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- EMDB-36482: cryoEM structure of ERGIC-53 deltaH34 mutant with MCFD2 -

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Basic information

Entry
Database: EMDB / ID: EMD-36482
TitlecryoEM structure of ERGIC-53 deltaH34 mutant with MCFD2
Map dataraw map
Sample
  • Complex: ERGIC-53-MCFD2 complex
    • Other: ERGIC-53Vesicular-tubular cluster
    • Other: MCFD2
Keywordscargo receptor / calcium / zinc / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsWatanabe S / Inaba K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18K06075 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP21H05253 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-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36482.png

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Map

FileDownload / File: emd_36482.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationraw map
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AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 320 pix.
= 441.28 Å		1.38 Å/pix.
x 320 pix.
= 441.28 Å		1.38 Å/pix.
x 320 pix.
= 441.28 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.379 Å
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Contour LevelBy AUTHOR: 0.163
Minimum - Maximum-0.62073267 - 1.5625061
Average (Standard dev.)0.0001017218 (±0.031108651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 441.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36482_msk_1.map
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Additional map: component III first

Fileemd_36482_additional_1.map
Annotationcomponent III first
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Fileemd_36482_additional_2.map
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Additional map: component II 1st

Fileemd_36482_additional_4.map
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Additional map: component II last

Fileemd_36482_additional_5.map
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Fileemd_36482_additional_6.map
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Half map: half map1

Fileemd_36482_half_map_1.map
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Fileemd_36482_half_map_2.map
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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
    • Other: ERGIC-53Vesicular-tubular cluster
    • Other: MCFD2

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Supramolecule #1: ERGIC-53-MCFD2 complex

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

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Macromolecule #1: ERGIC-53

MacromoleculeName: ERGIC-53 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAGSRQRGLR ARVRPLFCAL LLSLGRFVRG DGVGGDPAVA LPHRRFEYK YSFKGPHLVQ SDGTVPFWAH AGNAIPSSDQ I RVAPSLKS QRGSVWTKTK AAFENWEVEV TFRVTGRGRI GA DGLAIWY AENQGLEGPV FGSADLWNGV GIFFDSFDND GKK NNPAIV ...String:
MAGSRQRGLR ARVRPLFCAL LLSLGRFVRG DGVGGDPAVA LPHRRFEYK YSFKGPHLVQ SDGTVPFWAH AGNAIPSSDQ I RVAPSLKS QRGSVWTKTK AAFENWEVEV TFRVTGRGRI GA DGLAIWY AENQGLEGPV FGSADLWNGV GIFFDSFDND GKK NNPAIV IIGNNGQIHY DHQNDGASQA LASCQRDFRN KPYP VRAKI TYYQNTLTVM INNGFTPDKN DYEFCAKVEN MIIPA QGHF GISAATGGLA DDHDVLSFLT FQLTEPGKEP PTPDKE ISE KEKEKYQEEF EHFQQELDKK KEEFQKGHPD LQGQPAE EI FESVGDRELR QVFEGQNRIH LEIKQLNRQL DMILDEQR R YVSSLTEEIS SNEKPKCPEL PPFPSCLSTV HFIIFVVVQ TVLFIGYIMY RSQQEAAAKK FFDYKDDDDK
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #2: MCFD2

MacromoleculeName: MCFD2 / type: other / ID: 2 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GSHMEEPAAS FSQPGSMGLD KNTVHDQEHI MEHLEGVINK PEAEMSPQEL QLHYFKMHDY DGNNLLDGLE LSTAITHVHK EEGSEQAPLM SEDELINIID GVLRDDDKNN DGYIDYAEFA KSLQ
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138608
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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