PDB-7th2: Single-domain VHH intrabodies neutralize ricin toxin

ID or keywords:

Entry

Database: PDB / ID: 7th2

Title

Single-domain VHH intrabodies neutralize ricin toxin

Components

Ricin A chain
VHH antibody

Keywords

IMMUNE SYSTEM/TOXIN / Antibody-antigen complex / IMMUNE SYSTEM / IMMUNE SYSTEM-TOXIN complex

Function / homology

Function and homology information

rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function

Biological species

Ricinus communis (castor bean)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.838 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins.
Authors: Czajka, T.F. / Vance, D.J. / Davis, S. / Rudolph, M.J. / Mantis, N.J.

History

Deposition	Jan 10, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7th2.cif.gz	460.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7th2.ent.gz	383.1 KB	Display	PDB format
PDBx/mmJSON format	7th2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7th2_validation.pdf.gz	478.9 KB	Display	wwPDB validaton report
Full document	7th2_full_validation.pdf.gz	484.1 KB	Display
Data in XML	7th2_validation.xml.gz	35.9 KB	Display
Data in CIF	7th2_validation.cif.gz	51.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/7th2 ftp://data.pdbj.org/pub/pdb/validation_reports/th/7th2	HTTPS FTP

-
Related structure data

Related structure data	7tgfC 7tgiC 7th3C 1rtcS 4lgrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (15) #69 - Sep 2005 Cholera Toxin similarity (15) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Ricin A chain

B: Ricin A chain

C: VHH antibody

D: VHH antibody

hetero molecules

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

1

A: Ricin A chain

C: VHH antibody

hetero molecules

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

2

B: Ricin A chain

D: VHH antibody

hetero molecules

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

Unit cell

Length a, b, c (Å)	60.644, 63.812, 99.298
Angle α, β, γ (deg.)	90.000, 107.120, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid -1 through 84 or resid 86...
2	1	(chain B and (resid -1 through 84 or resid 86...
1	2	(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))
2	2	(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	TYR	TYR	(chain A and (resid -1 through 84 or resid 86...	A	A	-1 - 84	1 - 86
1	2	1	ALA	ALA	TYR	TYR	(chain A and (resid -1 through 84 or resid 86...	A	A	86 - 123	88 - 125
1	3	1	ARG	ARG	GLY	GLY	(chain A and (resid -1 through 84 or resid 86...	A	A	125 - 158	127 - 160
1	4	1	GLN	GLN	ARG	ARG	(chain A and (resid -1 through 84 or resid 86...	A	A	160 - 258	162 - 260
2	1	1	ALA	ALA	TYR	TYR	(chain B and (resid -1 through 84 or resid 86...	B	B	-1 - 84	1 - 86
2	2	1	ALA	ALA	TYR	TYR	(chain B and (resid -1 through 84 or resid 86...	B	B	86 - 123	88 - 125
2	3	1	ARG	ARG	GLY	GLY	(chain B and (resid -1 through 84 or resid 86...	B	B	125 - 158	127 - 160
2	4	1	GLN	GLN	ARG	ARG	(chain B and (resid -1 through 84 or resid 86...	B	B	160 - 258	162 - 260
1	1	2	GLN	GLN	SER	SER	(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	C	C	3 - 48	3 - 48
1	2	2	ILE	ILE	VAL	VAL	(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	C	C	50 - 104	50 - 104
1	3	2	THR	THR	SER	SER	(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	C	C	106 - 124	106 - 124
2	1	2	GLN	GLN	SER	SER	(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	D	D	3 - 48	3 - 48
2	2	2	ILE	ILE	VAL	VAL	(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	D	D	50 - 104	50 - 104
2	3	2	THR	THR	SER	SER	(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))	D	D	106 - 124	106 - 124

NCS ensembles :

ID
1
2

-
Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein	Ricin A chain / rRNA N-glycosidase Mass: 30139.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody	VHH antibody Mass: 14266.763 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG'

-
Non-polymers , 5 types, 570 molecules

#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM MES pH 6.5, 200 mM sodium thiocyanate, 8% dioxane, 1740 mM ammonium sulfate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.83→50 Å / Num. obs: 61630 / % possible obs: 98 % / Redundancy: 6.1 % / R_merge(I) obs: 0.115 / R_pim(I) all: 0.051 / R_rim(I) all: 0.126 / Χ²: 1.369 / Net I/σ(I): 8.5 / Num. measured all: 372877

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.83-1.86	6.1	0.907	3023	0.841	0.392	0.991	0.436	96.8
1.86-1.9	6.1	0.743	3004	0.87	0.323	0.812	0.497	96.8
1.9-1.93	6	0.61	3066	0.913	0.266	0.667	0.574	98.5
1.93-1.97	6.1	0.477	3066	0.93	0.209	0.522	0.609	98.1
1.97-2.01	6.2	0.41	3080	0.957	0.179	0.449	0.658	98.3
2.01-2.06	6	0.349	3102	0.958	0.154	0.383	0.748	99
2.06-2.11	6	0.3	3062	0.965	0.134	0.329	0.752	98.6
2.11-2.17	5.9	0.241	3098	0.976	0.108	0.265	0.842	98.5
2.17-2.23	5.6	0.218	3088	0.963	0.1	0.241	0.95	98.2
2.23-2.31	5.3	0.177	2889	0.98	0.084	0.197	1.083	92.3
2.31-2.39	6.3	0.178	3070	0.985	0.078	0.194	1.011	98.6
2.39-2.48	6.5	0.159	3129	0.988	0.068	0.173	1.101	99.1
2.48-2.6	6.4	0.143	3115	0.988	0.062	0.156	1.312	99.1
2.6-2.73	6.2	0.128	3138	0.988	0.057	0.141	1.539	99.1
2.73-2.9	6.1	0.111	3091	0.99	0.049	0.122	1.831	98.8
2.9-3.13	5.9	0.092	3105	0.993	0.042	0.101	2.238	98.8
3.13-3.44	5.4	0.075	2996	0.993	0.036	0.084	2.715	94.8
3.44-3.94	6.4	0.063	3179	0.996	0.027	0.069	2.922	99.7
3.94-4.97	6.2	0.053	3150	0.996	0.023	0.058	2.844	99.2
4.97-50	6.1	0.046	3179	0.998	0.02	0.051	2.524	97.3

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RTC, 4LGR

1rtc

4lgr

Resolution: 1.838→47.449 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1874	3189	5.18 %
R_work	0.1487	58396	-
obs	0.1507	61585	97.35 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 153.55 Å² / B_iso mean: 31.9007 Å² / B_iso min: 8.23 Å²

Refinement step

Cycle: final / Resolution: 1.838→47.449 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6034	0	106	542	6682
B_iso mean	-	-	54.85	35.11	-
Num. residues	-	-	-	-	773

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6265
X-RAY DIFFRACTION	f_angle_d	0.911	8529
X-RAY DIFFRACTION	f_chiral_restr	0.054	930
X-RAY DIFFRACTION	f_plane_restr	0.007	1117
X-RAY DIFFRACTION	f_dihedral_angle_d	11.04	3726

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3116	X-RAY DIFFRACTION	7.659	TORSIONAL
1	2	B	3116	X-RAY DIFFRACTION	7.659	TORSIONAL
2	1	C	1354	X-RAY DIFFRACTION	7.659	TORSIONAL
2	2	D	1354	X-RAY DIFFRACTION	7.659	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.838-1.8652	0.244	127	0.1929	2111	83
1.8652-1.8944	0.2262	147	0.1752	2487	96
1.8944-1.9254	0.2234	136	0.1711	2539	98
1.9254-1.9586	0.2143	164	0.1543	2541	98
1.9586-1.9942	0.196	122	0.1573	2542	99
1.9942-2.0326	0.2416	148	0.154	2555	98
2.0326-2.0741	0.1921	142	0.1531	2581	99
2.0741-2.1192	0.1772	136	0.1462	2542	99
2.1192-2.1685	0.1695	136	0.143	2561	98
2.1685-2.2227	0.1933	131	0.1455	2572	99
2.2227-2.2828	0.185	151	0.1401	2459	95
2.2828-2.35	0.2017	134	0.1456	2434	95
2.35-2.4258	0.1813	134	0.1454	2605	99
2.4258-2.5125	0.201	128	0.1514	2599	99
2.5125-2.6131	0.1769	135	0.1454	2578	99
2.6131-2.732	0.1602	122	0.1505	2583	99
2.732-2.8761	0.184	128	0.1496	2615	99
2.8761-3.0562	0.2049	133	0.1534	2590	99
3.0562-3.2921	0.2045	154	0.1532	2485	96
3.2921-3.6233	0.1716	153	0.1417	2531	97
3.6233-4.1474	0.18	155	0.1341	2619	100
4.1474-5.2242	0.1497	148	0.1269	2619	99
5.2242-47.449	0.213	125	0.1777	2648	97

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	1.1228	-0.6222	-0.7038	1.2748	0.4553	0.5032	0.0537	-0.137	0.1351	0.0325	0.0033	-0.1615	-0.0862	-0.0635	-0.034	0.1328	-0.0071	-0.0004	0.129	0.0077	0.148	-41.6903	-4.0049	82.6405
2	4.095	1.7593	2.6755	2.5261	2.3983	4.7541	-0.0918	-0.0963	0.2079	0.0027	-0.0416	0.0918	-0.1794	-0.2184	0.1443	0.0859	0.004	0.019	0.0754	0.0061	0.1055	-48.7732	-5.1162	87.9982
3	3.8092	-0.0946	-1.1913	3.9683	0.3479	2.2253	0.1319	-0.145	0.1804	0.3689	-0.0174	0.2644	-0.1506	-0.2127	-0.0448	0.1328	0.0112	0.0328	0.1421	0.0146	0.1456	-55.6487	-7.5955	95.3284
4	1.9153	-0.4353	-0.3028	0.8269	-0.3037	1.3692	-0.0715	0.0811	-0.3073	-0.0547	-0.0219	0.1537	0.2059	-0.2318	0.1045	0.1299	-0.0388	0.0116	0.1281	-0.028	0.1737	-50.9172	-21.0994	82.696
5	2.2152	-0.0014	0.3159	3.15	0.4038	2.5735	-0.0966	-0.258	-0.1828	0.2493	0.0631	-0.1953	0.2411	0.2759	0.0263	0.1628	0.0402	-0.0034	0.1725	0.051	0.1579	-30.1585	-22.2008	91.5513
6	1.3917	0.6576	0.5469	2.7127	1.2997	2.0817	0.0997	0.2858	-0.3308	-0.1396	-0.0747	-0.0249	0.0738	-0.3416	-0.084	0.1304	0.0032	-0.0255	0.2013	-0.032	0.1401	-30.8791	-5.5772	59.5686
7	4.9537	2.4786	1.9859	3.343	1.929	3.171	-0.0154	0.4462	-0.4477	-0.3211	0.0879	-0.6097	0.1396	0.3566	-0.0611	0.3164	0.0155	0.0706	0.4615	-0.0071	0.2876	-19.6025	-0.2821	45.9103
8	3.3335	-1.2049	0.022	1.7939	0.063	2.4288	0.1271	0.7568	0.0402	-0.3616	-0.1121	0.0761	0.1229	-0.1667	0.0274	0.1818	0.0043	-0.0266	0.3609	0.0265	0.1346	-39.8446	1.7771	49.2498
9	3.1193	-0.0655	-0.1222	0.7566	-0.1783	1.3195	-0.0666	0.1277	0.6126	0.0384	0.0582	0.0282	-0.1882	-0.2263	0.0365	0.1618	0.0281	-0.0083	0.1473	0.0386	0.2149	-36.2865	11.6486	62.2309
10	1.7759	0.028	1.0859	2.2598	0.0843	0.627	-0.0404	0.7198	0.6645	-0.365	-0.0325	-0.3901	-0.277	0.3426	-0.0545	0.2421	-0.054	0.0341	0.3373	0.1528	0.4084	-15.3666	16.0452	53.8002
11	2.6811	1.7091	-0.3635	5.3129	-1.6474	7.1644	-0.0466	0.7704	-0.2053	-0.3295	0.0086	0.61	0.4763	-0.4213	0.1512	0.2249	-0.0463	-0.0387	0.2166	-0.1109	0.2443	-26.9224	-22.6098	60.733
12	6.0136	0.3264	3.0589	1.9502	0.6729	3.2897	-0.0579	0.1994	0.3509	-0.1569	-0.0523	-0.056	-0.1111	0.2876	0.0889	0.1321	-0.0159	0.0233	0.134	0.0162	0.1261	-11.5574	-17.7044	64.1149
13	4.5699	-2.1428	1.3626	2.7748	-1.4372	4.9347	0.0022	-0.1395	-0.3004	-0.0447	0.0636	0.3307	-0.0984	-0.3396	-0.0518	0.0986	-0.0283	0.0093	0.0692	-0.0366	0.1351	-26.0081	-21.0606	68.4388
14	3.712	-3.365	-2.9663	6.0327	4.2555	3.2287	-0.1692	-0.3274	-0.4602	0.0331	0.0649	0.0309	0.6313	0.4092	0.0124	0.2687	0.0689	0.0198	0.1333	0.0149	0.2497	-16.7038	-28.7045	73.2186
15	2.8401	-4.5633	-0.1469	8.0065	0.1373	5.8577	-0.0182	-0.3355	0.0483	0.1396	0.0718	0.1427	-0.0347	0.2702	-0.0739	0.1311	-0.0178	0.0226	0.1066	-0.0021	0.1413	-21.4373	-17.5145	78.8197
16	7.63	-3.8993	6.5928	4.0383	-2.8316	7.848	-0.1111	-0.0131	0.0559	0.0142	0.1459	-0.0305	-0.233	0.0086	0.0197	0.11	-0.025	0.022	0.1052	-0.0175	0.1125	-19.0144	-13.9109	69.8358
17	5.9405	1.4683	-1.2146	0.8319	0.1155	1.0883	-0.0468	-0.0962	-0.1809	0.144	0.0514	-0.0331	0.0185	0.1007	0.0275	0.1414	0.0288	0.0078	0.0793	0.0042	0.1479	-18.0443	-24.7141	72.8829
18	5.6773	0.2087	-0.9773	5.8712	-0.1126	8.0879	-0.0962	0.0849	-0.6238	0.0759	0.0668	0.5316	0.6126	-0.5084	0.1635	0.1517	-0.0376	0.0186	0.1022	-0.0668	0.2617	-27.0858	-28.9834	68.1712
19	1.99	-0.3685	-2.2534	4.5754	-0.9257	2.9645	-0.2948	0.6713	-0.6865	0.144	0.1761	-0.6754	-0.0362	0.9418	0.1209	0.1783	-0.0176	0.0134	0.4138	-0.0604	0.2745	-0.5305	-23.1637	64.7216
20	5.1629	-0.248	0.7971	4.0811	-0.048	4.3497	-0.0982	-0.0098	-0.2699	0.1183	0.0225	0.2026	0.1582	-0.1221	0.0959	0.1314	-0.0049	-0.01	0.1054	0.0222	0.1123	0.9289	3.32	79.4443
21	0.851	-0.7931	-0.8712	3.8256	-2.0538	3.5656	0.7068	-1.777	-0.8727	0.774	-0.6761	0.3155	0.5797	-0.5155	-0.2132	0.2955	-0.1576	-0.0431	0.5147	0.096	0.345	-18.4369	2.3117	77.1874
22	5.7779	4.0792	1.5317	5.9073	0.3836	2.0766	-0.121	-0.232	0.8209	0.2697	-0.126	0.2193	-0.0896	-0.0744	0.1139	0.1186	0.0093	-0.0191	0.0792	-0.0242	0.1705	-4.4296	11.8293	75.1715
23	1.7306	1.8105	3.2255	1.9683	3.3742	6.0188	-0.3045	-0.1669	0.8278	-0.0611	-0.3214	-0.11	-0.9087	0.0591	0.3596	0.3212	-0.0588	-0.1273	0.1496	-0.0324	0.4769	-2.0195	16.1299	73.9507
24	5.5764	0.7322	2.3563	1.6107	0.882	3.2581	-0.0784	0.4621	0.2175	0.0116	-0.026	0.0273	-0.0834	0.2653	0.0713	0.1437	0.0029	-0.0113	0.1526	0.0311	0.1732	-4.1906	7.5657	64.6763
25	4.4166	-1.2697	-1.3313	1.9463	-1.2765	6.4032	0.0949	0.0008	-0.4521	-0.044	0.0653	0.1999	0.6277	-0.307	0.0039	0.2244	-0.0237	-0.0288	0.1705	0.0176	0.2355	-5.7006	-0.1021	72.9333
26	7.6703	-1.6336	0.4449	1.5275	1.0782	2.3566	-0.1099	-0.1284	0.3604	-0.0323	0.0227	-0.1106	-0.0932	0.18	0.0851	0.1507	-0.0233	-0.0064	0.106	0.0178	0.1588	3.1001	10.3253	75.5217
27	6.904	-0.3996	-0.7237	2.9856	-1.8187	4.9705	-0.1839	0.0424	0.6686	-0.1887	-0.1846	-0.1064	-0.2716	0.105	0.2806	0.187	0.0222	-0.0671	0.1184	-0.0098	0.2598	-13.2288	15.2886	68.0047
28	2.8304	0.2888	-0.9674	4.0405	2.2511	2.3304	-0.2135	-0.7053	0.3131	0.1159	-0.0933	0.319	-0.7524	-0.5813	-0.1419	0.1999	0.071	-0.0267	0.2768	-0.1222	0.2518	-12.1755	14.5854	78.6472
29	4.5473	-0.6019	-1.3681	7.591	-0.548	6.2391	-0.1948	-0.5775	0.4621	-0.0751	0.1361	-0.4727	0.0557	0.8954	0.0372	0.1182	0.0037	-0.0289	0.2124	-0.0195	0.1578	9.4314	8.9493	81.2352

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 44 )	A	-1 - 44
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 75 )	A	45 - 75
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 122 )	A	76 - 122
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 123 through 201 )	A	123 - 201
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 202 through 258 )	A	202 - 258
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -1 through 33 )	B	-1 - 33
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 34 through 56 )	B	34 - 56
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 57 through 122 )	B	57 - 122
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 123 through 201 )	B	123 - 201
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 202 through 261 )	B	202 - 261
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 7 )	C	1 - 7
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 8 through 25 )	C	8 - 25
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 26 through 38 )	C	26 - 38
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 39 through 50 )	C	39 - 50
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 51 through 63 )	C	51 - 63
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 64 through 82 )	C	64 - 82
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 83 through 107 )	C	83 - 107
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 108 through 117 )	C	108 - 117
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 118 through 128 )	C	118 - 128
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 3 through 24 )	D	3 - 24
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 25 through 31 )	D	25 - 31
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 32 through 38 )	D	32 - 38
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 39 through 50 )	D	39 - 50
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 51 through 66 )	D	51 - 66
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 67 through 82 )	D	67 - 82
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 83 through 98 )	D	83 - 98
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 99 through 107 )	D	99 - 107
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 108 through 117 )	D	108 - 117
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 118 through 124 )	D	118 - 124

-
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://pdbjlvh1.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

-
Protein / Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 5 types, 570 molecules

-
Details

-
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

-Protein / Antibody , 2 types, 4 molecules ABCD

-Non-polymers , 5 types, 570 molecules

-Details

-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

-
Protein / Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 5 types, 570 molecules

-
Details

-
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