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- EMDB-50841: Structure of methylamine activated CD109 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50841
TitleStructure of methylamine activated CD109
Map data
Sample
  • Complex: Monomeric methylamine non-GPI bounded CD109
    • Protein or peptide: CD109 antigen
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsProtease inhibitor / thioester activation / intermediate conformation / alpha-macroglobulin / IMMUNE SYSTEM
Function / homology
Function and homology information


osteoclast fusion / regulation of keratinocyte differentiation / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of wound healing / platelet alpha granule membrane / keratinocyte proliferation / hair follicle development / negative regulation of keratinocyte proliferation / negative regulation of stem cell proliferation / side of membrane ...osteoclast fusion / regulation of keratinocyte differentiation / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of wound healing / platelet alpha granule membrane / keratinocyte proliferation / hair follicle development / negative regulation of keratinocyte proliferation / negative regulation of stem cell proliferation / side of membrane / stem cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / serine-type endopeptidase inhibitor activity / Platelet degranulation / cell surface / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain ...Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAlmeida AV / Andersen GR
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-2032-00111B Denmark
CitationJournal: To Be Published
Title: Structure of methylamine activated CD109
Authors: Almeida AV / Andersen GR
History
DepositionJul 1, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50841.png

Downloads & links

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Map

FileDownload / File: emd_50841.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.38104862 - 1.0514208
Average (Standard dev.)-0.00047043178 (±0.019912945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50841_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_50841_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 : Monomeric methylamine non-GPI bounded CD109

EntireName: Monomeric methylamine non-GPI bounded CD109
Components
  • Complex: Monomeric methylamine non-GPI bounded CD109
    • Protein or peptide: CD109 antigen
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Monomeric methylamine non-GPI bounded CD109

SupramoleculeName: Monomeric methylamine non-GPI bounded CD109 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: C-terminal GPI-motif (residues 1421-1445) was removed
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 165 KDa

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Macromolecule #1: CD109 antigen

MacromoleculeName: CD109 antigen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.449797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SGSVAPGPRF LVTAPGIIRP GGNVTIGVEL LEHCPSQVTV KAELLKTASN LTVSVLEAEG VFEKGSFKTL TLPSLPLNSA DEIYELRVT GRTQDEILFS NSTRLSFETK RISVFIQTDK ALYKPKQEVK FRIVTLFSDF KPYKTSLNIL IKDPKSNLIQ Q WLSQQSDL ...String:
SGSVAPGPRF LVTAPGIIRP GGNVTIGVEL LEHCPSQVTV KAELLKTASN LTVSVLEAEG VFEKGSFKTL TLPSLPLNSA DEIYELRVT GRTQDEILFS NSTRLSFETK RISVFIQTDK ALYKPKQEVK FRIVTLFSDF KPYKTSLNIL IKDPKSNLIQ Q WLSQQSDL GVISKTFQLS SHPILGDWSI QVQVNDQTYY QSFQVSEYVL PKFEVTLQTP LYCSMNSKHL NGTITAKYTY GK PVKGDVT LTFLPLSFWG KKKNITKTFK INGSANFSFN DEEMKNVMDS SNGLSEYLDL SSPGPVEILT TVTESVTGIS RNV STNVFF KQHDYIIEFF DYTTVLKPSL NFTATVKVTR ADGNQLTLEE RRNNVVITVT QRNYTEYWSG SNSGNQKMEA VQKI NYTVP QSGTFKIEFP ILEDSSELQL KAYFLGSKSS MAVHSLFKSP SKTYIQLKTR DENIKVGSPF ELVVSGNKRL KELSY MVVS RGQLVAVGKQ NSTMFSLTPE NSWTPKACVI VYYIEDDGEI ISDVLKIPVQ LVFKNKIKLY WSKVKAEPSE KVSLRI SVT QPDSIVGIVA VDKSVNLMNA SNDITMENVV HELELYNTGY YLGMFMNSFA VFQECGLWVL TDANLTKDYI DGVYDNA EY AERENLYFQG HIVDIHDFSL GSSPHVRKHF PETWIWLDTN MGYRIYQEFE VTVPDSITSW VATGFVISED LGLGLTTT P VELQAFQPFF IFLNLPYSVI RGEEFALEIT IFNYLKDATE VKVIIEKSDK FDILMTSNEI NATGHQQTLL VPSEDGATV LFPIRPTHLG EIPITVTALS PTASDAVTQM ILVKAEGIEK SYSQSILLDL TDNRLQSTLK TLSFSFPPNT VTGSERVQIT AIGDVLGPS INGLASLIRM PYGCGEQNMI NFAPNIYILD YLTKKKQLTD NLKEKALSFM RQGYQRELLY QREDGSFSAF G NYDPSGST WLSAFVLRCF LEADPYIDID QNVLHRTYTW LKGHQKSNGE FWDPGRVIHS ELQGGNKSPV TLTAYIVTSL LG YRKYQPN IDVQESIHFL ESEFSRGISD NYTLALITYA LSSVGSPKAK EALNMLTWRA EQEGGMQFWV SSESKLSDSW QPR SLDIEV AAYALLSHFL QFQTSEGIPI MRWLSRQRNS LGGFASTQDT TVALKALSEF AALMNTERTN IQVTVTGPSS PSPV KFLID THNRLLLQTA ELAVVQPTAV NISANGFGFA ICQLNVVYNV KASGSSRR

UniProtKB: CD109 antigen

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration5.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
4.0 mMC32H58N2O7SCHAPS
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Support film - Film thickness: 1200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsMonodisperse sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11076 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2305684
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.04) / Number images used: 230644
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.04)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 230644 / Software - Name: cryoSPARC (ver. 4.04)

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Atomic model buiding 1

Initial modelPDB ID:

yhk3


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9fx2:
Structure of methylamine activated CD109

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