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Yorodumi- PDB-8cmt: Structure of the plasma coagulation Factor XIII A2B2 heterotetram... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cmt | |||||||||
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Title | Structure of the plasma coagulation Factor XIII A2B2 heterotetrameric complex. | |||||||||
Components |
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Keywords | BLOOD CLOTTING / Factor XIII heterotetrameric complex | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Singh, S. / Ugurlar, D. / Hagelueken, G. / Geyer, M. / Biswas, A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: To Be Published Title: The cryo-EM structure of plasma coagulation Factor XIII heterotetrameric 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cmt.cif.gz | 408.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cmt.ent.gz | 330.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cmt_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8cmt_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8cmt_validation.xml.gz | 72 KB | Display | |
Data in CIF | 8cmt_validation.cif.gz | 109.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/8cmt ftp://data.pdbj.org/pub/pdb/validation_reports/cm/8cmt | HTTPS FTP |
-Related structure data
Related structure data | 16745MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | Mass: 75600.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05160 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Factor XIII A2B2 heterotetramer / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20436 / Symmetry type: POINT |