1WAA

IG27 protein domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis.

Stacklies, W.Vega, M.C.Wilmanns, M.Grater, F.

(2009) PLoS Comput Biol 5: 00306

  • DOI: 10.1371/journal.pcbi.1000306
  • Primary Citation of Related Structures:  
    1WAA

  • PubMed Abstract: 
  • The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins. How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown ...

    The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins. How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown. We present a new method based on molecular dynamics simulations to disclose the distribution of strain in protein structures, here for the newly determined high-resolution crystal structure of I27, a titin immunoglobulin (IG) domain. We obtain a sparse, spatially connected, and highly anisotropic mechanical network. This allows us to detect load-bearing motifs composed of interstrand hydrogen bonds and hydrophobic core interactions, including parts distal to the site to which force was applied. The role of the force distribution pattern for mechanical stability is tested by in silico unfolding of I27 mutants. We then compare the observed force pattern to the sparse network of coevolved residues found in this family. We find a remarkable overlap, suggesting the force distribution to reflect constraints for the evolutionary design of mechanical resistance in the IG family. The force distribution analysis provides a molecular interpretation of coevolution and opens the road to the study of the mechanism of signal propagation in proteins in general.


    Organizational Affiliation

    CAS-MPG Partner Institute for Computational Biology, Shanghai, People's Republic of China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TITINA, B, C, D93Homo sapiensMutation(s): 0 
Gene Names: TTN
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
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Go to UniProtKB:  Q8WZ42
PHAROS:  Q8WZ42
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TITINE93Homo sapiensMutation(s): 0 
Gene Names: TTN
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WZ42 (Homo sapiens)
Explore Q8WZ42 
Go to UniProtKB:  Q8WZ42
PHAROS:  Q8WZ42
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TITINF93Homo sapiensMutation(s): 0 
Gene Names: TTN
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WZ42 (Homo sapiens)
Explore Q8WZ42 
Go to UniProtKB:  Q8WZ42
PHAROS:  Q8WZ42
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth F] , CA [auth F] , DA [auth F] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
AA [auth E],  BA [auth F],  CA [auth F],  DA [auth F],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth C],  R [auth C],  S [auth C],  T [auth C],  U [auth C],  V [auth D],  W [auth D],  X [auth D],  Y [auth E],  Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.24α = 90
b = 75.99β = 90
c = 134.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-05
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection