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Yorodumi- PDB-8jp6: Cryo-EM structures of the head region of full-length ERGIC-53 wit... -
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Entry | Database: PDB / ID: 8jp6 | ||||||
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Title | Cryo-EM structures of the head region of full-length ERGIC-53 with MCFD2 (Substate A) | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / cargo receptor / calcium / zinc | ||||||
Function / homology | Function and homology information Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Golgi organization / RHOC GTPase cycle ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Golgi organization / RHOC GTPase cycle / D-mannose binding / RHOG GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / 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 / unfolded protein binding / blood coagulation / protein folding / protein transport / 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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
Authors | Watanabe, S. / Inaba, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 8jp6.cif.gz | 357.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jp6.ent.gz | 279.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/8jp6 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/8jp6 | HTTPS FTP |
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-Related structure data
Related structure data | 36469MC 8jp4C 8jp5C 8jp7C 8jp8C 8jp9C 8jpgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
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