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- EMDB-16745: Structure of the plasma coagulation Factor XIII A2B2 heterotetram... -

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Basic information

Entry
Database: EMDB / ID: EMD-16745
TitleStructure of the plasma coagulation Factor XIII A2B2 heterotetrameric complex.
Map dataLow resolution reconstruction of FactorXIII A2B2 heterotetramer. No symmetry imposed.
Sample
  • Complex: Factor XIII A2B2 heterotetramer
    • Protein or peptide: Coagulation factor XIII A chain
    • Protein or peptide: Coagulation factor XIII B chain
KeywordsFactor XIII heterotetrameric complex / BLOOD CLOTTING
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsSingh S / Ugurlar D / Hagelueken G / Geyer M / Biswas A
Funding support Germany, 2 items
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 plasma coagulation Factor XIII heterotetrameric complex at 2.68 Angstrom resolution.
Authors: Singh S / Urgular D / Hagelueken G / Ramaraje Urs SU / Javed H / Imhof D / Geyer M / Oldenburg J / Biswas A
History
DepositionFeb 21, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16745.png

Downloads & links

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Map

FileDownload / File: emd_16745.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow resolution reconstruction of FactorXIII A2B2 heterotetramer. No symmetry imposed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 512 pix.
= 356.864 Å		0.7 Å/pix.
x 512 pix.
= 356.864 Å		0.7 Å/pix.
x 512 pix.
= 356.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0344
Minimum - Maximum-0.17571369 - 0.36917463
Average (Standard dev.)0.0001334518 (±0.008664222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 356.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Low resolution reconstruction of FactorXIII A2B2 heterotetramer. No...

Fileemd_16745_additional_1.map
AnnotationLow resolution reconstruction of FactorXIII A2B2 heterotetramer. No symmetry imposed.Sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16745_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16745_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Factor XIII A2B2 heterotetramer

EntireName: Factor XIII A2B2 heterotetramer
Components
  • Complex: Factor XIII A2B2 heterotetramer
    • Protein or peptide: Coagulation factor XIII A chain
    • Protein or peptide: Coagulation factor XIII B chain

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Supramolecule #1: Factor XIII A2B2 heterotetramer

SupramoleculeName: Factor XIII A2B2 heterotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coagulation factor XIII A chain

MacromoleculeName: Coagulation factor XIII A chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-glutamine gamma-glutamyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.365109 KDa
SequenceString: MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT NKVDHHTDKY ENNKLIVRRG QSFYVQIDF SRPYDPRRDL FRVEYVIGRY PQENKGTYIP VPIVSELQSG KWGAKIVMRE DRSVRLSIQS SPKCIVGKFR M YVAVWTPY ...String:
MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT NKVDHHTDKY ENNKLIVRRG QSFYVQIDF SRPYDPRRDL FRVEYVIGRY PQENKGTYIP VPIVSELQSG KWGAKIVMRE DRSVRLSIQS SPKCIVGKFR M YVAVWTPY GVLRTSRNPE TDTYILFNPW CEDDAVYLDN EKEREEYVLN DIGVIFYGEV NDIKTRSWSY GQFEDGILDT CL YVMDRAQ MDLSGRGNPI KVSRVGSAMV NAKDDEGVLV GSWDNIYAYG VPPSAWTGSV DILLEYRSSE NPVRYGQCWV FAG VFNTFL RCLGIPARIV TNYFSAHDND ANLQMDIFLE EDGNVNSKLT KDSVWNYHCW NEAWMTRPDL PVGFGGWQAV DSTP QENSD GMYRCGPASV QAIKHGHVCF QFDAPFVFAE VNSDLIYITA KKDGTHVVEN VDATHIGKLI VTKQIGGDGM MDITD TYKF QEGQEEERLA LETALMYGAK KPLNTEGVMK SRSNVDMDFE VENAVLGKDF KLSITFRNNS HNRYTITAYL SANITF YTG VPKAEFKKET FDVTLEPLSF KKEAVLIQAG EYMGQLLEQA SLHFFVTARI NETRDVLAKQ KSTVLTIPEI IIKVRGT QV VGSDMTVTVE FTNPLKETLR NVWVHLDGPG VTRPMKKMFR EIRPNSTVQW EEVCRPWVSG HRKLIASMSS DSLRHVYG E LDVQIQRRPS M

UniProtKB: Coagulation factor XIII A chain

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Macromolecule #2: Coagulation factor XIII B chain

MacromoleculeName: Coagulation factor XIII B chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.600594 KDa
SequenceString: MRLKNLTFII ILIISGELYA EEKPCGFPHV ENGRIAQYYY TFKSFYFPMS IDKKLSFFCL AGYTTESGRQ EEQTTCTTEG WSPEPRCFK KCTKPDLSNG YISDVKLLYK IQENMRYGCA SGYKTTGGKD EEVVQCLSDG WSSQPTCRKE HETCLAPELY N GNYSTTQK ...String:
MRLKNLTFII ILIISGELYA EEKPCGFPHV ENGRIAQYYY TFKSFYFPMS IDKKLSFFCL AGYTTESGRQ EEQTTCTTEG WSPEPRCFK KCTKPDLSNG YISDVKLLYK IQENMRYGCA SGYKTTGGKD EEVVQCLSDG WSSQPTCRKE HETCLAPELY N GNYSTTQK TFKVKDKVQY ECATGYYTAG GKKTEEVECL TYGWSLTPKC TKLKCSSLRL IENGYFHPVK QTYEEGDVVQ FF CHENYYL SGSDLIQCYN FGWYPESPVC EGRRNRCPPP PLPINSKIQT HSTTYRHGEI VHIECELNFE IHGSAEIRCE DGK WTEPPK CIEGQEKVAC EEPPFIENGA ANLHSKIYYN GDKVTYACKS GYLLHGSNEI TCNRGKWTLP PECVENNENC KHPP VVMNG AVADGILASY ATGSSVEYRC NEYYLLRGSK ISRCEQGKWS SPPVCLEPCT VNVDYMNRNN IEMKWKYEGK VLHGD LIDF VCKQGYDLSP LTPLSELSVQ CNRGEVKYPL CTRKESKGMC TSPPLIKHGV IISSTVDTYE NGSSVEYRCF DHHFLE GSR EAYCLDGMWT TPPLCLEPCT LSFTEMEKNN LLLKWDFDNR PHILHGEYIE FICRGDTYPA ELYITGSILR MQCDRGQ LK YPRCIPRQST LSYQEPLRT

UniProtKB: Coagulation factor XIII B chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Alphafold2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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