PDB-22zv: norovirus GII23 P domain

ID or keywords:

Entry

Database: PDB / ID: 22zv

Title

norovirus GII23 P domain

Components

Major capsid protein

Keywords

VIRAL PROTEIN / norovirus GII23 P domain

Function / homology

Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Major capsid protein

Function and homology information

Biological species

Norovirus GII

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	22zv.cif.gz	275.6 KB	Display	PDBx/mmCIF format
PDB format	pdb22zv.ent.gz	213.3 KB	Display	PDB format
PDBx/mmJSON format	22zv.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/22zv ftp://data.pdbj.org/pub/pdb/validation_reports/2z/22zv	HTTPS FTP

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Related structure data

Related structure data	22wzC 22xhC 22zwC 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

C: Major capsid protein

D: Major capsid protein

138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Major capsid protein

B: Major capsid protein

defined by author&software
Evidence: gel filtration
69 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Major capsid protein

D: Major capsid protein

defined by author&software
69 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.832, 107.313, 220.661
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 Mass: 34486.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6VXX1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H₂O
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: 2.61 Å³/Da / Density % sol: 52.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 10% (v/v) PEG 200, 0.1 M BIS-TRIS propane (pH 9.0), and 18% (w/v) PEG 8,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 98555 / % possible obs: 100 % / Redundancy: 9.8 % / CC_1/2: 0.997 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2→2.03 Å / Num. unique obs: 6811 / CC_1/2: 0.872

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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→47.761 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.927 / SU B: 4.547 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.228	4880	4.959 %
R_work	0.1824	93530	-
all	0.185	-	-
obs	-	98410	99.881 %

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: 25.828 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.613 Å²	-0 Å²	-0 Å²
2-	-	-1.757 Å²	0 Å²
3-	-	-	2.37 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.761 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9728	0	0	838	10566

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	10065
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9135
X-RAY DIFFRACTION	r_angle_refined_deg	1.397	1.662	13756
X-RAY DIFFRACTION	r_angle_other_deg	0.47	1.571	21133
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.084	5	1248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.706	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.416	10	1526
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.913	10	473
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1476
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12047
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2353
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	1693
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	8569
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	4961
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	5028
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	657
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.053	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.161	0.2	31
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.049	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.356	2.611	4989
X-RAY DIFFRACTION	r_mcbond_other	2.352	2.61	4989
X-RAY DIFFRACTION	r_mcangle_it	3.509	4.682	6238
X-RAY DIFFRACTION	r_mcangle_other	3.509	4.683	6239
X-RAY DIFFRACTION	r_scbond_it	3.134	2.915	5076
X-RAY DIFFRACTION	r_scbond_other	3.134	2.915	5077
X-RAY DIFFRACTION	r_scangle_it	4.836	5.213	7518
X-RAY DIFFRACTION	r_scangle_other	4.836	5.214	7519
X-RAY DIFFRACTION	r_lrange_it	6.716	27.494	10928
X-RAY DIFFRACTION	r_lrange_other	6.655	27.128	10782

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
2-2.052	0.29	370	0.236	6811	0.239	7181	0.94	0.959	100	0.212
2.052-2.108	0.271	334	0.239	6691	0.24	7025	0.943	0.953	100	0.213
2.108-2.169	0.261	342	0.208	6491	0.211	6833	0.953	0.97	100	0.183
2.169-2.236	0.247	321	0.207	6281	0.209	6603	0.961	0.969	99.9849	0.184
2.236-2.309	0.328	305	0.263	6046	0.266	6405	0.9	0.936	99.1569	0.23
2.309-2.39	0.27	279	0.194	5953	0.197	6232	0.952	0.975	100	0.169
2.39-2.48	0.26	300	0.194	5707	0.197	6009	0.956	0.975	99.9667	0.17
2.48-2.58	0.265	291	0.19	5514	0.194	5807	0.95	0.976	99.9656	0.166
2.58-2.695	0.236	275	0.178	5284	0.181	5560	0.965	0.98	99.982	0.155
2.695-2.826	0.252	268	0.18	5074	0.183	5342	0.959	0.979	100	0.158
2.826-2.978	0.23	246	0.181	4832	0.183	5078	0.965	0.978	100	0.161
2.978-3.158	0.225	252	0.178	4580	0.18	4832	0.968	0.978	100	0.163
3.158-3.375	0.235	208	0.184	4337	0.187	4548	0.957	0.978	99.934	0.172
3.375-3.644	0.23	206	0.193	4012	0.195	4222	0.965	0.977	99.9053	0.184
3.644-3.99	0.208	216	0.173	3707	0.175	3926	0.974	0.982	99.9236	0.17
3.99-4.457	0.184	184	0.142	3369	0.145	3553	0.979	0.987	100	0.147
4.457-5.139	0.164	170	0.133	3016	0.135	3193	0.986	0.99	99.7808	0.143
5.139-6.275	0.174	140	0.15	2570	0.151	2711	0.985	0.99	99.9631	0.157
6.275-8.799	0.188	109	0.145	2047	0.147	2157	0.978	0.988	99.9536	0.154
8.799-47.761	0.196	64	0.184	1208	0.184	1297	0.975	0.978	98.0725	0.2

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