PDBsum entry 2rik

Structural protein

PDB id: 2rik

Contents

Protein chain

283 a.a. *

Waters ×479

* Residue conservation analysis

PDB id:

2rik

Name:

Structural protein

Title:

I-band fragment i67-i69 from titin

Structure:

Titin. Chain: a. Fragment: i67-i69. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.171 R-free: 0.216

Authors:

M.Marino,E.Von Castelmur,D.Labeit,S.Labeit,O.Mayans

Key ref:

E.von Castelmur et al. (2008). A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain. Proc Natl Acad Sci U S A, 105, 1186-1191. PubMed id: 18212128 DOI: 10.1073/pnas.0707163105

Date:

11-Oct-07 Release date: 22-Jan-08

Protein chain

O97791  (O97791_RABIT) -  Titin (Fragment) from Oryctolagus cuniculus

Seq: 2000 a.a.

Struc: 283 a.a.*

* PDB and UniProt seqs differ at 218 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0707163105

Proc Natl Acad Sci U S A 105:1186-1191 (2008)

PubMed id: 18212128

A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain.

E.von Castelmur, M.Marino, D.I.Svergun, L.Kreplak, Z.Ucurum-Fotiadis, P.V.Konarev, A.Urzhumtsev, D.Labeit, S.Labeit, O.Mayans.

ABSTRACT

Myofibril elasticity, critical to muscle function, is dictated by the intrasarcomeric filament titin, which acts as a molecular spring. To date, the molecular events underlying the mechanics of the folded titin chain remain largely unknown. We have elucidated the crystal structure of the 6-Ig fragment I65-I70 from the elastic I-band fraction of titin and validated its conformation in solution using small angle x-ray scattering. The long-range properties of the chain have been visualized by electron microscopy on a 19-Ig fragment and modeled for the full skeletal tandem. Results show that conserved Ig-Ig transition motifs generate high-order in the structure of the filament, where conformationally stiff segments interspersed with pliant hinges form a regular pattern of dynamic super-motifs leading to segmental flexibility in the chain. Pliant hinges support molecular shape rearrangements that dominate chain behavior at moderate stretch, whereas stiffer segments predictably oppose high stretch forces upon full chain extension. There, librational entropy can be expected to act as an energy barrier to prevent Ig unfolding while, instead, triggering the unraveling of flanking springs formed by proline, glutamate, valine, and lysine (PEVK) sequences. We propose a mechanistic model based on freely jointed rigid segments that rationalizes the response to stretch of titin Ig-tandems according to molecular features.

Selected figure(s)

Figure 1.
Structural order in the poly-Ig from I-band titin. (A) Crystal structure of I65–I70. β-sheets are color coded to emphasize domain torsions. The FG β-hairpin, which claps against the Ig–Ig transition motif EPP, is colored black. (B) Modular composition of the I-band of soleus titin from rabbit (N2A and N2B elements are omitted). Ig domains are represented as boxes, where orange indicates Ig tightly connected and blue represents Ig containing a C-terminal three-residue linker. Annotations refer to conserved features at the Ig–Ig interfaces, where (i) an FG β-hairpin containing an NxxG sequence is marked by red asterisks, (ii) interdomain EPP motifs in green are listed vertically under each domain (Ig exhibiting a natural E-to-A mutation in this motif are colored salmon), and (iii) the conserved S/T residue in the BC loop is shown in red. These features are characteristic of the skeletal but not of the constitutive Ig tandems. Super-repeats of 6 or 10 Ig are indicated by capped bars. Domains with previously known structure are marked with a thick bar. (C) Frontal (Left) and lateral (Right) views of a predicted model of the complete skeletal Ig-tandem in one of its putative slack conformations in solution as calculated from linker arrangements in I65–I70. (D) Model in extended conformation (C and D are color coded as in B). (E) EM images (70 × 70 nm^2) of glycerol-sprayed/rotary shadowed I39–I57 accompanied by its corresponding model. The model (fragment indicated by arrows in C) has been oriented to match the micrographs, but no other manipulation has been applied (the 3D conformation of the I39–I57 model can be visualized in SI Movie 2).

Figure 2.
Molecular features of I65–I70. (A) Structure-based sequence alignment where orange and yellow represent >90% and >70% sequence identity, respectively, across all Ig of the skeletal tandem. Green indicates conserved hydrophobic positions. The EPP motif, NxxG sequence in β-hairpin FG, and the BC loop are boxed in black. To ease comparison, the E group in tight linkers is given as the last residue of the preceding domain. A conserved set of residues (KD at the CC′ region and Y at β-strand F) responsible for the conformation of the CC′D loop characteristic of this Ig type is boxed in blue. (B) Molecular surface of I65–I70 colored according to sequence conservation as in A. (C) I65–I66 long linker interface. The three inserted residues are in dark gray. The conserved E is now an integral part of the linker, whereas L, the last of the inserted residues, has replaced it at the N terminus of the following Ig. (D) I68–I69 interface representative of tight connections. The transition motif EPP, an integral part of the N terminus of I69, is in green. The conserved N residue from β-hairpin FG and the T group from the BC loop are in yellow; their interactions are conserved in all Ig constituents of I65–I70. Hydrogen bonds are shown as dashed lines (experimental electron density for both linkers is shown in SI Fig 6).

Figures were selected by an automated process.