PDB-9js5: Crystal structure of the ASFV-derived histone-like protein pA104R

ID or keywords:

Entry

Database: PDB / ID: 9js5

Title

Crystal structure of the ASFV-derived histone-like protein pA104R

Components

Viral histone-like protein

Keywords

DNA BINDING PROTEIN / ASFV / pA104R

Function / homology

Function and homology information

virion component / structural constituent of chromatin / DNA replication / DNA binding
Similarity search - Function

Biological species

African swine fever virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Li, Q. / Shao, H. / Yi, D. / Cen, S.

Funding support

China, 2items

Citation

Journal: Emerg Microbes Infect / Year: 2025
Title: Thonningianin A disrupts pA104R-DNA binding and inhibits African swine fever virus replication.
Authors: Li, Q.J. / Shao, H.H. / Zheng, L.L. / Liu, Q. / Huo, C.C. / Yi, D.R. / Feng, T. / Cen, S.

History

Deposition	Sep 30, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9js5.cif.gz	116.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9js5.ent.gz	74.6 KB	Display	PDB format
PDBx/mmJSON format	9js5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9js5_validation.pdf.gz	457.3 KB	Display	wwPDB validaton report
Full document	9js5_full_validation.pdf.gz	459.2 KB	Display
Data in XML	9js5_validation.xml.gz	13.3 KB	Display
Data in CIF	9js5_validation.cif.gz	17 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/9js5 ftp://data.pdbj.org/pub/pdb/validation_reports/js/9js5	HTTPS FTP

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Related structure data

Related structure data	6lmhS S: Starting model for refinement
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: Viral histone-like protein

B: Viral histone-like protein

hetero molecules

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

1

A: Viral histone-like protein

hetero molecules

A: Viral histone-like protein

hetero molecules

B: Viral histone-like protein

hetero molecules

B: Viral histone-like protein

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
47.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
defined by author&software

3

A: Viral histone-like protein

hetero molecules

B: Viral histone-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.648, 55.648, 152.345
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-339- HOH
2	1	A-347- HOH
3	1	A-356- HOH

#1: Protein	Viral histone-like protein / pA104R / DNA-binding protein pA104R Mass: 11630.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus Gene: A104R, A104R CDS, BA71V-A104R, AFSV47Ss_0056, ASFV-Georgia_4-058, ASFVARMWT4_00043 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E0L7
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.93 Å³/Da / Density % sol: 57.98 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2.6 M ammonium sulfate, 0.1M citric acid

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97851 Å / Relative weight: 1
Reflection	Resolution: 1.8→29.88 Å / Num. obs: 48848 / % possible obs: 99.87 % / Redundancy: 17.9 % / B_iso Wilson estimate: 33.63 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.07458 / Net I/σ(I): 23.24
Reflection shell	Resolution: 1.8→1.864 Å / R_merge(I) obs: 0.6258 / Num. unique obs: 3104 / CC_1/2: 0.945 / CC star: 0.986

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6LMH

6lmh

Resolution: 1.8→29.88 Å / SU ML: 0.1837 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 27.012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.239	2237	4.58 %
R_work	0.1983	46611	-
obs	0.2001	48848	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 40.7 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1554	0	38	146	1738

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1612
X-RAY DIFFRACTION	f_angle_d	0.943	2180
X-RAY DIFFRACTION	f_chiral_restr	0.0654	256
X-RAY DIFFRACTION	f_plane_restr	0.0082	272
X-RAY DIFFRACTION	f_dihedral_angle_d	5.6868	206

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 (%)
1.8-1.84	0.3062	128	0.251	2896	X-RAY DIFFRACTION	99.83
1.84-1.88	0.2581	174	0.2329	2858	X-RAY DIFFRACTION	99.87
1.88-1.93	0.2906	140	0.221	2947	X-RAY DIFFRACTION	100
1.93-1.98	0.2294	122	0.1979	2925	X-RAY DIFFRACTION	99.93
1.98-2.04	0.2671	130	0.228	2899	X-RAY DIFFRACTION	99.97
2.04-2.11	0.2688	170	0.2141	2893	X-RAY DIFFRACTION	100
2.11-2.18	0.278	114	0.205	2936	X-RAY DIFFRACTION	99.97
2.18-2.27	0.2139	114	0.1872	2929	X-RAY DIFFRACTION	99.97
2.27-2.37	0.2891	96	0.237	2951	X-RAY DIFFRACTION	99.97
2.37-2.5	0.2882	182	0.2417	2929	X-RAY DIFFRACTION	99.97
2.5-2.65	0.3046	156	0.2343	2908	X-RAY DIFFRACTION	100
2.65-2.86	0.282	152	0.2153	2892	X-RAY DIFFRACTION	100
2.86-3.14	0.2505	140	0.2402	2904	X-RAY DIFFRACTION	100
3.15-3.6	0.2566	123	0.2018	2937	X-RAY DIFFRACTION	100
3.6-4.53	0.188	144	0.1518	2892	X-RAY DIFFRACTION	100
4.53-29.88	0.1918	152	0.1675	2915	X-RAY DIFFRACTION	99.61

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.66467725808	-0.756149000149	0.0966897774896	1.92188538372	-0.829975072062	3.54091510762	0.109910391843	0.103141067627	0.0485694767168	-0.116999378683	-0.0946799036745	0.18832595036	0.192513827299	-0.257349016005	-0.0116798512843	0.274519095025	-0.00401422310388	-0.0135174403391	0.271867690793	-0.021518257121	0.329855495105	7.24154749292	-0.214618354514	10.9462430093
2	2.09798481502	1.83656703729	-2.54454692831	1.28827618219	-1.88237683083	2.91082451496	0.273048826147	0.229784488222	0.320260308962	0.183751499728	0.0716104765633	0.559306316533	-0.623518154553	-0.51886447197	-0.0931140436444	0.353076555076	0.0584138649221	-0.0122006689087	0.344465770924	-0.00148932340369	0.357431134683	14.8234612628	14.5697772379	9.28628028519
3	1.1902453302	0.447473117883	1.31181689571	-0.189481158863	0.334998440677	1.57441556462	-0.027720530683	0.170626509148	-0.012302031981	-0.0411323918544	-0.0316059487837	-0.0514830129717	-0.158526873993	0.246915444261	0.0186416571061	0.313649892417	-0.00931552692995	0.0330179046045	0.298672202911	0.0478331425566	0.295209724157	24.532165714	13.0435850314	-0.469128846268
4	4.37064562007	1.81475517065	2.26666798795	1.43787113227	2.29725854316	3.32740262326	-0.296828021484	0.00499089882153	0.13604437064	0.00477211904545	-0.0797447026323	0.234849769762	0.00997337029236	0.386639978473	0.000625363791989	0.356184849248	-0.0416236812278	-0.0261388056434	0.482626655628	0.112356516624	0.267656163367	11.0542573136	20.1225355868	-31.6310519588
5	4.48661168179	1.33616041735	5.27036951348	1.47797977233	1.64230332975	6.88286548018	-0.684777273704	0.114557029913	-0.0745896666272	0.252474727444	0.391020980625	0.461162133131	-1.38818082956	0.296214960411	0.0533550986106	0.444700283374	-0.0917510460389	-0.0662741979699	0.486661537193	0.0719917810006	0.379008759977	12.6649320464	23.9537655793	-24.4358787614
6	0.462351379167	-0.690108900373	0.416416946741	7.13937772585	-3.9985028926	2.92880592197	-0.0130605234677	0.333092382932	-0.196603045218	-0.399037135568	0.0680555078975	-0.263122112139	-0.0130432784535	0.171631048982	0.051266369307	0.337550600189	-0.0151561107617	0.0201331267502	0.359718341596	0.0170694146537	0.300441374794	22.5101430738	13.5832614819	-6.85735077897
7	1.05407093579	2.14596776475	0.340994655334	3.66686197587	0.606720271647	0.202227699696	-0.0640367364714	0.195353628438	-0.337910466599	-0.101093705256	0.085538650398	-0.675433723318	0.425844995014	0.183949964618	0.000390020091828	0.386417725012	0.0433011067365	-0.021978790682	0.353289303355	-0.0210243035443	0.413770581379	25.0699902904	-4.31127206094	0.695725295559
8	2.98559918349	1.05497880734	-1.51240715729	2.02803076736	-1.38421871568	3.61699363094	0.0633245982299	-0.136955234102	-0.0255976565185	0.15353083472	-0.205805101741	-0.0335040750654	-0.366250581851	0.0417669529041	-0.0407133847031	0.314517473679	-0.00565286179099	-0.0293076155284	0.265107949711	0.000476294100428	0.320501631423	23.6229116432	13.3869399507	14.3450852114
9	0.908380579611	1.17318776398	0.987997409598	3.37054686048	2.77828199835	4.0803839184	0.181350972352	-0.144036939763	0.118999160202	0.485268655813	-0.174521419689	0.12644004909	0.609660000249	0.0802288404723	-0.0508675522002	0.305258394159	0.0125412310932	0.0321224105402	0.231208698361	-0.00427831783486	0.268794686204	17.87095625	-1.54565016304	11.3949146476
10	1.2410301379	-0.0511628729409	-1.19513431229	1.3814797219	1.25272797655	1.89231569591	0.0519860116758	0.125987267475	0.0654608836928	-0.134071437348	-0.0471022269047	0.0678583533282	0.0826737821484	-0.419653300858	0.0388833877598	0.33291164911	0.00777681857273	-0.0281766503261	0.306654712327	0.0114456644561	0.356601767089	13.3121172645	-1.0506061781	-2.24751831776
11	2.0165370626	2.81184937141	0.0204798736951	2.73351347872	-1.28810686288	1.34570555657	-0.294658687649	0.798402434392	-0.402782229944	-0.0824352151252	0.299511371628	-0.283665750118	0.147095314329	-0.152203128703	-0.00663817538975	0.317414581821	-0.0420194166085	0.0618607632336	0.41773052477	-0.0430435575423	0.287997469524	35.240884004	0.0374927036607	-22.3142347275
12	4.37964731752	4.61525408058	-2.19938466526	4.63360281604	-2.58978807259	1.04051962021	0.425604548953	-0.593684736347	-0.779896960164	0.493704234216	-0.557434685961	-0.525897877584	-0.111990078886	0.353701909638	0.0702252903554	0.39228640305	-0.0552608094326	-0.00294763670042	0.366624867788	0.000471455911336	0.392838100972	33.4263936659	-5.90292840466	-17.317169937
13	0.933490261926	-2.83676055893	-1.27092213266	8.74689730508	3.51860704214	1.02987245376	0.231380125704	0.296811062665	-0.323087228097	-0.252357658002	-0.147932661639	0.88474701288	0.153387036208	-0.543071971918	-0.0269308642955	0.392361182309	0.0104176556213	-0.0233637900379	0.327737205313	0.0051816254304	0.328359450157	18.3498589009	-2.22168888092	-6.88186187385
14	2.09728165242	1.14705319804	-0.309932559026	2.66653146004	-0.525508442134	1.57969267131	-0.0429885939464	0.757584601343	1.01825633081	-0.632491316026	-0.143022278197	0.941348013068	-0.969989595964	-0.282702621581	0.00489843004626	0.512927259602	0.0633059205184	-0.0103811589922	0.384165160901	0.0896247968365	0.461972351818	13.250700359	16.1398248512	-4.47283723009

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 12 through 31 )	A	A	12 - 31	1 - 20
2	2	chain 'A' and (resid 32 through 52 )	A	A	32 - 52	21 - 41
3	3	chain 'A' and (resid 53 through 69 )	A	A	53 - 69	42 - 58
4	4	chain 'A' and (resid 70 through 84 )	A	A	70 - 84	59 - 73
5	5	chain 'A' and (resid 85 through 93 )	A	A	85 - 93	74 - 82
6	6	chain 'A' and (resid 94 through 101 )	A	A	94 - 101	83 - 90
7	7	chain 'A' and (resid 102 through 110 )	A	A	102 - 110	91 - 99
8	8	chain 'B' and (resid 12 through 31 )	B	B	12 - 31	1 - 20
9	9	chain 'B' and (resid 32 through 52 )	B	B	32 - 52	21 - 41
10	10	chain 'B' and (resid 53 through 69 )	B	B	53 - 69	42 - 58
11	11	chain 'B' and (resid 70 through 84 )	B	B	70 - 84	59 - 73
12	12	chain 'B' and (resid 85 through 93 )	B	B	85 - 93	74 - 82
13	13	chain 'B' and (resid 94 through 101 )	B	B	94 - 101	83 - 90
14	14	chain 'B' and (resid 102 through 110 )	B	B	102 - 110	91 - 99

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