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- EMDB-18803: STRUCTURE OF THE MOUSE FCGBP DIMER PROTEIN IN ITS SEMIEXTENDED CO... -

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Basic information

Entry
Database: EMDB / ID: EMD-18803
TitleSTRUCTURE OF THE MOUSE FCGBP DIMER PROTEIN IN ITS SEMIEXTENDED CONFORMATION
Map data
Sample
  • Complex: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN
    • Protein or peptide: Fc fragment of IgG binding protein
    • Protein or peptide: Fc fragment of IgG binding protein
    • Protein or peptide: Fc fragment of IgG binding protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsMUCUS / EPITHELIA / STRUCTURAL PROTEIN
Function / homology
Function and homology information


extracellular matrix
Similarity search - Function
TILa domain / TILa domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain ...TILa domain / TILa domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
Fc fragment of IgG binding protein / Fc fragment of IgG binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGallego P / Hansson GC / Johansson MEV
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Other private Sweden
CitationJournal: FEBS J / Year: 2025
Title: The structure of FCGBP is formed as a disulfide-mediated homodimer between its C-terminal domains.
Authors: Erik Ehrencrona / Pablo Gallego / Sergio Trillo-Muyo / Maria-Jose Garcia-Bonete / Christian V Recktenwald / Gunnar C Hansson / Malin E V Johansson /
Abstract: Mucus in the colon is crucial for intestinal homeostasis by forming a barrier that separates microbes from the epithelium. This is achieved by the structural arrangement of the major mucus proteins, ...Mucus in the colon is crucial for intestinal homeostasis by forming a barrier that separates microbes from the epithelium. This is achieved by the structural arrangement of the major mucus proteins, such as MUC2 and FCGBP, both of which are comprised of several von Willebrand D domains (vWD) and assemblies. Numerous disulfide bonds stabilise these domains, and intermolecular bonds generate multimers of MUC2. The oligomeric nature of FCGBP is not known. Human hFCGBP contains 13 vWD domains whereas mouse mFCGBP consists of only 7. We found unpaired cysteines in the vWD1 (human and mouse) and vWD5 (mouse)/vWD11 (human) assemblies which were not involved in disulfide bonds. However, the most C-terminal vWD domains, vWD7 (mouse)/vWD13 (human), formed disulfide-linked dimers. The intermolecular bond between C and C of human hFCGBP was observed by using mass spectrometry to generate the dimer. Cryo-EM structure analysis of recombinant mouse mFCGBP revealed a compact dimer with two symmetric intermolecular disulfide bonds between C and C, corresponding to the dimerising cysteines in the human hFCGBP. This compact conformation involves interactions between the vWD assemblies, but although the domains involved at the interface are the same, the nature of the interactions differ. Mouse mFCGBP was also found to exist in a semi-extended conformation. These different interactions offer insights into the dynamic nature of the FCGBP homodimer.
History
DepositionOct 31, 2023-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18803.png

Downloads & links

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Map

FileDownload / File: emd_18803.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0267
Minimum - Maximum-0.14109775 - 0.35729223
Average (Standard dev.)-0.00036500592 (±0.008924397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18803_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_18803_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 : DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN

EntireName: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN
Components
  • Complex: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN
    • Protein or peptide: Fc fragment of IgG binding protein
    • Protein or peptide: Fc fragment of IgG binding protein
    • Protein or peptide: Fc fragment of IgG binding protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN

SupramoleculeName: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP PROTEIN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Fc fragment of IgG binding protein

MacromoleculeName: Fc fragment of IgG binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 132.206906 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: SCQGIQCASG QRCQMVSGKA RCVAESTAVC RAQGDPHYTT FDGRRYDMMG TCSYTMAELC GSDETLPAFS VEAKNEHRGS RQVSYVGLV TVYAYSHSVS LVRGEIGFVR IDNQRSRLPA SLSEGRLRVH KSGTRGVIEM DFGLVVTYDW DGQLTLSLPK R FQDQVCGL ...String:
SCQGIQCASG QRCQMVSGKA RCVAESTAVC RAQGDPHYTT FDGRRYDMMG TCSYTMAELC GSDETLPAFS VEAKNEHRGS RQVSYVGLV TVYAYSHSVS LVRGEIGFVR IDNQRSRLPA SLSEGRLRVH KSGTRGVIEM DFGLVVTYDW DGQLTLSLPK R FQDQVCGL CGNYNGDPAD DFLTPDLDQA PDALEFANSW KLDDGDYLCD DGCHNSCPSC TPGQTQHYKG DRLCGMLTLS TG PFSACHE FLDPKPFLDD CVFDLCVTGG ERLSLCRSLS AYAQACVELG VTLENWRLPA SCPMSCPANS CYDPCSPACP PSC NSEAVP TNCSSRPCVE GCVCLPGFVA SGGDCVPVSS CGCIYQGRLL APGQEVFDDD RCRRRCTCDG ATQKVTCRDT TGCP SGERC NVQNGLLGCY PDNFASCQAS GDPHYVSFDG KRFDFMGTCT YLLVGSCGQN AALPAFKVLV ENEHRGSQTV SYTRA VRVV AHGVEVAVRR ENPGRVLVNG VLQYLPFQAA GGKIQVYRQG NDAIVSIDFG LTVTYNWDAH VTAKVPSSYA KDVCGL CGN FNGNPDDDLA LKGGGQASNV LDFGNSWQEE IIPGCGATEP GDCPQLDSLV TQQIQDKKEC GILADPEGPF RECHKLL NP QGAIRDCVYD LCLLPGQSGP LCDALAAYAA ACQAAGGTVH PWRSEELCPL TCPPNSHYEQ CSYGCPLSCG DLPVQGGC G SECREGCVCN EGFALSGESC VPLASCGCVH EGAYHAPGET FYPGPGCDSL CHCEEGGLVS CEPSSCGPQE ACQPSNGVL GCVAVGTTTC QASGDPHYVT FDGRRFDFMG TCVYVLAQTC GNRPGLHQFT VLQENEAWGN GKVSVTKVIT VLVANYTLRL EQSQWKVKV NGVDTKLPVM LDGGKIRVSQ HGSDVVIETD FGLRVAYDLV YYVRVTIPGN YYKQMCGLCG DYNGDPKDDF Q KPDGSQTT DPSDFGNSWE EAVPDSPCAP VPPCTGDDCD TECSPELQDK YHGEQFCGLL TSPTGPLAAC HKLLDPQGPL QD CVFDLCL GGGNQSILCN IIHAYVSACQ AAGGQVEPWR TETFCPMECP PHSHYEVCAD TCSLGCWALN TPQQCPEGCA EGC ECDSGF LYNGKACVPI EQCGCYHNGV YYEPEESVLI ENCQQHCVCQ PGKGMMCQDH SCKPGQVCEP SGGVLTCVTK DPCH GITCR PQETCKVQGG EGVCVPNYNS TCWLWGD

UniProtKB: Fc fragment of IgG binding protein

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Macromolecule #2: Fc fragment of IgG binding protein

MacromoleculeName: Fc fragment of IgG binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.236191 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: PHYNSFDGWS FDFQGTCNYL LAGTLCPGVN AEGLTPFTVT TKNENRGSPA VSYVRQVTVT TLNTNISIHK NEIGKVRVNG VLMALPVYL AGGRISVING GSKAVLETDF GLQVTYDWNW RVDVTLPSSY HGAVCGLCGN MDKNHQNDQV FPNGTMAPSI P TWGGSWQV ...String:
PHYNSFDGWS FDFQGTCNYL LAGTLCPGVN AEGLTPFTVT TKNENRGSPA VSYVRQVTVT TLNTNISIHK NEIGKVRVNG VLMALPVYL AGGRISVING GSKAVLETDF GLQVTYDWNW RVDVTLPSSY HGAVCGLCGN MDKNHQNDQV FPNGTMAPSI P TWGGSWQV PGWDPLCWHE CQGSCPTCPE DRVEEYEGPG FCGPLAPGTG SPFTSCHAHV PPESFFKGCV LDVCLGGGSK DI LCQALAA YAAACQAAGI KIEDWRTQAG CEITCPDNSH YELCGPPCPA SCPPPARHTA PTVCDGPCVE GCQCDEGFVL SAD QCVPLD GGCGCWVNGT YYEAGTEFWA DTTCSKRCHC GPGGDSLVCK PASCGLGEEC ALLPSGEIGC QPTSITECQA WGD

UniProtKB: Fc fragment of IgG binding protein

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Macromolecule #3: Fc fragment of IgG binding protein

MacromoleculeName: Fc fragment of IgG binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 98.653344 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: PHYTTLDGHR FDFQGTCEYL LSAPCHEPPT GTEYFNVTVA NEHRGSQAVS YTRSVTLQIY GLSLTLSAQW PRKLQVNGEF VALPFHLDQ KLSVYISGAD VVVNTASGVS LAFDGDSFVR LRVPAAYAGT LCGLCGNYNK NPNDDLTAVG GKPEGWKVGG A PGCDQCEP ...String:
PHYTTLDGHR FDFQGTCEYL LSAPCHEPPT GTEYFNVTVA NEHRGSQAVS YTRSVTLQIY GLSLTLSAQW PRKLQVNGEF VALPFHLDQ KLSVYISGAD VVVNTASGVS LAFDGDSFVR LRVPAAYAGT LCGLCGNYNK NPNDDLTAVG GKPEGWKVGG A PGCDQCEP EPCPKPCTPE EQEPFRGPDA CGIITAPEGP LAPCHSLVPP TQYFEACLLD ACQVQGHPGG LCPAIATYVA AC QAAGAQL GEWRKPDFCP LQCPAHSHYQ LCGDSCPVSC PSLSAPVGCE TICREGCVCD AGFVLSGDTC VPVGQCGCLY QGR YYVLGA TFYPGPECER LCECGPDGQV TCQEGADCEP YEECRIENGV QACHPTGCGH CLANGGLHYV TLDGRVYDLH GSCS YVLAS VCHPKPGDEE FSIVLEKNSA GDPQRVVVTV AGQVVGLARG PQVTVDGEVV TLPVATGHVS VTAEGRNIVL QTNKG MKVL FDGDAHILMS IPSSFRGRLC GLCGNFNGNW SDDFVLPSGA VAPNVEAFGT AWRAPGSSLG CGEGCGPQGC PVCLAE ETQ AYEKNDACGK IRDPHGPFAA CHKVLSPLEY FRQCVYDMCA HKGDKAYLCR SLAAYTAACQ AAGAAVKPWR TDSVCPL QC PAHSHYSICT RSCQGSCAAL SGLTGCTTRC FEGCECDDHF LLSHGVCIPA QDCGCVHNGQ YMPVNSSLMS SDCSERCF C SPNNGLTCHE AGCPSGHVCE IQAGVRECQA ARGLCSISVG ANLTTFDGAH NAISSPGVYE LSSRCPGLQK NVPWYRVLA DVQPCHNNDK IVSKVHIFFQ DGLVTVIPSK GAWVNGLRVD LPATVLTSVS VRRMPDGSML VHQKAGVTVW LGKDGLLDVM VGDDLAAML CGACGNFDGD QTNDAYGSQG KTPIEKWRAQ DFSPCSNTRT R

UniProtKB: Fc fragment of IgG binding protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167045
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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