8G0W | pdb_00008g0w

Crystal structure of human norovirus GII.4 P domain in complex with Nanobody M4

PDB DOI: https://doi.org/10.2210/pdb8G0W/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus, Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-01 Released: 2023-10-04
Deposition Author(s): Hu, L., Salmen, W., Sankaran, B., Prasad, B.V.V.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.294 (Depositor), 0.300 (DCC)
R-Value Work:
0.251 (Depositor), 0.250 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human norovirus GII.4 P domain in complex with Nanobody M4

Hu, L., Salmen, W., Sankaran, B., Prasad, B.V.V.

To be published.

Macromolecule Content

Total Structure Weight: 190.06 kDa
Atom Count: 12,812
Modeled Residue Count: 1,653
Deposited Residue Count: 1,724
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B, E, F	311	Norovirus	Mutation(s): 0
UniProt
Find proteins for K4LM89 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU) Explore K4LM89 Go to UniProtKB: K4LM89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K4LM89
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody M4	C, D, G, H	120	Lama glama	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: 2.87 Å
R-Value Free: 0.294 (Depositor), 0.300 (DCC)
R-Value Work: 0.251 (Depositor), 0.250 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.511	α = 90
b = 90.675	β = 113.26
c = 107.212	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

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 R01GM157729.