7B5F | pdb_00007b5f

Structure of echovirus 18 in complex with neonatal Fc receptor

• PDB DOI: https://doi.org/10.2210/pdb7B5F/pdb
• EM Map EMD-12028: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Echovirus E18, Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2020-12-03 Released: 2022-01-12 
• Deposition Author(s): Buchta, D., Levdansky, Y., Fuzik, T., Mukhamedova, L., Moravcova, J., Hrebik, D., Andersen, J.T., Plevka, P.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of echovirus 18 in complex with neonatal Fc receptor

Buchta, D., Levdansky, Y., Fuzik, T., Mukhamedova, L., Moravcova, J., Hrebik, D., Andersen, J.T., Plevka, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 136.86 kDa 
• Atom Count: 7,489 
• Modeled Residue Count: 958 
• Deposited Residue Count: 1,221 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Echovirus 18 viral protein 3	A [auth C]	239	Echovirus E18	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18) Explore Q8V635  Go to UniProtKB:  Q8V635

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Echovirus 18 viral protein 4	B [auth D]	69	Echovirus E18	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18) Explore Q8V635  Go to UniProtKB:  Q8V635

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Echovirus 18 viral protein 1	C [auth A]	287	Echovirus E18	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18) Explore Q8V635  Go to UniProtKB:  Q8V635

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Echovirus 18 viral protein 2	D [auth B]	260	Echovirus E18	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q8V635 (Echovirus E18) Explore Q8V635  Go to UniProtKB:  Q8V635

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG receptor FcRn large subunit p51	E [auth G]	267	Homo sapiens	Mutation(s): 0  Gene Names: FCGRT, FCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens) Explore P55899  Go to UniProtKB:  P55899
PHAROS:  P55899 GTEx:  ENSG00000104870

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	F [auth H]	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	G [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
GUN	H [auth B]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Buchta, D., Levdansky, Y., Fuzik, T., Mukhamedova, L., Moravcova, J., Hrebik, D., Andersen, J.T., Plevka, P.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	GX19-25982X

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2024-07-10
  Changes: Data collection, Derived calculations