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Yorodumi

- PDB-8khu: Hepatitis B virus core protein Y132A mutant in complex with THPP ... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8khu

Title

Hepatitis B virus core protein Y132A mutant in complex with THPP derivatives 48

Components

Capsid protein

Keywords

VIRAL PROTEIN / HBV capsid assembly mudulator / ANTIVIRAL PROTEIN

Function / homology

Function and homology information

microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function

Biological species

Hepatitis B virus adw/991

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zhou, Z. / Xu, Z.H.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Discovery of 4,5,6,7-Tetrahydropyrazolo[1.5-a]pyrizine Derivatives as Core Protein Allosteric Modulators (CpAMs) for the Inhibition of Hepatitis B Virus.
Authors: Kou, B. / Zhang, Z. / Han, X. / Zhou, Z. / Xu, Z. / Zhou, X. / Shen, F. / Zhou, Y. / Tian, X. / Yang, G. / Young, J.A.T. / Qiu, H. / Ottaviani, G. / Mayweg, A. / Zhu, W. / Shen, H.C. / Liu, H. / Hu, T.

History

Deposition	Aug 22, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	8khu.cif.gz	457.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8khu.ent.gz	313.5 KB	Display	PDB format
PDBx/mmJSON format	8khu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8khu_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8khu_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8khu_validation.xml.gz	40.1 KB	Display
Data in CIF	8khu_validation.cif.gz	53.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/8khu ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khu	HTTPS FTP

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Related structure data

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	#62 - Feb 2005 Major Histocompatibility Complex similarity (3) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

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Assembly

Deposited unit

A: Capsid protein

B: Capsid protein

C: Capsid protein

D: Capsid protein

E: Capsid protein

F: Capsid protein

G: Capsid protein

hetero molecules

125 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	66.207, 65.983, 86.412
Angle α, β, γ (deg.)	68.620, 68.420, 83.330
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1

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Components

#1: Protein	Capsid protein / Core antigen / Core protein / HBcAg / p21.5 Mass: 17486.916 Da / Num. of mol.: 7 / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus adw/991 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P03147
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O
#3: Chemical	ChemComp-VX0 / (6~{S},7~{R})-6,7-dimethyl-3-(2-oxidanylidenepyrrolidin-1-yl)-~{N}-[3,4,5-tris(fluoranyl)phenyl]-6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazine-5-carboxamide Mass: 407.390 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₉H₂₀F₃N₅O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM citrate, 21%(vol/vol) isopropanol, 1%(W/V) PEG 10000

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.97791 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97791 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 81798 / % possible obs: 96.6 % / Redundancy: 3.6 % / B_iso Wilson estimate: 35.09 Å² / CC_1/2: 0.5 / Net I/σ(I): 7.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	3.4	0.689	4005	0.748	0.925	0.427	0.814	0.484	94.4
2.03-2.07	3.4	0.61	3998	0.746	0.924	0.379	0.722	0.513	94.8
2.07-2.11	3.5	0.523	4015	0.841	0.956	0.325	0.619	0.539	95.1
2.11-2.15	3.3	0.427	4037	0.872	0.965	0.275	0.51	0.587	95.6
2.15-2.2	3.4	0.408	4105	0.879	0.967	0.258	0.486	0.578	95.6
2.2-2.25	3.6	0.35	4024	0.915	0.978	0.212	0.411	0.634	95.7
2.25-2.31	3.8	0.278	4035	0.958	0.989	0.161	0.322	0.701	95.8
2.31-2.37	3.8	0.247	4112	0.966	0.991	0.143	0.286	0.744	96.4
2.37-2.44	3.8	0.22	4081	0.966	0.991	0.128	0.255	0.766	95.7
2.44-2.52	3.8	0.201	4112	0.969	0.992	0.119	0.235	0.79	96.8
2.52-2.61	3.7	0.156	4086	0.983	0.996	0.092	0.181	0.908	97.3
2.61-2.71	3.6	0.139	4117	0.981	0.995	0.084	0.163	1.02	97.3
2.71-2.84	3.4	0.113	4145	0.987	0.997	0.072	0.135	1.186	97.5
2.84-2.99	3.7	0.103	4141	0.988	0.997	0.061	0.12	1.342	97.6
2.99-3.17	3.9	0.09	4106	0.99	0.998	0.052	0.104	1.548	97.7
3.17-3.42	3.8	0.077	4170	0.991	0.998	0.044	0.089	1.896	97.7
3.42-3.76	3.7	0.067	4087	0.993	0.998	0.04	0.079	2.172	97.1
3.76-4.31	3.4	0.062	4137	0.991	0.998	0.039	0.074	2.606	97.5
4.31-5.43	3.9	0.06	4136	0.992	0.998	0.035	0.07	2.472	97.2
5.43-50	3.7	0.063	4149	0.995	0.999	0.037	0.073	2.559	98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data scaling
HKL-3000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→43.04 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.3764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2131	2016	2.47 %
R_work	0.1792	79561	-
obs	0.18	81577	95.07 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.82 Å²

Refinement step

Cycle: LAST / Resolution: 2→43.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7005	0	208	301	7514

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0189	7491
X-RAY DIFFRACTION	f_angle_d	1.4937	10293
X-RAY DIFFRACTION	f_chiral_restr	0.0802	1151
X-RAY DIFFRACTION	f_plane_restr	0.0147	1298
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2063	2615

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 (%)
2-2.05	0.3053	113	0.2816	4556	X-RAY DIFFRACTION	76.6
2.05-2.1	0.2768	144	0.2505	5666	X-RAY DIFFRACTION	94.56
2.1-2.17	0.2782	146	0.2381	5657	X-RAY DIFFRACTION	95.05
2.17-2.23	0.2791	147	0.23	5741	X-RAY DIFFRACTION	95.55
2.23-2.31	0.2565	145	0.2016	5680	X-RAY DIFFRACTION	95.48
2.31-2.41	0.2084	141	0.1883	5747	X-RAY DIFFRACTION	96.04
2.41-2.52	0.2654	149	0.1941	5754	X-RAY DIFFRACTION	96.06
2.52-2.65	0.2273	150	0.1888	5821	X-RAY DIFFRACTION	96.77
2.65-2.82	0.2245	144	0.1887	5800	X-RAY DIFFRACTION	97.31
2.82-3.03	0.2606	144	0.1872	5831	X-RAY DIFFRACTION	97.33
3.03-3.34	0.1959	149	0.1768	5823	X-RAY DIFFRACTION	97.65
3.34-3.82	0.2204	146	0.1651	5821	X-RAY DIFFRACTION	97.34
3.82-4.81	0.1663	148	0.1457	5819	X-RAY DIFFRACTION	97.45
4.81-43.04	0.191	150	0.1724	5845	X-RAY DIFFRACTION	97.67

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	2.19997580229	-0.432019768681	-2.00095531178	0.23496475556	0.806092333562	4.23991194243	-0.372471263266	-0.34952829261	-0.225738120227	0.416939354097	0.236988266134	-0.213094209828	0.572247063957	0.944213890191	0.104283094578	0.43292232617	0.108904614903	-0.0177123712812	0.519329368403	0.00981397587348	0.318840848356	-32.1260735929	-5.3308922549	23.1357794816
2	2.72359317613	-2.43715063929	1.92189927115	2.33776660924	-1.35702612359	2.65947107252	-0.476915253189	-0.88778721347	-0.943454581219	0.68400497169	0.763435654199	0.289435091603	-0.10461156097	-0.776540041711	-0.199321143145	0.559460969116	0.142146871216	0.0695906559075	0.621850000352	0.159034763271	0.393071241712	-46.1508697906	-1.08761718138	29.5815122263
3	4.46973841574	0.62748410005	-2.91076424466	5.92565851604	-3.11547782137	7.2208662056	0.140284594711	0.243411977192	0.77235151941	0.104541276556	0.379480390291	0.331059667341	-1.00398651864	-0.888490537263	-0.383525043879	0.423666097456	0.0535922576242	0.0272279884806	0.327135649914	-0.0181347149219	0.291788088706	-46.3835749925	9.78524241275	16.2664283721
4	2.62783944436	-0.725900922726	-0.483898300837	2.52349450851	-0.36171087181	2.46927644503	0.0571536858416	0.197825349184	-0.0327393327309	-0.100939856797	0.158595624106	0.231352301548	-0.281783274798	-0.186477749255	-0.233058306064	0.347395668994	0.00290425656789	0.0332476793269	0.345469473417	0.00646880515075	0.339635362259	-43.1422438111	1.30849340917	9.60849344942
5	1.8979686615	-0.221696839673	-0.520071646093	0.153766813877	-0.151865864823	0.437966542032	0.414390664996	-0.797812126376	0.523363542976	0.0342340269933	-0.473180539442	1.78823604319	0.56843873101	-0.601890297095	-0.053989526168	0.661974574943	-0.0884456983525	0.00554409438803	0.891005266689	-0.185261684905	1.54016018875	-58.4757781877	-12.6683772264	14.9652161892
6	1.90955581217	-1.05151592718	0.327897575104	2.22305371276	-0.629044920027	3.72782988432	-0.453782099593	-0.385283117981	-0.144662414048	0.734045342175	0.685805244828	-0.730314493176	-0.198621219249	0.39611097235	-0.181485205638	0.465117796686	0.135354326686	-0.0475929519814	0.40758440458	-0.0505930985297	0.297092731341	-38.5770158842	2.46404042476	28.3548883272
7	1.05471961618	0.130581518299	0.355444827359	0.0136536793756	-0.0198420400454	1.21689977005	0.580138753171	-0.169951858024	1.05155210802	0.432450112836	0.406981021848	0.380094472948	-1.14229327539	-0.5750801278	-0.741483117713	1.00520113409	0.469410964318	0.141098253428	1.01433215282	-0.000729717809336	0.659390077334	-43.2797433441	4.27602797447	43.3578681366
8	2.63149687649	-0.618711028204	-0.915282361881	2.20083034644	-0.0336478695141	4.42056549261	0.415662443788	0.329033046465	0.201741212048	-0.299779418124	-0.37966209938	0.0875455366534	-0.430424006556	-0.842170837781	-0.119107632928	0.358266855046	0.024717891256	0.02199462276	0.35092717564	0.0304851355473	0.28905334707	-38.1369880626	0.892353245957	-3.4531985186
9	5.9226243119	0.428362463715	2.18701531853	3.73467266882	0.753064557988	7.55979255879	0.194878308028	0.348089384759	-0.387213519879	0.0332289794102	-0.0169529724268	-0.475200740273	0.913972147622	1.15447054721	-0.0551344547927	0.300651575309	0.0342831001364	0.00650062381259	0.404810054416	0.0142889750841	0.348670911651	-26.5903666238	-11.9870402583	5.41984175818
10	1.76530659857	-1.00905347588	-0.0509175596693	2.22115494534	-0.118154262257	2.95109479543	-0.0106211050692	-0.139478028876	-0.192434432734	0.117812654686	0.145016435288	0.0474067932676	0.133815195332	0.0660236474678	-0.128050240793	0.287328968862	-0.0496842047271	-0.00213861230399	0.332192535706	-0.00432321507918	0.306849210021	-36.3219707355	-8.21025809638	11.345697399
11	1.75078731213	0.94527011054	-1.07957200506	1.33073185358	-0.541534392935	0.678977069873	0.00117562767534	0.744339243626	-0.639978576011	-0.110148060452	0.213816693736	-0.301951929864	0.312606093455	-0.946702356319	0.00536430662286	0.520186202093	-0.336081524217	-0.0936117573288	0.687162779567	-0.00590292871643	0.75103832624	-52.3878847764	-18.5643987375	1.50757079632
12	2.08582834264	0.294473245208	0.521619842646	2.32498609502	-0.314237586927	1.92566113259	0.0969863344999	0.0224707562958	0.019993501919	-0.0352551701344	-0.0712166319391	-0.115893462389	0.0521449093944	0.156422639527	0.00213620093016	0.277096231227	-0.0189998613578	-0.00375633832952	0.294101333847	-0.0285586438039	0.288132265556	-32.8223947966	-4.62555023321	-0.643603549015
13	4.19990374757	-1.34860358985	0.746080802343	3.71734335257	-0.293501151693	6.23186591693	0.4787381408	0.279067398548	0.345614130082	-0.538392391676	-0.520560502058	-0.576059749702	-0.343422655294	0.74286090229	0.0778724953489	0.406340627954	0.0100779258367	0.0411856402549	0.402428630315	0.077211642354	0.315486025729	-30.2371751034	0.856065462829	-12.2580636036
14	1.91778707757	-0.633228261822	-0.160552780802	3.68884949583	-0.225113722812	4.55584913083	1.23597455223	0.969668240852	-0.363275158728	-0.687893927422	-0.486021173905	-0.705033687565	1.07538129762	1.15605270043	-0.497175687455	0.690261912922	0.258902863099	0.0984443988523	0.645556844168	0.0593102112875	0.487606938683	-27.5266561684	-5.11683312754	-20.4012094581
15	2.47019761003	2.90784475374	0.879938232168	3.72694080587	-0.241933021871	5.58836885693	0.303474857826	-0.500947075292	-0.0371662347884	0.0787060784371	-0.123702522827	-0.510668667022	0.536975176517	0.17127928103	-0.0456166466962	0.80674590801	-0.398328180596	0.156532412484	0.555444524693	-0.0997723026528	1.04658423601	-22.6422204994	10.445617198	7.25123830808
16	1.70652029739	-0.00175068279865	-0.0557527966558	4.93126202103	-4.02789209307	3.33377907082	0.0644164959851	-0.717559722252	0.0137348345303	0.564244951264	0.0615525668665	0.317384076603	-0.34838161269	-0.94420873232	-0.00697972043722	0.333775643223	-0.0379703727478	0.0445683888225	0.509734374463	0.023161640339	0.402330246248	-14.3990045885	-26.2214785238	15.2414902052
17	2.42078610753	-1.143249828	0.94249824347	0.966003132678	-1.26201984359	3.03270155313	-0.468641245997	-0.680586818067	0.240518092361	0.650132422525	0.279727161225	-0.465043325388	-0.973691638866	0.31034031136	0.102390646108	0.369963366256	-0.0899313472738	-0.0131365602672	0.291556486741	-0.0571475301265	0.425901007471	-10.4450917368	-20.9669918699	10.8605913157
18	7.15289047208	-4.0970951736	4.91568039569	6.89368761609	-2.45190461706	5.39178639701	0.178512862171	-1.12626266049	-0.192469494458	-0.216422756685	0.0885316138759	0.556829263989	-0.283119679249	-0.827564491099	-0.235402928767	0.332078972012	0.070876025625	0.0434077500772	0.412154056194	0.0391029726306	0.34843078661	-20.7578416727	-20.9975849679	4.91553659904
19	2.16334443208	-1.64459554351	-0.487648751474	3.8963032181	1.33303937831	1.5088299703	0.499221837653	0.536687147527	-0.329796164992	-0.733144109977	-0.435390569897	0.562371684382	-0.2195103546	-0.458006107353	-0.0392187756154	0.419067616987	0.0817243325498	-0.0421646410125	0.379409869255	0.0192562305845	0.404956270151	-19.97597572	-26.9461273115	-4.53879514851
20	8.28654559033	-1.05204908928	2.13677972372	2.54966983139	-0.181170836154	4.29623382017	0.117541992874	1.02978746984	-0.798620467151	-0.538705844564	-0.0752679287939	0.0680836032064	0.423749544679	0.470592657128	-0.0325637223485	0.453959132581	0.0416363655089	0.0544175866588	0.36412539099	0.0191617946347	0.316004037615	-4.66880606967	-34.8185660129	-4.49556116839
21	1.36560081996	-2.20374298702	-0.680465587854	3.64436028355	0.725227357612	1.72462207027	-0.370280717164	0.294160201099	0.275814539124	-0.495235353247	0.41099148577	0.485647187685	0.0625026486588	0.0606713989966	-0.0388684479719	0.267309811567	-0.0489403951752	0.0179698074264	0.522342446715	0.0703759226644	0.444446661851	5.55795880787	-32.3459128343	5.70978806309
22	2.59941039289	0.464515988035	-0.714347051482	2.02572669891	0.608173728325	2.69733893888	-0.194255739912	0.138783511097	-0.171382203942	0.287555982983	0.0500833321899	0.25207419588	0.413629848854	0.143611556805	0.0941979617639	0.297681809351	-0.010426142204	0.0211216477329	0.330773492488	-0.00322464656154	0.347113020236	-11.6038031179	-40.7612928136	5.4251863633
23	0.851323522789	1.15507951362	0.234991283128	1.55112753513	0.322260108726	0.0833165459357	-0.478077602447	0.473266940177	0.0895824011606	-0.551639267517	0.398715160808	1.05023278091	0.603844760656	-1.10458389199	0.158037186456	0.63705663565	-0.384331860283	-0.0472026646524	0.645057639035	0.014524672141	0.64930680932	-28.2580459107	-45.0847160961	1.15918435155
24	3.77443184951	-0.0555938384923	0.28774401804	2.18298412729	-0.268234074379	1.69418460906	0.327418493875	0.190280394809	0.286930327798	-0.151307891152	-0.186509474802	0.0473513173946	-0.00243998793496	0.13858419962	-0.162351076558	0.279982764828	-0.0136590310209	-0.0078549453853	0.307855543424	0.0166882923559	0.317127698791	-11.9244387061	-27.7957897001	0.760375234869
25	5.30867138206	-2.02859726279	-1.10428159294	3.19167645021	-0.609049878924	3.35946158612	0.53396888617	-0.00490212673872	0.21195889862	-0.306475021702	-0.380320064051	-0.596587331341	-0.616139813762	0.0407285884953	-0.160140264342	0.38812771325	0.0282089629142	0.0848404388434	0.264599210907	0.0413562536218	0.385786641304	-16.0756885838	-15.8166746538	-2.98974810526
26	0.373059113449	-0.418911260616	-0.130589267844	3.2320780653	-0.535314856821	3.90852674822	0.831645007822	1.02114849334	-0.287432965302	-1.17885141745	-0.700875867901	-0.18920813524	-0.768638506255	0.632681022334	0.00810290565467	0.845247985374	0.273482301948	0.0705499384625	0.612061410715	0.0021548800183	0.365356525676	-21.4545037066	-14.1263445159	-12.5088088827
27	2.82277423588	-1.33107848733	0.065516118189	2.67432267457	-1.14856777681	3.50606786852	-0.134564299325	-0.0965317240827	-0.0398963643641	0.192810410638	0.0946888101647	0.0112524567392	0.187793905719	0.285801316526	0.0350943298624	0.224673564908	0.00487148153271	-0.0238203094196	0.277878355678	0.000884099706309	0.217300139146	-3.30618277983	-37.5760883869	19.2370891615
28	1.4816894258	0.191804557128	-0.158465750831	1.4107186621	0.108373495808	1.7588418787	-0.0665092412029	0.0487939743984	-0.106560968683	0.10258552208	0.00532378514838	0.0978352724473	0.120051737729	-0.0636727226498	0.052955071516	0.303080482703	-0.0795918295034	-0.0197184865967	0.294377512519	-0.00123989488156	0.362266798953	-15.3016891219	-37.5800525128	14.2946140397
29	0.817572336714	0.215643799439	0.571457950389	0.133369881402	0.0207832380994	0.456068704092	0.64797893454	-0.608052414575	-0.30617825808	-0.393499340754	-0.48097194635	0.314406955808	1.20449717959	-0.378769702969	-0.108022753037	0.78088821699	-0.210147407408	-0.0116665157324	0.702784114502	0.124794240854	0.668707601164	-21.630538389	-52.9418852082	15.4449587124
30	2.52120266893	-1.82694133074	-0.0351823613245	4.15363737606	-0.31086603297	1.98614349426	-0.526661196511	-0.49741440703	0.0971614485117	0.543104436254	0.532115104345	-0.321311916507	0.388143423248	0.492070834961	0.0364509581367	0.431048323264	0.162586897867	-0.0146531465879	0.471479946704	-0.0186608622478	0.266376482991	3.9757930041	-45.2530805161	25.6422877556
31	1.80836172457	2.24843775136	0.376825749706	2.73340343245	0.59341302084	0.232553904214	-0.220594218421	-0.479428822736	0.940654552353	-0.695249278359	-0.530116562768	0.951000228057	-0.11668363642	0.224028747896	0.465518367272	0.730348210534	0.0161281994792	-0.148313944106	0.959117183769	-0.0972524130516	0.835531844621	16.4462651569	-27.643383201	35.7734858186
32	1.31122728463	-0.640752792591	-0.699921045765	2.70608716796	0.506270166845	1.55782011141	0.298954204745	0.959488005945	0.37737939265	-0.462281681084	-0.424665394045	0.00455859581126	-0.167459377443	-0.223863425246	0.0230683131425	0.598346391513	0.221588755778	0.0687112946291	0.66651198387	0.0467481318136	0.416826668252	-18.8571469757	-19.820764927	38.5394706989
33	6.06929520001	-2.81778444077	-3.30877126496	8.74436528392	1.3661524703	5.24797945152	0.0662996164173	0.177072789307	0.258729433753	-1.13736842132	-0.16290310057	0.498973364166	0.116396239059	-1.2932493245	0.196640085396	0.633477712014	0.298372519062	0.00716796505194	0.644157635572	0.0419478724759	0.358353760001	-15.1573548455	-30.7878504195	35.3550114849
34	1.81072073656	-0.907806571507	-0.0456359965933	2.06334982156	-1.46519947212	2.24961305892	-0.184852839023	-0.1355887039	0.0817692519389	0.49230126915	0.161223897961	-0.168231865744	0.215729140192	-0.0133672403104	0.0207720618805	0.415230231626	0.11707571884	-0.0148870230526	0.409316051688	-0.0343157461035	0.342048177747	-16.8364246465	-28.3515323665	55.107374667
35	2.58045956157	-1.03529235308	0.118034058836	2.75405306571	-0.333381010294	3.30094370384	0.185792548869	0.217827525815	-0.120105149722	0.199045403966	0.246989053239	0.382430944491	0.0698465258513	-0.629814105741	-0.400809072039	0.470585557755	0.118837259113	-0.0204789275987	0.478338603141	0.059598849879	0.401299656277	-29.2547580382	-27.3468601381	51.9574236132
36	3.08735919322	0.68225948861	-1.2226075874	0.196377712131	-0.0951791564111	1.01728770043	0.393481504792	0.754598693367	-0.817675277787	-0.712870643478	-0.0753942125345	1.30954946102	1.52418878475	-0.700065898078	-0.258628613192	1.01348516538	-0.211630203665	-0.18594877903	0.812983481803	0.0482544965062	1.25663089725	-36.4548488499	-41.5890500216	45.3994451258
37	1.16001563472	0.00905233280201	-0.551454916287	2.22303738763	0.798359570132	2.08658244286	0.0671112453302	0.195124379819	0.145182044917	0.115721536806	0.0404213574217	0.0760269810596	0.112593958289	0.271882675832	-0.0802809417827	0.497017079234	0.163505641416	0.0244955070936	0.447993186172	0.0180120296193	0.374646516887	-16.1189980439	-29.2196813504	47.0693620737
38	5.89899957207	-0.280225172688	0.966031965303	2.30447170404	1.73708994869	1.54053254768	-0.109155756695	-0.0934931120556	0.672742180243	0.0746162708662	-0.130238180555	-0.334919971995	0.773194472267	1.09899133464	-0.0725655982482	0.633171274171	0.245602941287	0.109613003754	0.743642760477	0.0775290176771	0.2583335898	-5.69573783696	-32.8396808074	39.5445874868
39	2.4131396466	-1.0630516073	-1.00229456133	3.23104324853	2.42614092144	4.4193942756	-0.220789092686	-0.476584487616	0.23902214173	0.978146600747	0.00990762706718	-0.257604342632	1.1159719451	1.05334582102	0.25220656147	1.0555694511	0.376172450247	0.0748820097211	0.751309893493	0.111649286396	0.489396691069	-1.14021149002	-41.8418762599	40.6938449442
40	3.284754638	-1.85542567825	-0.261541569731	1.76503234198	0.428318565831	0.31146198975	-0.796523266851	-0.544266289507	-0.338989016548	0.853443348756	0.653539750273	-0.0625437750559	0.347381495845	-0.0485521361741	0.0897464403883	0.6481617153	0.196280197033	0.0422407258242	0.438980514675	0.0102921973868	0.388742745943	-28.9150316103	-14.1609273151	60.1522806096
41	1.25552103423	-0.317344259109	-0.374855561888	1.056484562	0.880096029409	4.26986210858	0.183009685815	0.420009038218	0.0748333848903	0.168242834052	-0.3753125839	0.599538088475	-0.28700346275	-1.27761341431	0.0484785706038	0.569393199888	0.250649698411	0.114382673833	0.714514025766	0.038289025649	0.394304504489	-42.3904651326	-9.28109571207	52.0475274875
42	6.62439765147	0.678799281415	-2.1252972397	2.13319895639	-1.13213323658	1.95463853802	0.161834029879	1.58237326857	0.336158712104	-0.356901950282	-0.00708862526855	-0.15776353619	0.0275351387337	-0.467340236856	-0.135365525466	0.619995497175	0.216105931159	0.0755279059943	0.570015689591	0.0947444551153	0.405769245722	-31.4649316591	-10.0029905928	38.9359803268
43	2.79905843792	-1.64445211289	0.931055940652	2.73296907734	-0.38350571561	3.16216870694	0.259864881783	0.0720748236997	-0.180097793896	-0.419752143175	-0.142244717932	-0.0785953478961	0.0918209154333	-0.25599774884	-0.0868011412142	0.501337137131	0.145406087077	0.0399368738062	0.449550001073	0.0442968356136	0.376016367362	-28.5831185284	-20.5662709621	42.6488784767
44	1.64187708485	-0.0610965735022	-0.431499797137	1.08029849697	-0.285048422881	0.322719469591	0.000961037224078	0.39725988757	-0.629074159766	0.211114954587	0.237173408617	1.3648306915	1.32295319605	0.00257971929749	-0.306877405768	0.75242016124	-0.0156622004797	-0.146219103666	1.33752927846	0.0310946145919	1.01286610407	-47.6247588212	-29.3127964325	45.6416133545
45	2.87628236214	0.740148136324	-0.997093022644	2.49298711562	0.084748723944	2.39261689478	0.332234468054	0.0762886459356	0.0165797866422	0.102899415559	-0.287069442832	-0.275731382858	-0.332061616704	-0.231772787945	-0.0464147919233	0.519511983939	0.178130389366	0.0816825541435	0.46470715758	0.0693214220491	0.344654841596	-32.95849132	-10.5104617879	50.0779072592
46	3.56952958277	-1.06675442149	-2.27201911059	2.76527018595	0.0778546218999	3.56761104275	0.188581414168	-0.00601187136856	0.436799151365	-0.304330141572	0.0176109730628	-0.358212478493	-1.01938280285	-0.284192927016	-0.0842879429256	0.773607953429	0.181981060823	0.12405461795	0.466431327397	0.0281745956352	0.341929132469	-36.6393531906	-0.914030041047	58.6067319111
47	0.199114099824	0.401337800289	0.543243567205	1.78603459895	0.435023383237	1.74472927673	0.132011444844	0.893764584654	0.664324940791	-0.536325182324	0.0458031869678	0.0335575495129	-0.727331407348	-0.327304925445	-0.034109306921	1.04090409553	0.410346201436	0.10082668775	0.749350552945	0.159061132299	0.486108853729	-44.8944828046	5.4886914018	57.4767720354
48	1.23823736921	-0.621380628158	-0.197637291029	2.2336226031	0.0672323049447	3.76905159427	0.136814534743	-0.645529681171	-0.623878112911	0.370871829514	-0.235732671686	1.18811567844	1.12907852557	0.0407726108821	0.160584687958	1.06000198379	-0.115152691224	0.143144164566	0.728276990708	0.103749629032	0.90481960075	-22.1785424634	24.9429045768	54.7334173051
49	0.564578626238	-0.797237148292	-0.552057866505	1.92958935434	0.57891786072	0.597247823704	0.359546712369	-0.806278358686	-0.0524838663553	0.223545212943	-0.142382510408	-0.563632178208	0.32385236689	-0.0089462878269	0.0621280410383	0.9736894192	-0.46302045603	-0.159172052625	1.12536355422	0.380157047883	2.15012077003	6.77873584966	-22.1933672652	13.779633668

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 1 through 18 )	A	A	1 - 18	1 - 18
2	2	chain 'A' and (resid 19 through 26 )	A	A	19 - 26	19 - 26
3	3	chain 'A' and (resid 27 through 42 )	A	A	27 - 42	27 - 42
4	4	chain 'A' and (resid 43 through 74 )	A	A	43 - 74	43 - 74
5	5	chain 'A' and (resid 75 through 92 )	A	A	75 - 92	75 - 92
6	6	chain 'A' and (resid 93 through 127 )	A	A	93 - 127	93 - 127
7	7	chain 'A' and (resid 128 through 141 )	A	A	128 - 141	128 - 141
8	8	chain 'B' and (resid 1 through 26 )	B	B	1 - 26	1 - 26
9	9	chain 'B' and (resid 27 through 42 )	B	B	27 - 42	27 - 42
10	10	chain 'B' and (resid 43 through 75 )	B	B	43 - 75	43 - 75
11	11	chain 'B' and (resid 76 through 92 )	B	B	76 - 92	76 - 92
12	12	chain 'B' and (resid 93 through 110 )	B	B	93 - 110	93 - 110
13	13	chain 'B' and (resid 111 through 127 )	B	B	111 - 127	111 - 127
14	14	chain 'B' and (resid 128 through 142 )	B	B	128 - 142	128 - 142
15	15	chain 'B' and (resid 150 through 155 )	B	B	150 - 155	143 - 148
16	16	chain 'C' and (resid 1 through 6 )	C	C	1 - 6	1 - 6
17	17	chain 'C' and (resid 7 through 12 )	C	C	7 - 12	7 - 12
18	18	chain 'C' and (resid 13 through 18 )	C	C	13 - 18	13 - 18
19	19	chain 'C' and (resid 19 through 26 )	C	C	19 - 26	19 - 26
20	20	chain 'C' and (resid 27 through 42 )	C	C	27 - 42	27 - 42
21	21	chain 'C' and (resid 43 through 49 )	C	C	43 - 49	43 - 49
22	22	chain 'C' and (resid 50 through 75 )	C	C	50 - 75	50 - 75
23	23	chain 'C' and (resid 76 through 92 )	C	C	76 - 92	76 - 92
24	24	chain 'C' and (resid 93 through 110 )	C	C	93 - 110	93 - 110
25	25	chain 'C' and (resid 111 through 127 )	C	C	111 - 127	111 - 127
26	26	chain 'C' and (resid 128 through 141 )	C	C	128 - 141	128 - 141
27	27	chain 'D' and (resid 1 through 49 )	D	D	1 - 49	1 - 49
28	28	chain 'D' and (resid 50 through 75 )	D	D	50 - 75	50 - 75
29	29	chain 'D' and (resid 76 through 93 )	D	D	76 - 93	76 - 93
30	30	chain 'D' and (resid 94 through 137 )	D	D	94 - 137	94 - 137
31	31	chain 'D' and (resid 138 through 155 )	D	D	138 - 155	138 - 155
32	32	chain 'E' and (resid 1 through 12 )	E	E	1 - 12	1 - 12
33	33	chain 'E' and (resid 13 through 18 )	E	E	13 - 18	13 - 18
34	34	chain 'E' and (resid 19 through 49 )	E	E	19 - 49	19 - 49
35	35	chain 'E' and (resid 50 through 75 )	E	E	50 - 75	50 - 75
36	36	chain 'E' and (resid 76 through 92 )	E	E	76 - 92	76 - 92
37	37	chain 'E' and (resid 93 through 110 )	E	E	93 - 110	93 - 110
38	38	chain 'E' and (resid 111 through 127 )	E	E	111 - 127	111 - 127
39	39	chain 'E' and (resid 128 through 142 )	E	E	128 - 142	128 - 142
40	40	chain 'F' and (resid 1 through 18 )	F	F	1 - 18	1 - 18
41	41	chain 'F' and (resid 19 through 26 )	F	F	19 - 26	19 - 26
42	42	chain 'F' and (resid 27 through 42 )	F	F	27 - 42	27 - 42
43	43	chain 'F' and (resid 43 through 75 )	F	F	43 - 75	43 - 75
44	44	chain 'F' and (resid 76 through 92 )	F	F	76 - 92	76 - 92
45	45	chain 'F' and (resid 93 through 110 )	F	F	93 - 110	93 - 110
46	46	chain 'F' and (resid 111 through 127 )	F	F	111 - 127	111 - 127
47	47	chain 'F' and (resid 128 through 147 )	F	F	128 - 147	128 - 142
48	48	chain 'F' and (resid 148 through 155 )	F	F	148 - 155	143 - 150
49	49	chain 'G' and (resid 151 through 155 )	G	U	151 - 155	1 - 5

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

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