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- PDB-8cmu: High resolution structure of the coagulation Factor XIII A2B2 het... -

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Basic information

Entry
Database: PDB / ID: 8cmu
TitleHigh resolution structure of the coagulation Factor XIII A2B2 heterotetramer complex.
Components
  • Coagulation factor XIII A chain
  • Coagulation factor XIII B chain
KeywordsBLOOD CLOTTING / Factor XIII
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / blood microparticle / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. ...: / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Coagulation factor XIII A chain / Coagulation factor XIII B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsSingh, S. / Urgular, D. / Hagelueken, G. / Geyer, M. / Biswas, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)BI 1645/3-1 Germany
German Research Foundation (DFG)SI 2767-1/1 Germany
CitationJournal: To Be Published
Title: The cryo-EM structure of the plasma coagulation Factor XIII complex at 2.68 Angstrom resolution.
Authors: Singh, S. / Urgular, D. / Hagelueken, G. / Ramaraje Urs, S.U. / Javed, H. / Imhof, D. / Geyer, M. / Oldenburg, J. / Biswas, A.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XIII A chain
B: Coagulation factor XIII A chain
C: Coagulation factor XIII B chain
D: Coagulation factor XIII B chain


Theoretical massNumber of molelcules
Total (without water)317,9314
Polymers317,9314
Non-polymers00
Water13,475748
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Coagulation factor XIII A chain / Coagulation factor XIIIa / Protein-glutamine gamma-glutamyltransferase A chain / Transglutaminase A chain


Mass: 83365.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Protein Coagulation factor XIII B chain / Fibrin-stabilizing factor B subunit / Protein-glutamine gamma-glutamyltransferase B chain / ...Fibrin-stabilizing factor B subunit / Protein-glutamine gamma-glutamyltransferase B chain / Transglutaminase B chain


Mass: 75600.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05160
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Factor XIII A2B2 heterotetramer / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333272 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002813908
ELECTRON MICROSCOPYf_angle_d0.71218854
ELECTRON MICROSCOPYf_chiral_restr0.04962022
ELECTRON MICROSCOPYf_plane_restr0.01552452
ELECTRON MICROSCOPYf_dihedral_angle_d7.7181864

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