8CMT

Structure of the plasma coagulation Factor XIII A2B2 heterotetrameric complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the human native plasma coagulation factor XIII complex.

Singh, S.Hagelueken, G.Ugurlar, D.Urs, S.U.R.Sharma, A.Mahapatra, M.Drepper, F.Imhof, D.Huesgen, P.F.Oldenburg, J.Geyer, M.Biswas, A.

(2024) Blood 

  • DOI: https://doi.org/10.1182/blood.2024025369
  • Primary Citation of Related Structures:  
    8CMT, 8CMU

  • PubMed Abstract: 

    The structure of human coagulation factor XIII (FXIII), a heterotetrameric plasma pro-transglutaminase that covalently crosslinks pre-formed fibrin polymers, remains elusive until today. The heterotetrameric complex is composed of two catalytic FXIII-A and two protective FXIII-B subunits. Structural etiology underlying FXIII deficiency has so far been derived from crystallographic structures, all of which are currently available for the FXIII-A2 homodimer only. Here, we present the cryo-electron microscopy structure of a native, human plasma-derived FXIII-A2B2 complex at 2.4 Å resolution. The structure provides detailed information on FXIII subunit interacting interfaces as the two subunits interact strongly in plasma. The native FXIII-A2B2 complex reveals a pseudo-symmetric heterotetramer of two FXIII-B monomers intercalating with a symmetric FXIII-A2 dimer forming a "crown-like" assembly. The symmetry axes of the A2 and B2 homodimers are twisted relative to each other such that Sushi domain 1 interacts with the catalytic core of the A subunit and Sushi domain 2 with the symmetry related A' subunit and vice versa. We also report four novel mutations in the F13A1 gene encoding the FXIII-A subunit from a cohort of patients with severe FXIII deficiency. Our structure reveals the etiological basis of homozygous and heterozygous pathogenic mutations and explains the conditional dominant negative effects of heterozygous mutations. This atomistic description of complex interfaces is consistent with previous biochemical data and shows a congruence between the structural biochemistry of the FXIII complex and the clinical features of FXIII deficiency.


  • Organizational Affiliation

    Institute of Experimental Hematology and Transfusion Medicine, Bonn, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XIII A chain
A, B
732Homo sapiensMutation(s): 0 
EC: 2.3.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for P00488 (Homo sapiens)
Explore P00488 
Go to UniProtKB:  P00488
PHAROS:  P00488
GTEx:  ENSG00000124491 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00488
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XIII B chain
C, D
661Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05160 (Homo sapiens)
Explore P05160 
Go to UniProtKB:  P05160
PHAROS:  P05160
GTEx:  ENSG00000143278 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05160
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBI 1645/3-1
German Research Foundation (DFG)GermanySI 2767-1/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary