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- EMDB-36470: Cryo-EM structure of the head region of full-length ERGIC-53 with... -
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Basic information
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Title | Cryo-EM structure of the head region of full-length ERGIC-53 with MCFD2 (Substate B) | |||||||||
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![]() | cargo receptor / calcium / zinc / PROTEIN TRANSPORT | |||||||||
Function / homology | ![]() Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / 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 transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
![]() | Watanabe S / Inaba K | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 89.7 KB | ||
Masks | ![]() | 38.4 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() ![]() | 35.7 MB 35.7 MB 35.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jp7MC ![]() 8jp4C ![]() 8jp5C ![]() 8jp6C ![]() 8jp8C ![]() 8jp9C ![]() 8jpgC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Primary map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.996 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: raw map
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Annotation | raw map | ||||||||||||
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-Half map: half map 1
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-Half map: half map 2
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Annotation | half map 2 | ||||||||||||
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Sample components
-Entire : ERGIC-53-MCFD2 complex
Entire | Name: ERGIC-53-MCFD2 complex |
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Components |
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-Supramolecule #1: ERGIC-53-MCFD2 complex
Supramolecule | Name: ERGIC-53-MCFD2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Protein ERGIC-53
Macromolecule | Name: Protein ERGIC-53 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.766027 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: Multiple coagulation factor deficiency protein 2
Macromolecule | Name: Multiple coagulation factor deficiency protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.95222 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMEEPAAS FSQPGSMGLD KNTVHDQEHI MEHLEGVINK PEAEMSPQEL QLHYFKMHDY DGNNLLDGLE LSTAITHVHK EEGSEQAPL MSEDELINII DGVLRDDDKN NDGYIDYAEF AKSLQ UniProtKB: Multiple coagulation factor deficiency protein 2 |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8jp7: |