PDB-8xy4: Crystal structure of VACV N1 protein

ID or keywords:

Entry

Database: PDB / ID: 8xy4

Title

Crystal structure of VACV N1 protein

Components

N1L

Keywords

VIRAL PROTEIN / VACV / N1

Function / homology

Orthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / symbiont-mediated perturbation of host defense response / symbiont-mediated suppression of host NF-kappaB cascade / Protein OPG035

Function and homology information

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Ni, X.C. / Lei, J.

Funding support

China, 1items

Citation

Journal: Emerg Microbes Infect / Year: 2025
Title: Structural insights into MPXV P1 protein and its orthologs reveal conformational dynamics and a conserved antiviral pocket.
Authors: Ni, X. / Wang, Y. / Fan, X. / Yu, J. / Lei, J.

History

Deposition	Jan 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2025	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	8xy4.cif.gz	43.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8xy4.ent.gz	27.9 KB	Display	PDB format
PDBx/mmJSON format	8xy4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xy4_validation.pdf.gz	419.3 KB	Display	wwPDB validaton report
Full document	8xy4_full_validation.pdf.gz	419.9 KB	Display
Data in XML	8xy4_validation.xml.gz	8.4 KB	Display
Data in CIF	8xy4_validation.cif.gz	10.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xy/8xy4 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/8xy4	HTTPS FTP

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Related structure data

Related structure data	8xy1C 8xy2C 8xy3C 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

Deposited unit

A: N1L

16.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N1L

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

Unit cell

Length a, b, c (Å)	77.860, 77.860, 111.390
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-280- HOH

#1: Protein	N1L / N1L protein Mass: 16149.360 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus Gene: VACV_BRZ_SERRO2_026, N1L, 44/47.1_rMVA_020, List025, m8028L, mO028L Production host: Escherichia coli (E. coli) / References: UniProt: Q49PX0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.02 Å³/Da / Density % sol: 59.24 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97861 Å / Relative weight: 1
Reflection	Resolution: 2.42→42.94 Å / Num. obs: 8116 / % possible obs: 99.9 % / Redundancy: 35.7 % / CC_1/2: 0.999 / Net I/σ(I): 24.5
Reflection shell	Resolution: 2.42→2.51 Å / Num. unique obs: 826 / CC_1/2: 0.911

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
xia2		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.42→42.94 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.95 / SU B: 6.324 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2062	405	5.005 %
R_work	0.1701	7687	-
all	0.172	-	-
obs	-	8092	99.84 %

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: 43.187 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.969 Å²	0.484 Å²	-0 Å²
2-	-	0.969 Å²	-0 Å²
3-	-	-	-3.143 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→42.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1014	0	0	85	1099

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1055
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	977
X-RAY DIFFRACTION	r_angle_refined_deg	1.66	1.642	1429
X-RAY DIFFRACTION	r_angle_other_deg	1.412	1.589	2264
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.466	5	129
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.98	22.429	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.65	15	201
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.452	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	138
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1188
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	234
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	232
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	896
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	505
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	464
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	72
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.108	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	29
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	3.776	4.352	495
X-RAY DIFFRACTION	r_mcbond_other	3.763	4.346	494
X-RAY DIFFRACTION	r_mcangle_it	5.162	6.517	619
X-RAY DIFFRACTION	r_mcangle_other	5.164	6.525	620
X-RAY DIFFRACTION	r_scbond_it	4.81	4.782	560
X-RAY DIFFRACTION	r_scbond_other	4.778	4.77	558
X-RAY DIFFRACTION	r_scangle_it	6.615	6.973	806
X-RAY DIFFRACTION	r_scangle_other	6.613	6.975	806
X-RAY DIFFRACTION	r_lrange_it	8.436	50.254	1242
X-RAY DIFFRACTION	r_lrange_other	8.442	50.179	1235

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.42-2.483	0.328	34	0.246	536	X-RAY DIFFRACTION	99.1304
2.483-2.551	0.281	31	0.24	531	X-RAY DIFFRACTION	99.6454
2.551-2.625	0.33	28	0.22	525	X-RAY DIFFRACTION	100
2.625-2.705	0.25	20	0.187	514	X-RAY DIFFRACTION	99.8131
2.705-2.794	0.207	25	0.174	495	X-RAY DIFFRACTION	100
2.794-2.892	0.163	19	0.151	490	X-RAY DIFFRACTION	100
2.892-3.001	0.253	21	0.166	464	X-RAY DIFFRACTION	100
3.001-3.123	0.246	22	0.171	452	X-RAY DIFFRACTION	99.7895
3.123-3.261	0.201	19	0.177	431	X-RAY DIFFRACTION	100
3.261-3.42	0.242	23	0.173	412	X-RAY DIFFRACTION	100
3.42-3.605	0.17	21	0.18	399	X-RAY DIFFRACTION	100
3.605-3.823	0.25	24	0.18	368	X-RAY DIFFRACTION	99.7455
3.823-4.086	0.227	16	0.137	368	X-RAY DIFFRACTION	100
4.086-4.412	0.2	19	0.134	328	X-RAY DIFFRACTION	100
4.412-4.831	0.135	15	0.139	320	X-RAY DIFFRACTION	100
4.831-5.397	0.17	26	0.138	271	X-RAY DIFFRACTION	100
5.397-6.226	0.265	10	0.181	263	X-RAY DIFFRACTION	100
6.226-7.609	0.159	14	0.169	223	X-RAY DIFFRACTION	100
7.609-10.693	0.128	10	0.132	179	X-RAY DIFFRACTION	100
10.693-42.94	0.249	8	0.274	118	X-RAY DIFFRACTION	98.4375

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