8PMZ

HEV gt3 P domain in complex with glycan-insensitive nAb p61.15

PDB DOI: https://doi.org/10.2210/pdb8PMZ/pdb

Classification: VIRAL PROTEIN
Organism(s): Paslahepevirus balayani, 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: 1.91 Å
R-Value Free: 0.257
R-Value Work: 0.225
R-Value Observed: 0.226

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: 100.62 kDa
Atom Count: 6,163
Modelled Residue Count: 758
Deposited Residue Count: 932
Unique protein chains: 2

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, C	211	Paslahepevirus balayani	Mutation(s): 0
UniProt
Find proteins for C4B4T9 (Hepatitis E virus) Explore C4B4T9 Go to UniProtKB: C4B4T9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4B4T9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv_p61.15	B, D	255	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C]	E [auth A], F [auth C]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.257
R-Value Work: 0.225
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.59	α = 90
b = 178.77	β = 90
c = 49.66	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.