PDB-22zw: norovirus GII24 P domain

ID or keywords:

Entry

Database: PDB / ID: 22zw

Title

norovirus GII24 P domain

Components

Major capsid protein

Keywords

VIRAL PROTEIN / norovirus GII24 P domain

Function / homology

Function and homology information

virion component / host cell cytoplasm
Similarity search - Function

Biological species

Norovirus GII

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Duan, Z.J. / Cong, X.

Funding support

China, 1items

Citation

Journal: Front Microbiol / Year: 2026
Title: GII.23/24/25 noroviruses recognize glycans via a conventional glycan-binding site.
Authors: Li, H. / Cong, X. / Sun, X. / Qi, J. / Li, X. / Jin, M. / Duan, Z.

History

Deposition	Jan 29, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 25, 2026	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	22zw.cif.gz	142.5 KB	Display	PDBx/mmCIF format
PDB format	pdb22zw.ent.gz	105.3 KB	Display	PDB format
PDBx/mmJSON format	22zw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2z/22zw ftp://data.pdbj.org/pub/pdb/validation_reports/2z/22zw	HTTPS FTP

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Related structure data

Related structure data	22wzC 22xhC 22zvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: Major capsid protein

B: Major capsid protein

hetero molecules

69.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.629, 80.304, 134.287
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Major capsid protein / VP1 Mass: 34477.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus GII / Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0QSQ1
#2: Chemical	ChemComp-P / 2'-DEOXY-N1,N2-PROPANO GUANOSINE MONOPHOSPHATE Type: DNA linking / Mass: 387.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₈N₅O₇P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.33 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate trihydrate (pH 4.0) with 10% (w/v) PEG4,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.35→38.278 Å / Num. obs: 33685 / % possible obs: 99.7 % / Redundancy: 10 % / CC_1/2: 0.64 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.35→2.411 Å / Num. unique obs: 2452 / CC_1/2: 0.64

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
HKL-2000	HLK-2000	data reduction
HKL-2000	HLK-2000	data scaling
PHENIX	PHENIX	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→38.278 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.925 / SU B: 12.082 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.273
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.286	1662	4.934 %
R_work	0.2315	32023	-
all	0.234	-	-
obs	-	33685	99.372 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 39.572 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.021 Å²	-0 Å²	-0 Å²
2-	-	-1.3 Å²	0 Å²
3-	-	-	4.322 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→38.278 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4859	0	2	214	5075

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	5016
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4526
X-RAY DIFFRACTION	r_angle_refined_deg	1.325	1.666	6857
X-RAY DIFFRACTION	r_angle_other_deg	0.46	1.571	10442
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.654	5	623
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.957	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.422	10	742
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.955	10	242
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	731
X-RAY DIFFRACTION	r_chiral_restr_other	0.031	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6089
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1211
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	866
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	4254
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	2394
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	2580
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	193
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.004	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.237	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.235	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.107	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.174	4.071	2486
X-RAY DIFFRACTION	r_mcbond_other	3.174	4.071	2486
X-RAY DIFFRACTION	r_mcangle_it	4.93	7.318	3105
X-RAY DIFFRACTION	r_mcangle_other	4.929	7.318	3106
X-RAY DIFFRACTION	r_scbond_it	3.426	4.369	2530
X-RAY DIFFRACTION	r_scbond_other	3.425	4.369	2531
X-RAY DIFFRACTION	r_scangle_it	5.466	7.854	3750
X-RAY DIFFRACTION	r_scangle_other	5.465	7.853	3751
X-RAY DIFFRACTION	r_lrange_it	7.822	40.822	5280
X-RAY DIFFRACTION	r_lrange_other	7.791	40.772	5246

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.35-2.411	0.419	119	0.382	2333	0.384	2453	0.805	0.86	99.9592	0.336
2.411-2.477	0.419	117	0.354	2286	0.357	2404	0.874	0.892	99.9584	0.305
2.477-2.548	0.373	110	0.353	2224	0.353	2336	0.866	0.898	99.9144	0.313
2.548-2.626	0.395	79	0.322	2180	0.324	2263	0.871	0.915	99.8232	0.273
2.626-2.712	0.352	109	0.305	2087	0.307	2200	0.913	0.925	99.8182	0.257
2.712-2.807	0.352	87	0.263	2038	0.267	2127	0.912	0.949	99.906	0.217
2.807-2.912	0.315	100	0.248	1960	0.251	2063	0.94	0.96	99.8546	0.21
2.912-3.03	0.305	91	0.251	1900	0.253	1994	0.934	0.958	99.8495	0.215
3.03-3.164	0.319	94	0.23	1805	0.234	1903	0.941	0.967	99.7898	0.199
3.164-3.317	0.264	96	0.21	1732	0.213	1838	0.96	0.975	99.4559	0.188
3.317-3.495	0.332	81	0.231	1669	0.236	1760	0.94	0.97	99.4318	0.21
3.495-3.705	0.248	86	0.232	1533	0.233	1642	0.961	0.969	98.5993	0.214
3.705-3.958	0.281	80	0.23	1459	0.232	1558	0.947	0.969	98.7805	0.218
3.958-4.272	0.316	74	0.186	1384	0.192	1463	0.952	0.98	99.6582	0.18
4.272-4.674	0.193	73	0.154	1281	0.157	1364	0.985	0.987	99.2669	0.157
4.674-5.216	0.213	56	0.16	1169	0.162	1233	0.976	0.987	99.3512	0.163
5.216-6.004	0.286	65	0.188	1020	0.194	1099	0.966	0.982	98.7261	0.184
6.004-7.308	0.235	53	0.169	872	0.173	951	0.97	0.984	97.266	0.173
7.308-10.152	0.203	58	0.168	681	0.171	758	0.976	0.984	97.4934	0.181
10.152-38.278	0.253	34	0.257	410	0.256	478	0.975	0.963	92.887	0.278

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