8PMW

HEV gt3 P domain in complex with glycan-sensitive nAb p60.1

• PDB DOI: https://doi.org/10.2210/pdb8PMW/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Paslahepevirus balayani
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2023-06-29 Released: 2024-07-10 
• Deposition Author(s): Ssebyatika, G., Krey, T.
• Funding Organization(s): Volkswagen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.227 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

A novel class of broadly neutralizing hepatitis E virus-specific human antibodies

Ssebyatika, G., Dinkelborg, K., Stroeh, L.J., Hinte, F., Corneillie, L., Hueffner, L., Guzman, E.M., Nankya, P.L., Plueckebaum, N., Prallet, S., Mehnert, A.K., Verhoye, L., Juergens, C., Steinmann, E., Wedemeyer, H., Viejo-Borbolla, A., Dao Thi, L.V., Pietschmann, T., Luetgehetmann, M., Meuleman, P., Dandri, M., Krey, T., Behrendt, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 198.6 kDa 
• Atom Count: 8,498 
• Modelled Residue Count: 1,069 
• Deposited Residue Count: 1,848 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv_p60.1	A, B, G, H	251	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C, D, E, F	211	Paslahepevirus balayani	Mutation(s): 0
UniProt
Find proteins for C4B4T9 (Hepatitis E virus) Explore C4B4T9  Go to UniProtKB:  C4B4T9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], N [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	I [auth A], K [auth C], L [auth D], M [auth G]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.227 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.81	α = 90
b = 159.26	β = 90
c = 205.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Ssebyatika, G., Krey, T.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	9A888

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release