PDB-6id2: Crystal structure of H7 hemagglutinin mutant H7-AVTL (P221T) from...

ID or keywords:

Entry

Database: PDB / ID: 6id2

Title

Crystal structure of H7 hemagglutinin mutant H7-AVTL (P221T) from the influenza virus A/Anhui/1/2013 (H7N9)

Components

Hemagglutinin HA1 chain
Hemagglutinin HA2 chain

Keywords

VIRAL PROTEIN /

influenza virus /

H7N9 /

hemagglutinin

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane /

viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane /

metal ion binding
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.705 Å

Authors

Gao, G.F. / Xu, Y. / Qi, J.X.

Citation

Journal: Cell Rep / Year: 2019
Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.
Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / Gao, G.F.

History

Deposition	Sep 8, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6id2.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6id2.ent.gz	962.2 KB	Display	PDB format
PDBx/mmJSON format	6id2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/6id2 ftp://data.pdbj.org/pub/pdb/validation_reports/id/6id2	HTTPS FTP

-
Related structure data

Related structure data	6icwC 6icxC 6icyC 6id3C 6id5C 6id8C 6id9C 6idaC 6idbC 6iddC 6idzC 4kolS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4n61-2 6tvr-2 3eyk-1 6icx-1 5xl2-d 4ln4-5 6twh-1 4qy1-2 6tvs-d 4lkg-1 4ln8-5 4dj8-d 6icw-1 6d8b-d 6tws-d 4cyw-d 4xqu-d 4cz0-d 4lcx-d 6tvd-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (6) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

C: Hemagglutinin HA1 chain

D: Hemagglutinin HA2 chain

E: Hemagglutinin HA1 chain

F: Hemagglutinin HA2 chain

G: Hemagglutinin HA1 chain

H: Hemagglutinin HA2 chain

I: Hemagglutinin HA1 chain

J: Hemagglutinin HA2 chain

K: Hemagglutinin HA1 chain

L: Hemagglutinin HA2 chain

333 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

C: Hemagglutinin HA1 chain

D: Hemagglutinin HA2 chain

E: Hemagglutinin HA1 chain

F: Hemagglutinin HA2 chain

defined by author&software
Evidence: homology, gel filtration
166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Hemagglutinin HA1 chain

H: Hemagglutinin HA2 chain

I: Hemagglutinin HA1 chain

J: Hemagglutinin HA2 chain

K: Hemagglutinin HA1 chain

L: Hemagglutinin HA2 chain

defined by author&software
166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	165.187, 165.187, 191.251
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

#1: Protein	Hemagglutinin HA1 chain Mass: 34997.547 Da / Num. of mol.: 6 / Mutation: P221T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#2: Protein	Hemagglutinin HA2 chain Mass: 20442.463 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated ...Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated hemagglutinin used in this studay, which was derived from AH1-H7N9 virus, was identical with R4NN21_9INFA.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.53 Å³/Da / Density % sol: 72.84 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES pH 7.0, 12% w/v Polyethylene glycol 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97892 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97892 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 159187 / % possible obs: 100 % / Redundancy: 5.4 % / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.7→2.8 Å

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KOL

4kol

Resolution: 2.705→47.685 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 33

	R_factor	Num. reflection	% reflection
R_free	0.2902	7116	4.95 %
R_work	0.2636	-	-
obs	0.2649	143780	90.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.705→47.685 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22389	0	0	589	22978

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	22833
X-RAY DIFFRACTION	f_angle_d	0.599	30852
X-RAY DIFFRACTION	f_dihedral_angle_d	16.833	8520
X-RAY DIFFRACTION	f_chiral_restr	0.049	3318
X-RAY DIFFRACTION	f_plane_restr	0.003	4089

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 (%)
2.705-2.7357	0.424	107	0.3751	1877	X-RAY DIFFRACTION	37
2.7357-2.7679	0.3986	102	0.362	2077	X-RAY DIFFRACTION	41
2.7679-2.8017	0.4113	126	0.3562	2312	X-RAY DIFFRACTION	46
2.8017-2.8371	0.3956	124	0.3299	2578	X-RAY DIFFRACTION	51
2.8371-2.8745	0.4034	147	0.3168	3109	X-RAY DIFFRACTION	61
2.8745-2.9138	0.3789	190	0.3306	4135	X-RAY DIFFRACTION	81
2.9138-2.9554	0.349	238	0.3271	4667	X-RAY DIFFRACTION	93
2.9554-2.9996	0.3549	289	0.3281	4963	X-RAY DIFFRACTION	98
2.9996-3.0464	0.3778	249	0.3213	5023	X-RAY DIFFRACTION	100
3.0464-3.0964	0.363	270	0.3196	5005	X-RAY DIFFRACTION	100
3.0964-3.1497	0.3403	264	0.3173	5066	X-RAY DIFFRACTION	100
3.1497-3.207	0.3396	220	0.3242	5143	X-RAY DIFFRACTION	100
3.207-3.2687	0.3396	326	0.3177	4922	X-RAY DIFFRACTION	100
3.2687-3.3354	0.368	282	0.3054	5049	X-RAY DIFFRACTION	100
3.3354-3.4079	0.3542	270	0.2983	5104	X-RAY DIFFRACTION	100
3.4079-3.4871	0.3247	276	0.2903	4961	X-RAY DIFFRACTION	100
3.4871-3.5743	0.2986	324	0.2755	5024	X-RAY DIFFRACTION	100
3.5743-3.6709	0.2809	282	0.2672	5106	X-RAY DIFFRACTION	100
3.6709-3.7789	0.2868	228	0.2703	5013	X-RAY DIFFRACTION	100
3.7789-3.9008	0.2976	220	0.2513	5081	X-RAY DIFFRACTION	100
3.9008-4.0402	0.2594	228	0.2521	5090	X-RAY DIFFRACTION	100
4.0402-4.2018	0.2575	257	0.2332	5077	X-RAY DIFFRACTION	100
4.2018-4.3929	0.237	248	0.2156	5023	X-RAY DIFFRACTION	100
4.3929-4.6244	0.2085	256	0.1956	5064	X-RAY DIFFRACTION	100
4.6244-4.9138	0.234	294	0.2152	5037	X-RAY DIFFRACTION	100
4.9138-5.2928	0.2522	288	0.223	5048	X-RAY DIFFRACTION	100
5.2928-5.8245	0.2593	227	0.2371	5059	X-RAY DIFFRACTION	100
5.8245-6.6654	0.2614	300	0.2544	5024	X-RAY DIFFRACTION	100
6.6654-8.3903	0.2485	253	0.2522	5061	X-RAY DIFFRACTION	100
8.3903-47.6928	0.2609	231	0.2339	4966	X-RAY DIFFRACTION	98

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	0.7373	0.0506	0.2499	0.4608	-0.12	2.3243	0.1353	-0.3175	0.0546	0.0992	-0.1025	0.0663	0.246	-0.2723	-0.0173	0.3457	-0.0781	-0.0046	0.3492	-0.044	0.3747	40.0581	174.9778	-0.0726
2	1.1975	-0.3876	-0.4052	2.2149	-0.5327	1.2931	0.0565	0.1114	0.2056	-0.1001	-0.0807	0.0626	-0.056	-0.1511	-0.0814	0.2488	-0.0248	-0.0092	0.2506	-0.0217	0.4302	39.8149	183.1519	-30.6605
3	0.956	-0.263	0.7563	1.3171	-0.611	2.0979	-0.1753	-0.3138	0.0632	0.4123	-0.0374	-0.1194	0.2684	-0.5697	-0.0758	0.3266	-0.1253	0.0327	0.43	-0.0577	0.4104	34.5286	175.2591	-1.203
4	2.1217	-1.2046	0.7938	0.7769	-0.0366	2.3483	0.5696	-0.031	-0.3615	0.199	-0.0894	0.4574	0.621	-0.5847	0.0626	0.4522	-0.0996	0.0447	0.2643	0.0255	0.3256	44.4447	174.9277	11.3983
5	0.7587	0.256	-0.5965	0.8796	-0.1211	4.3898	0.0946	-0.5916	-0.2336	0.5428	-0.076	0.0064	0.2504	-0.1486	0.0052	0.4537	-0.1284	0.0514	0.5351	0.0393	0.3252	51.6103	173.6341	27.3723
6	0.9203	-0.0765	-0.4402	2.1312	-0.8082	0.5607	-0.1743	-0.5631	-0	0.2251	-0.155	-0.2204	0.4976	-0.2281	0.1066	0.7682	-0.2143	0.04	0.8512	0.1492	0.3867	43.2105	173.8716	45.582
7	2.7164	-0.3383	-1.5133	2.1554	1.4533	4.6145	-0.0974	0.2214	0.1871	0.4728	0.3604	0.3997	0.1501	-0.1776	-0.2945	0.3389	0.056	-0.0205	0.3467	-0.0717	0.3674	47.3019	179.9837	-2.4752
8	0.6226	0.3171	-0.1118	0.7633	-0.3382	1.3	0.469	-0.6955	-0.0413	0.5742	-0.2256	0.1349	-0.3531	-0.0357	0.2035	0.866	-0.3131	0.0897	0.8393	0.2429	-0.1262	48.7467	180.7257	47.0317
9	0.2642	0.0644	0.0329	0.5077	-0.6283	1.7569	0.2243	-0.2927	0.2112	0.3648	0.0145	0.3007	-0.3646	-0.1713	-0.0506	0.4802	0.0332	0.0609	0.4158	-0.04	0.3571	45.6534	209.7915	8.2832
10	1.3957	0.4864	-0.6445	2.3476	-0.7746	3.1894	0.0976	-0.434	0.2574	0.1926	-0.167	0.2279	-0.5002	0.2322	-0.05	0.2999	0.0064	-0.0311	0.2705	0.059	0.3121	57.7503	210.0156	-9.4448
11	1.1525	0.2228	-0.1472	1.4593	-0.1319	1.6969	0.2248	0.331	0.0934	0.0512	-0.1641	-0.1355	-0.0742	0.4226	-0.0501	0.2119	0.084	0.0276	0.3358	0.0331	0.3477	54.4432	215.2421	-32.8008
12	1.2393	0.0768	0.7904	1.4366	0.2976	2.6539	-0.1334	-0.1134	0.157	-0.1628	0.0602	-0.2661	-0.2033	0.1689	0.0231	0.2361	0.1095	0.0464	0.1481	-0.0313	0.3562	59.1879	207.6578	-27.7058
13	1.177	0.6685	0.6676	0.3786	0.3191	1.7436	0.4553	0.0414	-0.4936	0.1398	-0.0887	-0.2457	0.4332	-0.2011	0.0368	0.273	0.0509	-0.0445	0.225	0.0138	0.3206	57.8176	198.8325	-29.4258
14	2.075	0.1192	0.2597	0.6797	0.2434	1.7524	0.1414	-0.0761	-0.1837	0.124	-0.2026	-0.0945	0.0392	0.1798	0.0059	0.3056	0.029	-0.0205	0.1699	0.0259	0.3129	57.0631	206.4724	-24.5791
15	2.2918	0.5517	-1.0049	1.2673	-0.662	1.6396	-0.1243	-0.4381	0.0294	0.4229	-0.0647	0.3432	-0.4649	0.1168	-0.0956	0.5247	0.0794	-0.0026	0.3011	-0.0224	0.3447	51.9253	215.0682	1.1087
16	2.2541	0.5001	-1.5781	0.6532	-0.6925	1.3185	0.1354	-0.1754	0.3316	0.5091	0.34	0.3151	-0.5434	0.1118	0.0734	0.4649	0.0979	0.0281	0.3529	-0.079	0.2035	46.5706	206.0386	13.1446
17	1.0952	0.3575	-1.1967	1.4737	-1.1343	4.6487	0.0027	-0.6059	-0.0759	0.2514	-0.2243	0.2943	-0.5103	-0.0188	-0.1296	0.457	-0.0545	0.0778	0.5465	-0.0061	0.3845	41.8099	199.688	28.8051
18	0.4699	0.0203	-0.2244	0.1172	0.402	1.7892	0.0501	-0.4251	-0.0382	0.7225	-0.2836	0.1983	-0.7655	-0.1484	-0.1442	1.2417	-0.1838	0.2939	0.9491	-0.2077	0.4611	46.1328	205.1473	49.9598
19	0.8247	-0.5179	-1.7149	0.3332	1.0744	3.5654	0.3073	-0.1645	0.3278	0.1521	0.2373	-0.2071	-0.286	0.209	-0.2976	1.1192	-0.2257	0.0756	0.8617	-0.0558	0.757	56.4515	206.8769	19.6804
20	2.3748	-0.1835	1.3325	2.0965	0.6417	3.6407	0.0797	0.2073	0.2059	-0.1112	-0.221	0.3656	-0.2856	-0.0195	-0.0292	0.3831	0.0254	0.011	0.5235	0.0248	0.3596	49.3039	201.9088	-1.4648
21	0.5013	-0.292	-0.1458	0.6224	0.4758	2.6161	0.2924	-0.3793	0.2132	0.4738	-0.065	0.0535	0.0384	0.1543	0.0358	0.5426	-0.1861	0.1122	0.5886	-0.0298	0.2448	49.9817	193.7865	33.6163
22	0.072	0.1413	0.1534	0.2582	0.2951	0.3293	0.108	-0.2266	0.2212	0.3673	0.1231	-0.0181	-0.2074	0.2136	-0.0395	1.4467	-0.2969	0.3677	1.4734	-0.2929	0.3933	46.9286	202.9443	67.4086
23	0.2108	-0.3385	0.6601	0.5432	-1.0339	5.0406	0.2576	0.08	-0.135	0.2278	0.1394	-0.1877	0.3695	0.1676	-0.0574	1.6238	-0.4956	-0.0681	1.6703	-0.3262	0.6206	57.5559	204.7984	69.2562
24	1.4052	0.3393	0.9822	1.5551	1.6943	2.1288	0.0794	-0.2394	-0.0652	0.3693	0.1054	-0.1465	0.101	0.234	-0.0004	1.3778	0.0114	-0.0633	1.5315	-0.1543	0.2753	52.495	196.3408	78.919
25	0.0673	0.2117	-0.3377	0.526	-0.3222	2.2573	0.1868	-0.4163	-0.0361	0.3238	-0.0054	-0.3011	0.0156	0.4894	-0.0369	0.4731	-0.0909	-0.0355	0.6119	-0.001	0.3769	75.8106	189.6368	17.2362
26	0.6966	0.2523	-0.4988	0.6227	-0.294	1.1991	-0.0004	-0.1403	-0.2234	-0.1593	0.0313	-0.0548	0.3216	0.0375	-0.0729	0.2738	0.0511	0.0692	0.2256	0.0337	0.4492	76.0302	180.6583	-19.5671
27	1.2179	0.6225	0.0001	2.2985	-0.5421	1.3559	-0.0592	0.1007	-0.1422	0.0075	0.0638	0.0903	0.1736	-0.1399	0.007	0.2118	-0.0295	0.0149	0.2346	0.0211	0.3831	65.9633	181.0223	-29.7081
28	1.3064	0.2904	0.5475	1.5475	1.4823	1.4822	-0.0677	-0.4263	-0.1782	0.3994	-0.2214	-0.0981	0.3635	-0.0071	-0.0799	0.4324	0.0456	0.0399	0.3961	0.175	0.3949	77.7946	180.1559	-0.2237
29	0.2706	-0.2276	-0.1882	0.3785	0.7269	3.7728	0.247	-0.6098	0.0951	0.377	-0.1162	-0.2207	0.0332	0.461	0.0265	0.4337	-0.1602	0.0025	0.5727	0.0704	0.3175	71.0987	191.893	21.0423
30	0.5741	-0.1008	0.9137	0.0869	-0.1457	1.4584	-0.0631	-0.5356	0.4798	0.9679	-0.0672	-0.2406	0.0055	0.5537	0.3684	1.0503	-0.291	-0.1844	1.3623	0.0352	0.5612	74.5774	191.2974	55.5047
31	0.8137	0.1305	1.404	0.98	0.7	2.6961	0.2271	-0.5115	0.1365	0.1573	-0.4135	-0.3282	0.1185	0.69	0.1128	0.8141	-0.2051	-0.0399	0.9803	0.1179	0.4688	71.0509	181.943	42.6761
32	0.003	-0.0005	0.0114	0.0055	0.0116	0.0606	0.1309	0.2524	-0.5684	0.1187	0.1263	0.0689	0.7657	0.1079	-0.4103	1.5542	0.2248	-0.1583	1.0062	0.0911	0.716	68.7024	179.057	18.5956
33	2.8128	-0.3194	-0.2575	3.4915	-2.1394	4.3276	0.3788	0.059	-0.2664	0.0188	-0.4335	0.3182	0.5635	-0.0488	-0.2646	0.6144	0.0124	0.0324	0.4331	0.1052	0.4037	67.4876	189.0695	-1.9208
34	0.2947	0.0131	0.4945	0.2586	-0.7461	3.6814	0.2651	-0.379	0.1251	0.2884	-0.0917	0.0499	-0.0029	-0.0341	-0.0232	0.5701	-0.1645	0.0097	0.5094	0.0115	0.2008	60.7657	190.8805	28.5984
35	0.2148	-0.4538	-0.1287	1.0903	0.032	0.6232	-0.125	-0.5289	0.0865	0.4879	0.2741	-0.1985	0.0903	0.449	0.1441	1.3229	-0.2502	-0.2381	1.4874	0.0202	0.3614	68.2945	185.9074	67.2665
36	0.4896	-0.3746	-1.8689	0.2838	1.4272	7.2948	-0.0647	-0.2161	-0.1448	0.0555	0.1476	0.198	0.1678	-0.2532	-0.0333	1.3886	-0.2338	-0.2362	1.6533	0.3683	0.7397	67.2978	175.8307	68.1303
37	0.6043	0.2423	-0.0577	0.5851	-0.3821	0.7108	0.0203	-0.0724	-0.0127	0.1621	0.072	0.0574	0.0457	-0.0869	0.0548	1.7218	-0.0623	0.0133	1.7217	0.2853	0.2455	62.6474	183.7483	78.4288
38	0.6235	-0.2205	0.2179	0.4904	0.2954	3.5493	0.1541	0.1098	0.1224	0.093	-0.0297	0.1063	-0.8129	-0.3384	-0.0381	0.3741	-0.0161	-0.0823	0.2788	0.012	0.3426	34.2324	158.0726	-46.3291
39	0.2079	0.0281	-0.2789	0.3364	0.0161	0.3446	0.1718	0.1396	0.0572	-0.3253	0.05	-0.0892	-0.0147	1.1442	-0.0751	0.7194	-0.1046	0.1028	1.0438	0.0719	0.3573	48.3539	154.0938	-94.3164
40	1.5922	-0.688	1.2055	1.9297	-0.252	0.9822	0.061	0.6215	-0.1043	-0.5922	-0.0342	-0.0601	0.2465	0.6138	-0.0832	0.9281	0.0633	0.1211	1.1012	0.0715	0.3898	41.5677	145.5751	-115.9802
41	1.3621	-0.5237	0.1969	0.3545	-0.1726	0.0852	0.14	0.3892	-0.8433	0.0978	0.1026	0.331	0.5697	0.6114	0.034	0.8487	0.1338	0.0671	1.0281	-0.0961	0.5931	45.1057	138.962	-107.7293
42	1.0612	-0.504	-0.9626	0.2335	0.4485	0.8772	-0.0305	0.4076	-0.0207	-0.3386	-0.2401	-0.3918	-0.1157	0.8686	-0.1237	0.4375	-0.1901	0.0652	0.8255	0.1602	0.3528	43.4032	153.9583	-78.2839
43	0.301	0.2964	0.0398	0.7869	0.1628	0.2635	0.1215	-0.0562	-0.1055	0.0926	-0.1432	0.047	-0.0756	-0.0015	-0.5966	0.3751	-0.3487	-0.0109	-0.0756	0.246	0.1966	33.6732	157.8867	-55.4813
44	1.1408	0.6239	-0.0621	1.6875	0.2485	2.3592	0.0238	-0.0857	0.2716	-0.0953	-0.0547	-0.0711	-0.2688	-0.0609	0.0246	0.2656	-0.1573	-0.0341	0.2403	-0.0498	0.4697	38.2115	158.781	-37.4612
45	0.9588	0.0793	0.8931	0.9746	1.6812	5.5944	-0.1582	0.0155	0.1219	-0.1928	-0.0996	0.026	-0.2292	0.3875	0.1503	0.2182	-0.0642	-0.0353	0.29	0.027	0.4185	44.1636	151.2229	-39.132
46	0.0433	0.1709	0.303	0.6912	1.2177	2.1445	0.2794	-0.0528	-0.1726	0.0521	0.2405	0.0017	0.0926	0.1399	-0.1828	1.3109	-0.0448	0.0244	1.2815	0.1108	0.6693	43.626	143.5065	-69.0899
47	1.7533	0.2406	1.0514	3.1273	-2.0098	2.1333	0.5934	0.4796	-0.0941	-0.2484	0.0132	-0.0987	-0.1638	-0.0619	-0.4024	0.8329	0.1158	-0.044	0.8601	0.038	0.3292	35.6014	149.319	-89.7631
48	0.2673	-0.2389	0.9089	0.4588	0.2498	4.2108	0.1781	0.1306	-0.0938	-0.1175	0.1382	-0.0238	0.4829	-0.0456	-0.1334	0.2939	-0.0504	-0.0501	0.2298	0.0288	0.2316	30.2603	147.5861	-58.2983
49	2.2841	1.434	0.0637	1.3998	-0.6999	3.919	0.1207	-0.3496	0.1673	-0.0496	-0.1441	-0.2033	-0.2661	0.334	0.1018	0.419	0.0026	-0.1082	0.27	-0.0497	0.3362	41.2126	149.5223	-21.0308
50	5.7246	-1.0896	-0.9282	4.4547	0.2631	4.0272	0.4389	-0.7111	-0.65	1.3009	-0.1357	-0.6856	0.035	-0.0426	-0.2897	0.5811	-0.1247	-0.0697	0.4053	0.0536	0.3888	40.062	144.2971	-11.3387
51	0.513	-0.1797	0.1591	0.6158	-0.3592	1.3463	0.0313	-0.2015	0.0102	-0.0611	0.0687	0.0269	0.2556	0.2728	0.2671	0.147	0.077	-0.0204	0.1971	0.0482	0.3003	37.6106	127.9657	-45.7243
52	1.5738	0.8141	0.4197	2.1704	0.8039	3.1957	0.2999	0.3454	-0.2471	-0.484	0.0137	-0.0946	0.5651	-0.2757	0.4114	0.71	0.1434	-0.0486	0.4061	-0.1159	0.3142	26.9391	115.7109	-75.841
53	0.6317	0.2235	0.0641	0.2067	0.3347	0.8082	-0.2287	0.2829	0.0229	-0.7746	0.214	0.2318	0.8122	-0.2005	-0.1141	1.0467	-0.125	-0.1707	0.6952	-0.1775	0.5225	19.3979	119.1612	-101.911
54	1.1464	-0.3833	-0.9023	0.1614	0.4763	1.7315	-0.1619	0.51	-0.3721	-0.0414	0.0268	0.0884	0.8368	-0.2777	-0.2569	1.5737	-0.2011	-0.2169	0.9814	-0.2105	0.4925	21.3336	114.084	-115.2891
55	0.5016	0.2985	0.2233	0.7252	0.6265	0.5689	0.3233	1.0764	-0.392	-0.7341	-0.1418	0.4398	0.2598	-0.4213	-0.1062	1.3435	-0.149	-0.4692	1.3091	0.0754	0.5112	11.8956	125.9615	-116.2188
56	1.7529	1.5156	-0.2659	1.4543	0.1592	1.0579	-0.0363	0.3729	-0.0696	-0.5812	0.4637	0.3413	0.5811	0.4203	-0.3618	1.5172	0.1342	-0.0337	1.1898	-0.0411	0.5648	25.05	128.2984	-126.8783
57	1.0794	0.3421	-0.0392	1.6119	0.2807	1.406	0.1028	0.5305	0.0748	-0.4766	0.1203	0.1823	0.5478	-0.0441	-0.2934	0.997	-0.0978	-0.1976	0.9177	0.0364	0.5737	18.0436	129.9565	-112.7753
58	0.7995	0.5396	0.8288	0.8911	0.5692	1.338	0.1724	0.3077	-0.3555	-0.124	-0.1041	0.0778	1.0194	-0.2178	-0.0036	0.7403	-0.063	0.009	0.4965	-0.1162	0.4089	23.6809	119.8802	-81.8181
59	1.5099	-0.5606	0.037	0.8662	-0.573	1.3491	-0.0883	0.3732	0.1325	-0.327	-0.0803	-0.1298	0.1693	-0.0503	-0.711	0.0419	0.285	0.0232	0.1132	-0.0591	0.2723	35.1433	128.292	-58.9332
60	2.289	-1.336	0.9579	1.9157	1.3282	3.5259	0.2285	-0.1154	0.0317	0.1396	-0.0839	-0.2354	0.4146	0.0411	-0.2887	0.2487	0.083	0.0266	0.1994	0.0683	0.3322	36.2137	125.0482	-36.6841
61	1.03	-0.9261	1.5325	1.7394	-1.8796	7.5298	-0.3065	-0.2171	0.0679	-0.0527	0.0881	-0.1268	0.1786	-0.5101	0.1461	0.2138	-0.0713	-0.0317	0.2898	-0.0341	0.4129	26.6237	123.5507	-37.9901
62	0.1545	-0.3897	0.7052	1.0208	-1.7931	3.2188	0.0612	-0.2562	-0.3731	0.1371	0.2912	0.4346	0.251	-0.6033	-0.3283	1.3763	0.1423	-0.1968	0.944	0.0019	0.6717	19.0348	126.0992	-67.8447
63	0.6259	-0.1347	-0.07	0.7161	-0.9743	2.546	-0.0105	0.1924	-0.0091	-0.2498	0.0382	0.0752	0.149	-0.3012	0.1389	0.2745	-0.053	0.0207	0.2684	-0.0023	0.3023	29.1601	134.6587	-65.5117
64	1.5111	-0.6527	-0.5259	2.9032	2.0075	1.6986	0.0365	0.0468	-0.3224	0.7039	-0.2074	0.0995	0.3062	0.4716	-0.3736	0.3231	-0.0242	-0.1781	0.2892	0.1647	0.3408	28.8618	128.6271	-19.7562
65	1.9485	0.2668	2.2082	0.4901	1.0239	7.6357	0.2049	0.475	-0.6999	0.2467	-0.2348	0.4739	0.1803	-0.294	-0.0182	0.341	0.0266	0.1028	0.6005	0.124	0.5299	19.0378	127.688	-18.0899
66	5.9071	-2.7002	1.6858	1.661	-0.8494	2.0427	-0.1634	-0.5989	0.4339	0.5136	0.3563	0.0804	0.0504	-0.0321	-0.1448	0.7372	0.0101	0.2492	0.554	-0.0901	0.1549	26.2946	133.6841	-8.4022
67	1.0804	-0.1103	0.4219	1.5036	-0.5282	1.5177	0.0524	-0.0444	0.0259	-0.2888	0.1862	0.3437	0.0287	0.0423	0.4386	0.1311	-0.0297	0.075	0.2213	-0.0121	0.3543	9.6449	140.3959	-44.8392
68	0.61	-0.0963	0.0916	0.7422	-0.3447	0.8726	0.1111	0.3948	0.1037	-0.4812	0.0482	0.0841	-0.5441	-0.423	-0.0248	0.7543	0.0758	-0.1455	0.8312	0.174	0.4302	6.4537	156.9839	-103.0378
69	0.7553	-0.1861	-0.3359	0.3115	-0.4999	1.4319	-0.0629	0.3559	0.3319	-0.5214	0.146	0.3711	-0.5554	-0.4605	-0.1321	1.1553	0.0407	-0.0515	0.8347	0.1618	0.3748	16.1701	157.2417	-115.1965
70	3.2446	1.5454	0.7968	1.5619	0.4382	0.3018	0.0827	0.597	-0.1969	-0.2728	0.1341	-0.4417	0.041	0.1502	-0.0822	1.0452	-0.032	0.0716	0.8083	0.0283	0.5564	20.7078	149.8282	-117.8221
71	0.7484	-0.8713	0.1261	1.2951	-0.5638	0.6532	0.1224	0.4951	0.2563	-0.7838	-0.3808	-0.1779	-0.3898	-0.043	0.1957	0.7129	0.0033	-0.0375	0.9199	0.144	0.4412	15.4692	154.7633	-112.309
72	0.2543	-0.2791	-0.0104	1.094	-0.5176	1.1434	-0.1247	0.0426	-0.0098	-0.0093	0.1397	0.1481	-0.3972	-0.4877	0.1207	0.505	0.0748	-0.1339	0.5612	0.104	0.3021	7.4615	154.5308	-81.6298
73	0.0733	-0.0232	0.0708	0.1799	0.1119	0.6097	-0.112	-0.036	0.1528	-0.2477	-0.0398	0.1139	-0.0947	-0.0891	-0.4517	-0.0097	-0.1858	-0.1101	0.2554	-0.024	0.388	10.4846	141.7166	-58.1932
74	1.0971	0.3149	0.2607	0.3982	-0.3194	0.5524	-0.1232	0.2503	-0.2536	-0.012	0.0595	0.1922	0.0444	-0.237	-0.2933	0.055	0.1217	0.1198	0.5085	0.0225	0.664	7.997	143.7599	-35.9889
75	0.798	-0.0206	-1.1253	2.0157	0.4624	7.0921	-0.0962	0.0799	-0.1002	0.0163	-0.0277	0.314	-1.1721	-0.5174	0.0316	0.2887	0.0467	-0.0168	0.2974	0.0676	0.4712	11.3649	152.6352	-37.9319
76	0.0008	0.0018	-0.0081	0.0061	-0.0007	0.0451	0.3488	0.2685	0.365	0.0157	0.4192	0.1076	-0.4974	-0.1138	-0.696	1.7035	0.3022	-0.0858	1.0904	0.2718	0.8861	16.1641	156.2783	-68.2282
77	2.8204	0.4376	1.1695	2.4223	0.5214	3.2804	0.5018	0.4773	-0.1027	-0.0771	0.0626	-0.2685	-0.1499	0.275	-0.6685	0.8364	-0.09	-0.1906	0.6373	-0.0773	0.4742	13.696	146.5953	-88.7987
78	0.3188	-0.3239	-0.4725	0.4281	0.219	3.6596	-0.1264	0.0876	0.0751	-0.0689	0.102	0.1253	-0.08	0.4804	0.0622	0.2067	-0.1019	0.0015	0.2182	-0.0056	0.304	20.382	143.0256	-53.5667
79	2.2604	-0.8618	1.8559	1.0606	0.1315	2.5537	-0.4472	-0.2197	0.3713	0.1907	0.3255	0.2032	-0.2693	-0.7812	-0.0956	0.4728	0.0349	0.1372	0.2163	0.0567	0.3728	12.8467	149.9837	-19.9177
80	0.6988	0.415	0.0162	1.2421	-0.1828	0.0383	-0.1777	0.3168	0.0223	-0.2522	0.2981	-0.3307	-0.2234	0.1258	0.1381	0.8654	-0.2505	-0.0393	0.4286	-0.1125	0.5259	19.5107	158.3951	-18.7487
81	0.7722	-0.4727	-1.3541	1.6838	-0.9695	4.7048	-0.0724	-0.509	0.2493	0.3887	-0.2058	-0.2158	-0.3498	0.5643	0.0148	0.8394	-0.1499	-0.18	0.6711	-0.0516	0.1926	21.6092	149.31	-8.5813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 122 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 246 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 247 through 275 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 276 through 295 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 296 through 316 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 328 through 381 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 382 through 395 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 396 through 490 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 3 through 94 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 95 through 112 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 113 through 154 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 155 through 186 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 187 through 211 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 212 through 246 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 247 through 275 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 276 through 295 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 296 through 316 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 328 through 376 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 377 through 381 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 382 through 395 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 396 through 453 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 454 through 474 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 475 through 483 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 484 through 490 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 3 through 66 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 67 through 143 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 144 through 246 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 247 through 275 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 276 through 316 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 328 through 352 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 353 through 376 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 377 through 381 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 382 through 395 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 396 through 446 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 447 through 474 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 475 through 483 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 484 through 490 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 1 through 31 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 32 through 89 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 90 through 228 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 229 through 259 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 260 through 299 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 300 through 316 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 328 through 342 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 343 through 376 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 377 through 381 )
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 382 through 395 )
48	X-RAY DIFFRACTION	48	chain 'H' and (resid 396 through 447 )
49	X-RAY DIFFRACTION	49	chain 'H' and (resid 448 through 479 )
50	X-RAY DIFFRACTION	50	chain 'H' and (resid 480 through 490 )
51	X-RAY DIFFRACTION	51	chain 'I' and (resid 1 through 31 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 32 through 47 )
53	X-RAY DIFFRACTION	53	chain 'I' and (resid 48 through 122 )
54	X-RAY DIFFRACTION	54	chain 'I' and (resid 123 through 143 )
55	X-RAY DIFFRACTION	55	chain 'I' and (resid 144 through 175 )
56	X-RAY DIFFRACTION	56	chain 'I' and (resid 176 through 192 )
57	X-RAY DIFFRACTION	57	chain 'I' and (resid 193 through 246 )
58	X-RAY DIFFRACTION	58	chain 'I' and (resid 247 through 295 )
59	X-RAY DIFFRACTION	59	chain 'I' and (resid 296 through 316 )
60	X-RAY DIFFRACTION	60	chain 'J' and (resid 328 through 342 )
61	X-RAY DIFFRACTION	61	chain 'J' and (resid 343 through 376 )
62	X-RAY DIFFRACTION	62	chain 'J' and (resid 377 through 381 )
63	X-RAY DIFFRACTION	63	chain 'J' and (resid 382 through 446 )
64	X-RAY DIFFRACTION	64	chain 'J' and (resid 447 through 474 )
65	X-RAY DIFFRACTION	65	chain 'J' and (resid 475 through 483 )
66	X-RAY DIFFRACTION	66	chain 'J' and (resid 484 through 490 )
67	X-RAY DIFFRACTION	67	chain 'K' and (resid 1 through 31 )
68	X-RAY DIFFRACTION	68	chain 'K' and (resid 32 through 154 )
69	X-RAY DIFFRACTION	69	chain 'K' and (resid 155 through 185 )
70	X-RAY DIFFRACTION	70	chain 'K' and (resid 186 through 211 )
71	X-RAY DIFFRACTION	71	chain 'K' and (resid 212 through 246 )
72	X-RAY DIFFRACTION	72	chain 'K' and (resid 247 through 295 )
73	X-RAY DIFFRACTION	73	chain 'K' and (resid 296 through 316 )
74	X-RAY DIFFRACTION	74	chain 'L' and (resid 328 through 342 )
75	X-RAY DIFFRACTION	75	chain 'L' and (resid 343 through 376 )
76	X-RAY DIFFRACTION	76	chain 'L' and (resid 377 through 381 )
77	X-RAY DIFFRACTION	77	chain 'L' and (resid 382 through 395 )
78	X-RAY DIFFRACTION	78	chain 'L' and (resid 396 through 453 )
79	X-RAY DIFFRACTION	79	chain 'L' and (resid 454 through 474 )
80	X-RAY DIFFRACTION	80	chain 'L' and (resid 475 through 483 )
81	X-RAY DIFFRACTION	81	chain 'L' and (resid 484 through 490 )

-
News

-
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

-
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

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi