F.A.Tezcan (2008).
Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation.
  J Am Chem Soc, 130, 6082-6084.
PDB codes: 3c62 3c63
19206287 T.F.Chou, C.So, B.R.White, J.C.Carlson, M.Sarikaya, and C.R.Wagner (2008).
Enzyme nanorings.
  ACS Nano, 2, 2519-2525.  
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.