1MQK

Crystal structure of the unliganded Fv-fragment of the anti-cytochrome C oxidase antibody 7E2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.

Essen, L.O.Harrenga, A.Ostermeier, C.Michel, H.

(2003) Acta Crystallogr D Biol Crystallogr 59: 677-687

  • DOI: https://doi.org/10.1107/s0907444903002233
  • Primary Citation of Related Structures:  
    1MQK

  • PubMed Abstract: 

    The antibody Fv fragment 7E2 has previously been employed in the induced crystallization of the integral membrane protein cytochrome c oxidase from Paracoccus denitrificans. The 1.3 A X-ray structure of the uncomplexed antibody fragment reveals conserved water networks on the surfaces of the framework regions. A novel consensus motif for water coordination, XX(S/T), is found along the edges of the beta-sandwich, where a water molecule forms hydrogen bonds to the carbonyl O atom of a residue at position N and the OG hydroxyl groups of conserved serines or threonines at position N + 2. Multiple conformations were found in the hydrophobic core for residues IleL21, LeuL33 and the disulfide bridges. An internal water molecule that is compatible with only one of the three packing states of the V(L) core suggests local 'breathing' of the variable domain. TrpH47, a conserved key residue of the V(H)/V(L) interface, is crucially involved in the formation of the antigen-binding site by adopting a novel conformation that specifically stabilizes the non-canonical CDR-L3 loop. Finally, a comparison with 7E2-cytochrome c oxidase complexes demonstrates that binding of this membrane-bound antigen proceeds without major conformational changes of the 7E2 antibody fragment.


  • Organizational Affiliation

    Department of Chemsitry, Philipps University, Marburg, Germany. essen@chemie.uni-marburg.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antibody 7E2 FV fragment, light chainA [auth L]120Mus musculusMutation(s): 0 
UniProt
Find proteins for P01636 (Mus musculus)
Explore P01636 
Go to UniProtKB:  P01636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01636
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody 7E2 FV fragment, heavy chainB [auth H]127Mus musculusMutation(s): 0 
UniProt
Find proteins for P18525 (Mus musculus)
Explore P18525 
Go to UniProtKB:  P18525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18525
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.436α = 90
b = 56.045β = 90
c = 99.846γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLORmodel building
SHELXLrefinement
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary