8JP6

Cryo-EM structures of the head region of full-length ERGIC-53 with MCFD2 (Substate A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport.

Watanabe, S.Kise, Y.Yonezawa, K.Inoue, M.Shimizu, N.Nureki, O.Inaba, K.

(2024) Nat Commun 15: 2404-2404

  • DOI: https://doi.org/10.1038/s41467-024-46747-1
  • Primary Citation of Related Structures:  
    8JP4, 8JP5, 8JP6, 8JP7, 8JP8, 8JP9, 8JPG

  • PubMed 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 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 2+ -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.


  • Organizational Affiliation

    Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan. satoshi.watanabe.c1@tohoku.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ERGIC-53
A, B, E, F
522Homo sapiensMutation(s): 0 
Gene Names: LMAN1ERGIC53F5F8D
UniProt & NIH Common Fund Data Resources
Find proteins for P49257 (Homo sapiens)
Explore P49257 
Go to UniProtKB:  P49257
PHAROS:  P49257
GTEx:  ENSG00000074695 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49257
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multiple coagulation factor deficiency protein 2
C, D, G, H
124Homo sapiensMutation(s): 0 
Gene Names: MCFD2SDNSF
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI22 (Homo sapiens)
Explore Q8NI22 
Go to UniProtKB:  Q8NI22
PHAROS:  Q8NI22
GTEx:  ENSG00000180398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NI22
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth H],
O [auth C],
R [auth D],
Y [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
J [auth A]
K [auth B]
L [auth B]
AA [auth H],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth G],
X [auth G],
Z [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP18K06075

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary