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- EMDB-19070: STRUCTURE OF THE MOUSE FCGBP DIMER PROTEIN IN ITS COMPACT CONFORMATION -

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Basic information

Entry
Database: EMDB / ID: EMD-19070
TitleSTRUCTURE OF THE MOUSE FCGBP DIMER PROTEIN IN ITS COMPACT CONFORMATION
Map data
Sample
  • Complex: DISULFIDE-COVALENT HOMODIMER STRUCTURE OF THE MOUSE FCGBP 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGallego P / Hansson GC / Johansson MEV
Funding support1 items
OrganizationGrant numberCountry
Other private
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
DepositionDec 8, 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_19070.png

Downloads & links

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Map

FileDownload / File: emd_19070.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: 0.0495
Minimum - Maximum-0.13199697 - 0.34023425
Average (Standard dev.)0.00006649698 (±0.01181967)
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_19070_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_19070_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
  • 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
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 275.970312 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGSPWKWWAL WAGATLLWAL LTPAEASCQG IQCASGQRCQ MVSGKARCVA ESTAVCRAQG DPHYTTFDGR RYDMMGTCSY TMAELCGSD ETLPAFSVEA KNEHRGSRQV SYVGLVTVYA YSHSVSLVRG EIGFVRIDNQ RSRLPASLSE GRLRVHKSGT R GVIEMDFG ...String:
MGSPWKWWAL WAGATLLWAL LTPAEASCQG IQCASGQRCQ MVSGKARCVA ESTAVCRAQG DPHYTTFDGR RYDMMGTCSY TMAELCGSD ETLPAFSVEA KNEHRGSRQV SYVGLVTVYA YSHSVSLVRG EIGFVRIDNQ RSRLPASLSE GRLRVHKSGT R GVIEMDFG LVVTYDWDGQ LTLSLPKRFQ DQVCGLCGNY NGDPADDFLT PDLDQAPDAL EFANSWKLDD GDYLCDDGCH NS CPSCTPG QTQHYKGDRL CGMLTLSTGP FSACHEFLDP KPFLDDCVFD LCVTGGERLS LCRSLSAYAQ ACVELGVTLE NWR LPASCP MSCPANSCYD PCSPACPPSC NSEAVPTNCS SRPCVEGCVC LPGFVASGGD CVPVSSCGCI YQGRLLAPGQ EVFD DDRCR RRCTCDGATQ KVTCRDTTGC PSGERCNVQN GLLGCYPDNF ASCQASGDPH YVSFDGKRFD FMGTCTYLLV GSCGQ NAAL PAFKVLVENE HRGSQTVSYT RAVRVVAHGV EVAVRRENPG RVLVNGVLQY LPFQAAGGKI QVYRQGNDAI VSIDFG LTV TYNWDAHVTA KVPSSYAKDV CGLCGNFNGN PDDDLALKGG GQASNVLDFG NSWQEEIIPG CGATEPGDCP QLDSLVT QQ IQDKKECGIL ADPEGPFREC HKLLNPQGAI RDCVYDLCLL PGQSGPLCDA LAAYAAACQA AGGTVHPWRS EELCPLTC P PNSHYEQCSY GCPLSCGDLP VQGGCGSECR EGCVCNEGFA LSGESCVPLA SCGCVHEGAY HAPGETFYPG PGCDSLCHC EEGGLVSCEP SSCGPQEACQ PSNGVLGCVA VGTTTCQASG DPHYVTFDGR RFDFMGTCVY VLAQTCGNRP GLHQFTVLQE NEAWGNGKV SVTKVITVLV ANYTLRLEQS QWKVKVNGVD TKLPVMLDGG KIRVSQHGSD VVIETDFGLR VAYDLVYYVR V TIPGNYYK QMCGLCGDYN GDPKDDFQKP DGSQTTDPSD FGNSWEEAVP DSPCAPVPPC TGDDCDTECS PELQDKYHGE QF CGLLTSP TGPLAACHKL LDPQGPLQDC VFDLCLGGGN QSILCNIIHA YVSACQAAGG QVEPWRTETF CPMECPPHSH YEV CADTCS LGCWALNTPQ QCPEGCAEGC ECDSGFLYNG KACVPIEQCG CYHNGVYYEP EESVLIENCQ QHCVCQPGKG MMCQ DHSCK PGQVCEPSGG VLTCVTKDPC HGITCRPQET CKVQGGEGVC VPNYNSTCWL WGDPHYNSFD GWSFDFQGTC NYLLA GTLC PGVNAEGLTP FTVTTKNENR GSPAVSYVRQ VTVTTLNTNI SIHKNEIGKV RVNGVLMALP VYLAGGRISV INGGSK AVL ETDFGLQVTY DWNWRVDVTL PSSYHGAVCG LCGNMDKNHQ NDQVFPNGTM APSIPTWGGS WQVPGWDPLC WHECQGS CP TCPEDRVEEY EGPGFCGPLA PGTGSPFTSC HAHVPPESFF KGCVLDVCLG GGSKDILCQA LAAYAAACQA AGIKIEDW R TQAGCEITCP DNSHYELCGP PCPASCPPPA RHTAPTVCDG PCVEGCQCDE GFVLSADQCV PLDGGCGCWV NGTYYEAGT EFWADTTCSK RCHCGPGGDS LVCKPASCGL GEECALLPSG EIGCQPTSIT ECQAWGDPHY TTLDGHRFDF QGTCEYLLSA PCHEPPTGT EYFNVTVANE HRGSQAVSYT RSVTLQIYGL SLTLSAQWPR KLQVNGEFVA LPFHLDQKLS VYISGADVVV N TASGVSLA FDGDSFVRLR VPAAYAGTLC GLCGNYNKNP NDDLTAVGGK PEGWKVGGAP GCDQCEPEPC PKPCTPEEQE PF RGPDACG IITAPEGPLA PCHSLVPPTQ YFEACLLDAC QVQGHPGGLC PAIATYVAAC QAAGAQLGEW RKPDFCPLQC PAH SHYQLC GDSCPVSCPS LSAPVGCETI CREGCVCDAG FVLSGDTCVP VGQCGCLYQG RYYVLGATFY PGPECERLCE CGPD GQVTC QEGADCEPYE ECRIENGVQA CHPTGCGHCL ANGGLHYVTL DGRVYDLHGS CSYVLASVCH PKPGDEEFSI VLEKN SAGD PQRVVVTVAG QVVGLARGPQ VTVDGEVVTL PVATGHVSVT AEGRNIVLQT NKGMKVLFDG DAHILMSIPS SFRGRL CGL CGNFNGNWSD DFVLPSGAVA PNVEAFGTAW RAPGSSLGCG EGCGPQGCPV CLAEETQAYE KNDACGKIRD PHGPFAA CH KVLSPLEYFR QCVYDMCAHK GDKAYLCRSL AAYTAACQAA GAAVKPWRTD SVCPLQCPAH SHYSICTRSC QGSCAALS G LTGCTTRCFE GCECDDHFLL SHGVCIPAQD CGCVHNGQYM PVNSSLMSSD CSERCFCSPN NGLTCHEAGC PSGHVCEIQ AGVRECQAAR GLCSISVGAN LTTFDGAHNA ISSPGVYELS SRCPGLQKNV PWYRVLADVQ PCHNNDKIVS KVHIFFQDGL VTVIPSKGA WVNGLRVDLP ATVLTSVSVR RMPDGSMLVH QKAGVTVWLG KDGLLDVMVG DDLAAMLCGA CGNFDGDQTN D AYGSQGKT PIEKWRAQDF SPCSNTRTR

UniProtKB: Fc fragment of IgG binding protein

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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: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / 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
GridDetails: 15MM
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184178
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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