PDB-6qqo: Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyri...

ID or keywords:

Entry

Database: PDB / ID: 6qqo

Title

Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (3)

Components

Soluble acetylcholine receptor

Keywords

SIGNALING PROTEIN / AChBP /

Acetylcholine

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity /

membrane / identical protein binding /

metal ion binding
Similarity search - Function

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Bueno, R.V. / Davis, S. / Dawson, A. / Hunter, W.N.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Interactions between 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors
Authors: Bueno, R.V. / Davis, S. / Dawson, A. / Ondachi, P.W. / Carroll, F.I. / Hunter, W.N.

History

Deposition	Feb 18, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Mar 2, 2022	Group: Database references / Structure summary Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Jan 24, 2024	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

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Download

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Validation report

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

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Related structure data

Related structure data	6qkkC 6qqpC 5o87S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qkk-1 6sgv-1 6sh0-2 6sh0-1 6qkk-2 5oa0-d 5oan-d 5oal-2 2y58-d 4bqt-d 5o87-2 6qqp-2 2y54-d 2yme-1 5obg-d 5o87-1 5obh-d 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

6qkkC

6qqpC

5o87S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4)

Deposited unit

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

293 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

hetero molecules

defined by author&software
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

defined by author&software
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	209.826, 134.060, 131.719
Angle α, β, γ (deg.)	90.00, 102.56, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	20 - 224	20 - 224
2	1	ARG	ARG	B	B	20 - 224	20 - 224
1	2	ARG	ARG	A	A	20 - 224	20 - 224
2	2	ARG	ARG	C	C	20 - 224	20 - 224
1	3	GLU	GLU	A	A	20 - 223	20 - 223
2	3	GLU	GLU	D	D	20 - 223	20 - 223
1	4	GLU	GLU	A	A	20 - 223	20 - 223
2	4	GLU	GLU	E	E	20 - 223	20 - 223
1	5	ARG	ARG	A	A	20 - 224	20 - 224
2	5	ARG	ARG	F	F	20 - 224	20 - 224
1	6	GLU	GLU	A	A	20 - 223	20 - 223
2	6	GLU	GLU	G	G	20 - 223	20 - 223
1	7	ARG	ARG	A	A	20 - 224	20 - 224
2	7	ARG	ARG	H	H	20 - 224	20 - 224
1	8	ARG	ARG	A	A	20 - 224	20 - 224
2	8	ARG	ARG	I	I	20 - 224	20 - 224
1	9	ARG	ARG	A	A	20 - 224	20 - 224
2	9	ARG	ARG	J	J	20 - 224	20 - 224
1	10	ARG	ARG	B	B	20 - 224	20 - 224
2	10	ARG	ARG	C	C	20 - 224	20 - 224
1	11	GLU	GLU	B	B	20 - 223	20 - 223
2	11	GLU	GLU	D	D	20 - 223	20 - 223
1	12	GLU	GLU	B	B	20 - 223	20 - 223
2	12	GLU	GLU	E	E	20 - 223	20 - 223
1	13	ARG	ARG	B	B	20 - 224	20 - 224
2	13	ARG	ARG	F	F	20 - 224	20 - 224
1	14	GLU	GLU	B	B	20 - 223	20 - 223
2	14	GLU	GLU	G	G	20 - 223	20 - 223
1	15	ARG	ARG	B	B	20 - 224	20 - 224
2	15	ARG	ARG	H	H	20 - 224	20 - 224
1	16	ARG	ARG	B	B	20 - 224	20 - 224
2	16	ARG	ARG	I	I	20 - 224	20 - 224
1	17	ARG	ARG	B	B	20 - 224	20 - 224
2	17	ARG	ARG	J	J	20 - 224	20 - 224
1	18	GLU	GLU	C	C	20 - 223	20 - 223
2	18	GLU	GLU	D	D	20 - 223	20 - 223
1	19	GLU	GLU	C	C	20 - 223	20 - 223
2	19	GLU	GLU	E	E	20 - 223	20 - 223
1	20	ARG	ARG	C	C	20 - 224	20 - 224
2	20	ARG	ARG	F	F	20 - 224	20 - 224
1	21	GLU	GLU	C	C	20 - 223	20 - 223
2	21	GLU	GLU	G	G	20 - 223	20 - 223
1	22	ARG	ARG	C	C	20 - 224	20 - 224
2	22	ARG	ARG	H	H	20 - 224	20 - 224
1	23	ARG	ARG	C	C	20 - 224	20 - 224
2	23	ARG	ARG	I	I	20 - 224	20 - 224
1	24	ARG	ARG	C	C	20 - 224	20 - 224
2	24	ARG	ARG	J	J	20 - 224	20 - 224
1	25	ARG	ARG	D	D	20 - 225	20 - 225
2	25	ARG	ARG	E	E	20 - 225	20 - 225
1	26	GLU	GLU	D	D	20 - 223	20 - 223
2	26	GLU	GLU	F	F	20 - 223	20 - 223
1	27	ARG	ARG	D	D	20 - 225	20 - 225
2	27	ARG	ARG	G	G	20 - 225	20 - 225
1	28	GLU	GLU	D	D	20 - 223	20 - 223
2	28	GLU	GLU	H	H	20 - 223	20 - 223
1	29	GLU	GLU	D	D	20 - 223	20 - 223
2	29	GLU	GLU	I	I	20 - 223	20 - 223
1	30	GLU	GLU	D	D	20 - 223	20 - 223
2	30	GLU	GLU	J	J	20 - 223	20 - 223
1	31	GLU	GLU	E	E	20 - 223	20 - 223
2	31	GLU	GLU	F	F	20 - 223	20 - 223
1	32	ARG	ARG	E	E	20 - 225	20 - 225
2	32	ARG	ARG	G	G	20 - 225	20 - 225
1	33	GLU	GLU	E	E	20 - 223	20 - 223
2	33	GLU	GLU	H	H	20 - 223	20 - 223
1	34	GLU	GLU	E	E	20 - 223	20 - 223
2	34	GLU	GLU	I	I	20 - 223	20 - 223
1	35	GLU	GLU	E	E	20 - 223	20 - 223
2	35	GLU	GLU	J	J	20 - 223	20 - 223
1	36	GLU	GLU	F	F	20 - 223	20 - 223
2	36	GLU	GLU	G	G	20 - 223	20 - 223
1	37	ARG	ARG	F	F	20 - 224	20 - 224
2	37	ARG	ARG	H	H	20 - 224	20 - 224
1	38	ARG	ARG	F	F	20 - 224	20 - 224
2	38	ARG	ARG	I	I	20 - 224	20 - 224
1	39	ARG	ARG	F	F	20 - 224	20 - 224
2	39	ARG	ARG	J	J	20 - 224	20 - 224
1	40	GLU	GLU	G	G	20 - 223	20 - 223
2	40	GLU	GLU	H	H	20 - 223	20 - 223
1	41	GLU	GLU	G	G	20 - 223	20 - 223
2	41	GLU	GLU	I	I	20 - 223	20 - 223
1	42	GLU	GLU	G	G	20 - 223	20 - 223
2	42	GLU	GLU	J	J	20 - 223	20 - 223
1	43	ARG	ARG	H	H	20 - 224	20 - 224
2	43	ARG	ARG	I	I	20 - 224	20 - 224
1	44	ARG	ARG	H	H	20 - 224	20 - 224
2	44	ARG	ARG	J	J	20 - 224	20 - 224
1	45	ARG	ARG	I	I	20 - 224	20 - 224
2	45	ARG	ARG	J	J	20 - 224	20 - 224

NCS ensembles :

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

#1: Protein

Soluble acetylcholine receptor

Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: The sequence conflicts are because we have used the AChBP gene sequence provided in the Aplysia californica genome (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=589127391_ ...
Source: (gene. exp.)

Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8

#5: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 726 molecules

#2: Chemical	ChemComp-JC8 / 6-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]pyridine-3-carboxamide Mass: 312.341 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₇H₁₇FN₄O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.49 Å³/Da / Density % sol: 64.79 % / Description: Block
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Reservoir: 0.2 M NaCl 0.1 M Phosphate/citrate pH 4.2 10% PEG 8000 Buffer: 50 mM Tris 250 mM NaCl Protein concentration 4 mg/ml Microseeded

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96858 Å / Relative weight: 1
Reflection	Resolution: 2.5→46.4 Å / Num. obs: 109552 / % possible obs: 89.7 % / Redundancy: 2.3 % / B_iso Wilson estimate: 13.6 Å² / CC_1/2: 0.93 / R_merge(I) obs: 0.118 / Net I/σ(I): 6.9
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.559 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 12673 / CC_1/2: 0.46 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5o87

5o87

Resolution: 2.5→46.4 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.902 / SU B: 7.279 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21161	5421	4.9 %	RANDOM
R_work	0.1928	-	-	-
obs	0.19372	104105	89.09 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 20.005 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.7 Å²	-0 Å²	-0.44 Å²
2-	-	1.62 Å²	-0 Å²
3-	-	-	1.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→46.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16381	0	613	659	17653

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	17477
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15419
X-RAY DIFFRACTION	r_angle_refined_deg	1.561	1.965	23838
X-RAY DIFFRACTION	r_angle_other_deg	0.93	3.001	35898
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.961	5.017	2069
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.513	24.481	790
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.681	15	2731
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.087	15	93
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2654
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	19819
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3498
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.603	1.88	8278
X-RAY DIFFRACTION	r_mcbond_other	1.603	1.88	8275
X-RAY DIFFRACTION	r_mcangle_it	2.826	2.81	10335
X-RAY DIFFRACTION	r_mcangle_other	2.826	2.81	10335
X-RAY DIFFRACTION	r_scbond_it	2.278	2.243	9198
X-RAY DIFFRACTION	r_scbond_other	2.278	2.244	9199
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.831	3.262	13502
X-RAY DIFFRACTION	r_long_range_B_refined	6.392	21.586	17917
X-RAY DIFFRACTION	r_long_range_B_other	6.372	21.584	17865
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12926	0.03
1	2	B	12926	0.03
2	1	A	12950	0.03
2	2	C	12950	0.03
3	1	A	12742	0.03
3	2	D	12742	0.03
4	1	A	12754	0.04
4	2	E	12754	0.04
5	1	A	12930	0.03
5	2	F	12930	0.03
6	1	A	12820	0.02
6	2	G	12820	0.02
7	1	A	12896	0.04
7	2	H	12896	0.04
8	1	A	12904	0.04
8	2	I	12904	0.04
9	1	A	12884	0.03
9	2	J	12884	0.03
10	1	B	12958	0.02
10	2	C	12958	0.02
11	1	B	12710	0.03
11	2	D	12710	0.03
12	1	B	12758	0.03
12	2	E	12758	0.03
13	1	B	12934	0.03
13	2	F	12934	0.03
14	1	B	12798	0.02
14	2	G	12798	0.02
15	1	B	12854	0.04
15	2	H	12854	0.04
16	1	B	12934	0.03
16	2	I	12934	0.03
17	1	B	12900	0.03
17	2	J	12900	0.03
18	1	C	12752	0.03
18	2	D	12752	0.03
19	1	C	12766	0.04
19	2	E	12766	0.04
20	1	C	12964	0.02
20	2	F	12964	0.02
21	1	C	12840	0.02
21	2	G	12840	0.02
22	1	C	12880	0.04
22	2	H	12880	0.04
23	1	C	12938	0.03
23	2	I	12938	0.03
24	1	C	12932	0.03
24	2	J	12932	0.03
25	1	D	12816	0.05
25	2	E	12816	0.05
26	1	D	12728	0.04
26	2	F	12728	0.04
27	1	D	12872	0.04
27	2	G	12872	0.04
28	1	D	12696	0.04
28	2	H	12696	0.04
29	1	D	12744	0.03
29	2	I	12744	0.03
30	1	D	12746	0.03
30	2	J	12746	0.03
31	1	E	12742	0.04
31	2	F	12742	0.04
32	1	E	12874	0.05
32	2	G	12874	0.05
33	1	E	12696	0.04
33	2	H	12696	0.04
34	1	E	12724	0.05
34	2	I	12724	0.05
35	1	E	12748	0.04
35	2	J	12748	0.04
36	1	F	12820	0.03
36	2	G	12820	0.03
37	1	F	12894	0.04
37	2	H	12894	0.04
38	1	F	12914	0.03
38	2	I	12914	0.03
39	1	F	12924	0.03
39	2	J	12924	0.03
40	1	G	12790	0.04
40	2	H	12790	0.04
41	1	G	12802	0.04
41	2	I	12802	0.04
42	1	G	12808	0.03
42	2	J	12808	0.03
43	1	H	12936	0.04
43	2	I	12936	0.04
44	1	H	12920	0.04
44	2	J	12920	0.04
45	1	I	12892	0.02
45	2	J	12892	0.02

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	416	-
R_work	0.274	7813	-
obs	-	-	91.2 %

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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

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

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Non-polymers , 4 types, 726 molecules

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-Validation report

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-Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

-Non-polymers , 4 types, 726 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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

-
Non-polymers , 4 types, 726 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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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

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

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Jul 12, 2017. Major update of PDB

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Yorodumi