PDB-3ria: C. elegans glutamate-gated chloride channel (GluCl) in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 3ria

Title

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and iodide.

Components

(Mouse monoclonal Fab fragment, ...) x 2
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

Keywords

TRANSPORT PROTEIN/IMMUNE SYSTEM /

Membrane protein /

transport protein /

Cys-loop receptor /

ligand-gated ion channel /

neurotransmitter receptor /

Ivermectin /

Picrotoxin /

Glycosylation / TRANSPORT PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich /

Immunoglobulins / Up-down Bundle /

Immunoglobulin-like /

Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology

Biological species

Caenorhabditis elegans (invertebrata)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.8 Å

Authors

Hibbs, R.E. / Gouaux, E.

Citation

Journal: Nature / Year: 2011
Title: Principles of activation and permeation in an anion-selective Cys-loop receptor.
Authors: Hibbs, R.E. / Gouaux, E.

History

Deposition	Apr 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 19, 2011	Group: Database references
Revision 1.3	Aug 23, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ria.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb3ria.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	3ria.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/3ria ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3ria	HTTPS FTP

-
Related structure data

Related structure data	3rhwSC 3ri5C 3rifC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3rhw-d 3ri5-d 3rif-d 4tnw-1 4tnw-2 4tnv-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1)

Deposited unit

A: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

B: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

C: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

D: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

E: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

F: Mouse monoclonal Fab fragment, heavy chain

G: Mouse monoclonal Fab fragment, heavy chain

H: Mouse monoclonal Fab fragment, heavy chain

I: Mouse monoclonal Fab fragment, heavy chain

J: Mouse monoclonal Fab fragment, heavy chain

K: Mouse monoclonal Fab fragment, light chain

L: Mouse monoclonal Fab fragment, light chain

M: Mouse monoclonal Fab fragment, light chain

N: Mouse monoclonal Fab fragment, light chain

O: Mouse monoclonal Fab fragment, light chain

hetero molecules

438 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	155.099, 155.099, 578.257
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 1:340 ) and (not element H)
2	1	1	chain B and (resseq 1:340 ) and (not element H)
3	1	1	chain C and (resseq 1:339 ) and (not element H)
4	1	1	chain D and (resseq 1:340 ) and (not element H)
5	1	1	chain E and (resseq 1:340 ) and (not element H)
1	1	2	chain F and (resseq 1:120 ) and (not element H)
2	1	2	chain G and (resseq 1:120 ) and (not element H)
3	1	2	chain H and (resseq 1:120 ) and (not element H)
4	1	2	chain I and (resseq 1:120 ) and (not element H)
5	1	2	chain J and (resseq 1:120 ) and (not element H)
1	1	3	chain K and (resseq 1:108 ) and (not element H)
2	1	3	chain L and (resseq 1:108 ) and (not element H)
3	1	3	chain M and (resseq 1:108 ) and (not element H)
4	1	3	chain N and (resseq 1:108 ) and (not element H)
5	1	3	chain O and (resseq 1:108 ) and (not element H)
1	1	4	A348
2	1	4	C349
3	1	4	C350
4	1	4	E348
5	1	4	E349

NCS ensembles :

ID
1
2
3
4

-
Antibody , 2 types, 10 molecules FGHIJKLMNO

#2: Antibody	Mouse monoclonal Fab fragment, heavy chain Mass: 23921.744 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Antibody	Mouse monoclonal Fab fragment, light chain Mass: 22618.156 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: HYBRIDOMA

-
Protein / Sugars , 2 types, 8 molecules ABCDE

#1: Protein	Avermectin-sensitive glutamate-gated chloride channel GluCl alpha Mass: 39636.629 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: glc-1, F11A5.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O17793
#5: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM

-
Non-polymers , 5 types, 14 molecules

#4: Chemical	ChemComp-IVM / (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside / 22,23-DIHYDROAVERMECTIN B1A / IVERMECTIN / Ivermectin Mass: 875.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄₈H₇₄O₁₄ / Comment: antiparasitic*YM
#6: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#7: Chemical	ChemComp-OCT / N-OCTANE / Octane Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈
#8: Chemical	ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₄
#9: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4 Å³/Da / Density % sol: 69.23 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 21-23% PEG 400, 50 mM sodium citrate pH 4.5, 70 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.49 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2010 Details: Mirrors: bent cylinders, stripes of Pt, Rh and clear
Radiation	Monochromator: Cryo-cooled double Si(111) crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.49 Å / Relative weight: 1
Reflection	Resolution: 3.8→40 Å / Num. all: 69600 / Num. obs: 69600 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / R_merge(I) obs: 0.142 / Net I/σ(I): 11.6
Reflection shell	Resolution: 3.8→3.94 Å / Redundancy: 5 % / R_merge(I) obs: 0.672 / Mean I/σ(I) obs: 2.7 / % possible all: 97.7

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RHW

3rhw

Resolution: 3.8→38.775 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 25.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2803	3349	5.04 %
R_work	0.2664	-	-
obs	0.2671	66435	93.9 %
all	-	66437	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 12.442 Å² / k_sol: 0.28 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.5452 Å²	0 Å²	-0 Å²
2-	-	2.5452 Å²	-0 Å²
3-	-	-	-5.0903 Å²

Refinement step

Cycle: LAST / Resolution: 3.8→38.775 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28730	0	429	0	29159

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	29952
X-RAY DIFFRACTION	f_angle_d	0.728	40892
X-RAY DIFFRACTION	f_dihedral_angle_d	13.983	10752
X-RAY DIFFRACTION	f_chiral_restr	0.048	4788
X-RAY DIFFRACTION	f_plane_restr	0.003	5044

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2716	X-RAY DIFFRACTION	POSITIONAL
1	2	B	2716	X-RAY DIFFRACTION	POSITIONAL	0.016
1	3	C	2706	X-RAY DIFFRACTION	POSITIONAL	0.017
1	4	D	2716	X-RAY DIFFRACTION	POSITIONAL	0.016
1	5	E	2716	X-RAY DIFFRACTION	POSITIONAL	0.017
2	1	F	949	X-RAY DIFFRACTION	POSITIONAL
2	2	G	949	X-RAY DIFFRACTION	POSITIONAL	0.025
2	3	H	949	X-RAY DIFFRACTION	POSITIONAL	0.014
2	4	I	949	X-RAY DIFFRACTION	POSITIONAL	0.01
2	5	J	949	X-RAY DIFFRACTION	POSITIONAL	0.012
3	1	K	804	X-RAY DIFFRACTION	POSITIONAL
3	2	L	804	X-RAY DIFFRACTION	POSITIONAL	0.013
3	3	M	804	X-RAY DIFFRACTION	POSITIONAL	0.012
3	4	N	804	X-RAY DIFFRACTION	POSITIONAL	0.011
3	5	O	804	X-RAY DIFFRACTION	POSITIONAL	0.048
4	1	A	62	X-RAY DIFFRACTION	POSITIONAL
4	2	B	62	X-RAY DIFFRACTION	POSITIONAL	0.01
4	3	C	62	X-RAY DIFFRACTION	POSITIONAL	0.009
4	4	D	62	X-RAY DIFFRACTION	POSITIONAL	0.01
4	5	E	62	X-RAY DIFFRACTION	POSITIONAL	0.009

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 (%)
3.8-3.8535	0.3151	129	0.327	2273	X-RAY DIFFRACTION	83
3.8535-3.9109	0.3288	127	0.3289	2338	X-RAY DIFFRACTION	85
3.9109-3.972	0.3508	114	0.3213	2394	X-RAY DIFFRACTION	86
3.972-4.0371	0.3347	138	0.2961	2427	X-RAY DIFFRACTION	89
4.0371-4.1066	0.2837	111	0.2826	2502	X-RAY DIFFRACTION	90
4.1066-4.1812	0.2907	130	0.2644	2535	X-RAY DIFFRACTION	91
4.1812-4.2615	0.2579	134	0.2569	2526	X-RAY DIFFRACTION	92
4.2615-4.3484	0.2815	121	0.2496	2587	X-RAY DIFFRACTION	94
4.3484-4.4428	0.255	121	0.2404	2616	X-RAY DIFFRACTION	93
4.4428-4.546	0.2292	129	0.235	2604	X-RAY DIFFRACTION	95
4.546-4.6595	0.2377	132	0.2255	2627	X-RAY DIFFRACTION	95
4.6595-4.7853	0.2381	154	0.2128	2638	X-RAY DIFFRACTION	95
4.7853-4.9258	0.2136	157	0.2115	2638	X-RAY DIFFRACTION	96
4.9258-5.0845	0.2429	158	0.23	2657	X-RAY DIFFRACTION	96
5.0845-5.2658	0.2579	142	0.2317	2687	X-RAY DIFFRACTION	96
5.2658-5.476	0.2635	135	0.2483	2706	X-RAY DIFFRACTION	97
5.476-5.7245	0.272	138	0.2695	2699	X-RAY DIFFRACTION	96
5.7245-6.0253	0.3377	160	0.2879	2689	X-RAY DIFFRACTION	96
6.0253-6.4012	0.3016	143	0.2807	2721	X-RAY DIFFRACTION	97
6.4012-6.8929	0.3539	158	0.2945	2755	X-RAY DIFFRACTION	97
6.8929-7.5819	0.2956	145	0.258	2801	X-RAY DIFFRACTION	98
7.5819-8.6683	0.2379	155	0.2423	2848	X-RAY DIFFRACTION	99
8.6683-10.881	0.2584	188	0.2311	2857	X-RAY DIFFRACTION	99
10.881-38.7768	0.3602	130	0.357	2961	X-RAY DIFFRACTION	95

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	0.5865	-0.126	0.0269	2.8536	-0.4429	0.9892	0.0173	-0.0605	0.07	0.2873	0.0703	0.2478	0.0234	-0.1112	-0	0.7517	-0.0719	-0.0209	0.877	-0.0143	0.7088	-2.2137	74.4988	38.5492
2	0.9832	0.22	-0.1187	2.7697	-0.7087	1.0675	-0.0258	0.1228	-0.0732	0.0192	0.2409	0.0126	0.2087	-0.0264	0	0.7819	-0.0221	-0.0292	0.9288	-0.1276	0.7195	22.854	71.9542	35.2644
3	0.9612	-0.397	0.2554	2.9004	-1.2221	1.804	0.0739	0.1103	-0.0082	-0.0682	-0.0263	-0.0789	0.1937	0.1256	-0	0.7758	-0.054	-0.0305	0.8338	-0.169	0.8807	34.3174	81.2064	55.7977
4	1.408	0.2304	-0.1197	1.8162	-0.9115	1.4585	0.0237	-0.21	-0.062	0.1395	-0.04	-0.091	0.055	0.0687	-0	0.956	-0.0181	-0.0296	0.863	-0.2019	0.7988	16.5794	89.6278	71.8078
5	1.106	0.5336	0.0632	2.5734	-0.7483	1.3069	-0.0292	-0.0859	0.0984	0.3973	0.0717	0.1036	-0.06	-0.0524	0	0.8158	0.0994	0.1124	0.8398	-0.1271	0.8681	-6.1374	85.4807	61.1974
6	0.0241	0.0575	-0.0089	0.0006	-0.0214	0.0202	0.3805	0.3095	-1.3427	-0.6585	-0.3117	-0.3796	0.4452	0.5476	-0	0.6484	-0.1585	-0.0051	1.2522	0.004	0.5419	10.9761	92.4924	21.367
7	0.0041	0.0391	0.021	0.0843	0.0747	0.0488	0.1919	-0.0297	-0.3202	0.4268	-0.3895	-0.257	0.0959	0.8936	0	0.8976	-0.21	-0.0597	1.1039	0.0696	1.0042	34.5382	97.1105	33.4207
8	0.0204	-0.0566	0.0442	0.0455	-0.0011	-0.0333	-0.3783	-1.1572	0.2859	0.2891	-0.3179	0.514	0.3902	0.6873	-0	1.3696	-0.264	-0.4081	-1.7221	-2.026	0.3742	29.8859	108.9688	57.2847
9	0.0113	-0.0301	0.0561	0.0399	-0.0353	0.0566	0.2784	-0.4368	0.1141	-0.2666	-0.8892	0.572	0.1966	-0.2216	0	1.0457	-0.0265	0.2388	1.095	-0.068	1.3245	2.8918	111.3169	60.2502
10	0.0347	0.0148	-0.1121	0.0121	-0.0332	0.1023	-0.5007	-0.237	-0.0006	0.1403	-0.9833	0.0597	0.6825	-0.3653	-0	0.7587	0.0476	-0.1159	1.0011	0.01	0.9233	-8.7833	101.2709	37.9733
11	3.1551	0.4551	-0.6036	2.9024	-0.8339	1.1486	-0.0535	0.7049	-0.4724	-0.2606	0.2362	-0.9277	0.3042	0.4984	-0	1.1379	0.1119	-0.0143	1.4505	-0.4258	1.2982	52.6478	47.0273	33.4516
12	0.2998	-0.4727	0.2726	-1.013	0.0317	0.0005	-0.1006	-0.1771	-0.8392	-0.4216	0.2513	-0.4488	-0.1468	0.4073	0	2.1669	0.1384	-0.0597	2.5421	-0.1237	2.3578	82.8667	36.7888	24.1788
13	4.6045	-0.5911	0.7594	2.6307	0.8576	3.9377	-0.2503	0.0106	-0.0075	0.0718	0.2038	-0.3308	0.0067	0.3965	-0	0.9119	0.0696	-0.1065	0.8635	-0.1176	0.8617	54.4955	73.192	87.8137
14	3.1976	0.5079	-1.7295	1.7148	-1.2369	3.0131	0.0862	-0.1139	-0.1282	0.2865	-0.1058	-0.1397	-0.4312	-0.4319	-0	1.2654	0.0263	-0.2862	1.0588	-0.0917	1.0879	76.2022	71.1443	111.0509
15	6.2628	0.4496	0.1869	2.0054	1.3928	3.329	-0.1167	0.4209	-0.2138	0.015	0.0639	0.0869	0.0383	-0.0053	0	0.7555	-0.0156	-0.0924	0.7136	0.0225	0.6828	-5.0028	42.0017	17.6872
16	3.5421	-0.4203	-0.4326	3.872	0.6471	2.2372	-0.0083	0.5458	-0.4883	-0.2727	0.1163	0.0705	0.4429	-0.1872	0	0.9529	-0.0625	-0.1381	1.2347	-0.1573	0.9766	-12.7849	20.3622	-7.2556
17	2.9442	-1.0998	-0.4281	1.818	0.2867	2.7269	0.0653	-0.5365	0.2664	0.4398	-0.1039	0.1064	0.0901	-0.305	-0	1.3049	-0.1585	0.1591	1.4612	-0.2626	0.9489	-1.2494	84.2508	105.5537
18	0.3144	0.3874	-0.9063	-0.476	-0.0245	-0.2131	-0.052	-3.7536	0.5348	0.0176	-1.6169	-0.2636	2.2557	-4.6589	0	3.176	-2.1077	0.5339	6.1887	-1.4558	1.4472	-11.1475	85.1165	138.5171
19	3.8445	0.5493	0.4673	1.9399	0.319	3.5258	0.0513	0.1425	0.0033	0.1019	0.0468	0.6792	0.0433	-0.4633	0	0.9309	-0.0853	0.1585	0.8715	-0.0507	1.2156	-38.7705	64.175	62.3948
20	0.7928	0.7806	0.0911	0.428	0.7376	1.1528	-0.0884	-0.1941	-0.6813	-0.0852	-0.2187	0.9781	0.3271	-0.8563	-0	1.6407	0.0813	0.4532	1.5729	-0.0239	2.45	-68.4291	50.0224	66.4757

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	A348
7	X-RAY DIFFRACTION	7	C349
8	X-RAY DIFFRACTION	8	C350
9	X-RAY DIFFRACTION	9	E348
10	X-RAY DIFFRACTION	10	E349
11	X-RAY DIFFRACTION	11	(chain F and resid 1:120) or (chain N and
12	X-RAY DIFFRACTION	12	(chain F and resid 126:221) or (chain N and
13	X-RAY DIFFRACTION	13	(chain G and resid 1:120) or (chain K and
14	X-RAY DIFFRACTION	14	(chain G and resid 126:221) or (chain K and
15	X-RAY DIFFRACTION	15	(chain H and resid 1:120) or (chain L and
16	X-RAY DIFFRACTION	16	(chain H and resid 126:221) or (chain L and
17	X-RAY DIFFRACTION	17	(chain I and resid 1:120) or (chain O and
18	X-RAY DIFFRACTION	18	(chain I and resid 126:221) or (chain O and
19	X-RAY DIFFRACTION	19	(chain J and resid 1:120) or (chain M and
20	X-RAY DIFFRACTION	20	(chain J and resid 126:221) or (chain M and

-
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

-
Antibody , 2 types, 10 molecules FGHIJKLMNO

-
Protein / Sugars , 2 types, 8 molecules ABCDE

-
Non-polymers , 5 types, 14 molecules

-
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

-Antibody , 2 types, 10 molecules FGHIJKLMNO

-Protein / Sugars , 2 types, 8 molecules ABCDE

-Non-polymers , 5 types, 14 molecules

-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

-
Antibody , 2 types, 10 molecules FGHIJKLMNO

-
Protein / Sugars , 2 types, 8 molecules ABCDE

-
Non-polymers , 5 types, 14 molecules

-
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