8PMX

rat HEV P domain in complex with glycan-sensitive nAb p60.12

PDB DOI: https://doi.org/10.2210/pdb8PMX/pdb

Classification: VIRAL PROTEIN
Organism(s): Hepatitis E virus rat/R63/DEU/2009, Homo sapiens
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free: 0.361
R-Value Work: 0.300
R-Value Observed: 0.304

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 83.73 kDa
Atom Count: 5,572
Modelled Residue Count: 735
Deposited Residue Count: 780
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pro-secreted protein ORF2	A, B	165	Hepatitis E virus rat/R63/DEU/2009	Mutation(s): 0
UniProt
Find proteins for E0XL23 (Hepatitis E virus rat/R63/DEU/2009) Explore E0XL23 Go to UniProtKB: E0XL23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E0XL23
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab p60.12-HC	C [auth H]	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab p60.12-LC	D [auth L]	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.92 Å
R-Value Free: 0.361
R-Value Work: 0.300
R-Value Observed: 0.304
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.856	α = 90
b = 112.856	β = 90
c = 184.439	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	9A888

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.