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- EMDB-36479: Cryo-EM structure of full-length ERGIC-53 with MCFD2 -

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Basic information

Entry
Database: EMDB / ID: EMD-36479
TitleCryo-EM structure of full-length ERGIC-53 with MCFD2
Map dataprimary map (raw map)
Sample
  • Complex: ERGIC-53-MCFD2 complex
    • Protein or peptide: Protein ERGIC-53
    • Protein or peptide: Multiple coagulation factor deficiency protein 2
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
Keywordscargo receptor / calcium / zinc / PROTEIN TRANSPORT
Function / homology
Function and homology information


Transport to the Golgi and subsequent modification / positive regulation of organelle organization / : / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / : / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / Golgi organization / D-mannose binding / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / blood coagulation / unfolded protein binding / protein folding / protein transport / : / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / metal ion binding / membrane
Similarity search - Function
: / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...: / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Protein ERGIC-53 / Multiple coagulation factor deficiency protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.76 Å
AuthorsWatanabe S / Inaba K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18K06075 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport.
Authors: Satoshi Watanabe / Yoshiaki Kise / Kento Yonezawa / Mariko Inoue / Nobutaka Shimizu / Osamu Nureki / Kenji Inaba /
Abstract: ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional ...ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
History
DepositionJun 12, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36479.png

Downloads & links

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Map

FileDownload / File: emd_36479.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map (raw map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.49 Å/pix.
x 240 pix.
= 597.6 Å		2.49 Å/pix.
x 240 pix.
= 597.6 Å		2.49 Å/pix.
x 240 pix.
= 597.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.74709904 - 3.7616332
Average (Standard dev.)-0.0006036067 (±0.0847711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 597.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36479_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_36479_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36479_half_map_2.map
Projections & Slices
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Sample components

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Entire : ERGIC-53-MCFD2 complex

EntireName: ERGIC-53-MCFD2 complex
Components
  • Complex: ERGIC-53-MCFD2 complex
    • Protein or peptide: Protein ERGIC-53
    • Protein or peptide: Multiple coagulation factor deficiency protein 2
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: ERGIC-53-MCFD2 complex

SupramoleculeName: ERGIC-53-MCFD2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein ERGIC-53

MacromoleculeName: Protein ERGIC-53 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.766027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGSRQRGLR ARVRPLFCAL LLSLGRFVRG DGVGGDPAVA LPHRRFEYKY SFKGPHLVQS DGTVPFWAHA GNAIPSSDQI RVAPSLKSQ RGSVWTKTKA AFENWEVEVT FRVTGRGRIG ADGLAIWYAE NQGLEGPVFG SADLWNGVGI FFDSFDNDGK K NNPAIVII ...String:
MAGSRQRGLR ARVRPLFCAL LLSLGRFVRG DGVGGDPAVA LPHRRFEYKY SFKGPHLVQS DGTVPFWAHA GNAIPSSDQI RVAPSLKSQ RGSVWTKTKA AFENWEVEVT FRVTGRGRIG ADGLAIWYAE NQGLEGPVFG SADLWNGVGI FFDSFDNDGK K NNPAIVII GNNGQIHYDH QNDGASQALA SCQRDFRNKP YPVRAKITYY QNTLTVMINN GFTPDKNDYE FCAKVENMII PA QGHFGIS AATGGLADDH DVLSFLTFQL TEPGKEPPTP DKEISEKEKE KYQEEFEHFQ QELDKKKEEF QKGHPDLQGQ PAE EIFESV GDRELRQVFE GQNRIHLEIK QLNRQLDMIL DEQRRYVSSL TEEISKRGAG MPGQHGQITQ QELDTVVKTQ HEIL RQVNE MKNSMSETVR LVSGMQHPGS AGGVYETTQH FIDIKEHLHI VKRDIDNLVQ RNMPSNEKPK CPELPPFPSC LSTVH FIIF VVVQTVLFIG YIMYRSQQEA AAKKFFGVAM PGAEDDVV

UniProtKB: Protein ERGIC-53

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Macromolecule #2: Multiple coagulation factor deficiency protein 2

MacromoleculeName: Multiple coagulation factor deficiency protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.95222 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMEEPAAS FSQPGSMGLD KNTVHDQEHI MEHLEGVINK PEAEMSPQEL QLHYFKMHDY DGNNLLDGLE LSTAITHVHK EEGSEQAPL MSEDELINII DGVLRDDDKN NDGYIDYAEF AKSLQ

UniProtKB: Multiple coagulation factor deficiency protein 2

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29762
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8jpg:
Cryo-EM structure of full-length ERGIC-53 with MCFD2

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