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), 0.296 (DCC)
R-Value Work:
0.251 (Depositor), 0.252 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K4LM89
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody M4	C, D, G, H	120	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.294 (Depositor), 0.296 (DCC)
R-Value Work: 0.251 (Depositor), 0.252 (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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.