PDB-4fyw: E. coli Aspartate Transcarbamoylase complexed with CTP

ID or keywords:

Entry

Database: PDB / ID: 4fyw

Title

E. coli Aspartate Transcarbamoylase complexed with CTP

Components

Aspartate carbamoyltransferase catalytic chain
Aspartate carbamoyltransferase regulatory chain

Keywords

TRANSFERASE / pyrimidine nucleotide biosynthesis /

feedback inhibition /

allostery

Function / homology

Function and homology information

aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process /

aspartate carbamoyltransferase /

aspartate carbamoyltransferase activity /

amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Cockrell, G.M. / Kantrowitz, E.R.

Citation

Journal: Biochemistry / Year: 2012
Title: Metal Ion Involvement in the Allosteric Mechanism of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Kantrowitz, E.R.

History

Deposition	Jul 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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	4fyw.cif.gz	205.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4fyw.ent.gz	162.6 KB	Display	PDB format
PDBx/mmJSON format	4fyw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/4fyw ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fyw	HTTPS FTP

-
Related structure data

Related structure data	4fyvC 4fyxC 4fyyC 1za1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3at1-1 2qg9-1 5at1-1 2atc-1 1rae-1 2fzk-1 1tu0-1 2qgf-1 1i5o-1 9atc-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (20)

Deposited unit

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

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

1

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

defined by author&software
312 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.297, 121.297, 142.251
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-569- HOH
2	1	A-574- HOH
3	1	A-578- HOH
4	1	A-581- HOH
5	1	C-508- HOH
6	1	C-579- HOH

#1: Protein	Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase Mass: 34337.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein	Aspartate carbamoyltransferase regulatory chain Mass: 17143.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7F3
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.08 %
Crystal grow	Temperature: 298 K / Method: microdialysis / pH: 5.7 Details: 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM CTP, pH 5.7, MICRODIALYSIS, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 25, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.542 Å / Relative weight: 1

Reflection

Redundancy: 5.35 % / Number: 381122 / R_merge(I) obs: 0.057 / Χ²: 0.94 / D res high: 2.1 Å / D res low: 43.22 Å / Num. obs: 70735 / % possible obs: 99.7

Diffraction reflection shell

ID: 1

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	R_merge(I) obs	Chi squared	Redundancy	Rejects
4.52	43.22	99.4	0.037	0.69	5.33	280
3.59	4.52	99.4	0.046	0.67	5.44	428
3.14	3.59	99.2	0.059	0.73	5.43	619
2.85	3.14	99.3	0.084	0.82	5.4	596
2.65	2.85	99.5	0.12	0.89	5.37	446
2.49	2.65	99.8	0.168	0.99	5.33	279
2.37	2.49	100	0.234	1.06	5.32	120
2.26	2.37	100	0.296	1.12	5.31	54
2.18	2.26	100	0.369	1.19	5.28	23
2.1	2.18	100	0.45	1.3	5.28	15

Reflection

Resolution: 2.1→43.22 Å / Num. all: 70735 / Num. obs: 70735 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.35 % / R_merge(I) obs: 0.057 / Χ²: 0.94 / Net I/σ(I): 10.7 / Scaling rejects: 2860

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
2.1-2.18	5.28	0.45	2.6	36859	6982	1.3	100
2.18-2.26	5.28	0.369	3.2	37165	7030	1.19	100
2.26-2.37	5.31	0.296	3.8	37262	7010	1.12	100
2.37-2.49	5.32	0.234	4.6	37636	7058	1.06	100
2.49-2.65	5.33	0.168	6.4	37712	7027	0.99	99.8
2.65-2.85	5.37	0.12	8.6	38192	7033	0.89	99.5
2.85-3.14	5.4	0.084	11.7	38475	7014	0.82	99.3
3.14-3.59	5.43	0.059	16.2	38958	7061	0.73	99.2
3.59-4.52	5.44	0.046	21.1	39380	7158	0.67	99.4
4.52-43.22	5.33	0.037	26.9	39483	7362	0.69	99.4

-
Processing

Software

Name	Version	Classification
d*TREK	9.9.8.8D	data scaling
d*TREK	9.9.8.8D	data reduction
PHENIX		refinement
PDB_EXTRACT	3.11	data extraction
CrystalClear		data collection
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZA1

1za1

Resolution: 2.1→43.218 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 26.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2291	3569	5.05 %	Random
R_work	0.1838	-	-	-
obs	0.186	70722	99.64 %	-
all	-	70735	-	-

Solvent computation

Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 180.62 Å² / B_iso mean: 30.0296 Å² / B_iso min: 3.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→43.218 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7083	0	60	571	7714

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7269
X-RAY DIFFRACTION	f_angle_d	1.128	9870
X-RAY DIFFRACTION	f_chiral_restr	0.078	1146
X-RAY DIFFRACTION	f_plane_restr	0.005	1277
X-RAY DIFFRACTION	f_dihedral_angle_d	14.243	2707

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1288	0.3248	131	0.2637	2666	2797	100
2.1288-2.1592	0.262	143	0.2499	2634	2777	100
2.1592-2.1914	0.3272	143	0.2516	2658	2801	100
2.1914-2.2257	0.3057	155	0.2416	2663	2818	100
2.2257-2.2621	0.3465	149	0.2559	2668	2817	100
2.2621-2.3011	0.3464	120	0.2589	2686	2806	100
2.3011-2.343	0.3151	160	0.2513	2653	2813	100
2.343-2.3881	0.3303	146	0.2369	2657	2803	100
2.3881-2.4368	0.2591	129	0.2367	2686	2815	100
2.4368-2.4898	0.2695	143	0.2392	2687	2830	100
2.4898-2.5477	0.331	142	0.2231	2660	2802	100
2.5477-2.6114	0.264	149	0.2076	2640	2789	100
2.6114-2.682	0.3239	156	0.2157	2681	2837	100
2.682-2.7609	0.266	145	0.2154	2675	2820	100
2.7609-2.85	0.2473	139	0.207	2673	2812	100
2.85-2.9518	0.2652	151	0.2054	2669	2820	99
2.9518-3.07	0.257	132	0.2011	2668	2800	99
3.07-3.2097	0.261	156	0.192	2662	2818	99
3.2097-3.3788	0.2953	139	0.1902	2688	2827	99
3.3788-3.5904	0.226	116	0.1721	2693	2809	99
3.5904-3.8675	0.2124	138	0.1569	2717	2855	99
3.8675-4.2564	0.147	116	0.1429	2727	2843	99
4.2564-4.8715	0.1654	167	0.1357	2734	2901	100
4.8715-6.1348	0.1723	169	0.1643	2724	2893	100
6.1348-43.2272	0.1856	135	0.1683	2884	3019	99

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	0.0525	0.0758	0.0241	0.1226	0.0636	0.1331	0.0118	0.0526	-0.0258	-0.0622	0.1067	0.0242	-0.062	-0.0984	0.1972	0.0276	0.011	-0.0158	0.0812	0.0175	0.0331	43.3099	36.5873	2.851
2	0.0075	0.0003	0.0017	0.0091	-0.0097	0.0101	0.0179	-0.0449	0.0117	0.0433	-0.0106	-0.0574	-0.0421	0.0151	-0.0022	0.1098	-0.0433	0.0067	0.165	0.0448	0.1393	55.1435	43.8092	17.8651
3	0.1238	0.1193	-0.0024	0.2245	-0.0806	0.1696	-0.0104	0.0479	0.0832	0.0304	0.0869	0.1805	-0.0712	-0.1642	0.1483	-0.0536	0.0328	0.087	0.1344	0.0086	-0.0189	33.718	36.0734	14.073
4	0.0052	0.0567	0.0353	0.6146	0.3773	0.2354	-0.0455	-0.0789	-0.1126	0.314	0.1703	-0.0058	0.136	-0.055	0.0811	0.1652	0.0075	-0.0047	0.2839	0.0758	0.1524	28.1629	21.5513	24.726
5	0.1579	-0.0055	-0.009	0.1119	0.0152	0.06	-0.0445	0.0585	-0.0727	-0.0667	0.0162	0.0462	0.0918	-0.0484	-0.0717	0.0609	-0.0611	0.0075	0.0764	0.0103	0.088	37.2864	21.163	9.7078
6	0.0036	-0.003	0.0009	0.0037	-0.0036	0.0061	0.004	0.0109	-0.008	-0.0005	0.0076	-0.0048	-0.0016	0.0037	0.0004	0.682	0.1741	0.0635	0.6116	0.0658	0.6078	20.7707	87.7828	23.2782
7	0.0299	-0.0184	0.0141	0.0403	0.0094	0.0168	0.0234	0.0223	0.0508	-0.0548	0.005	0.0009	-0.1005	-0.0715	0.011	0.2305	0.1329	-0.0304	0.19	-0.061	0.25	23.8696	75.6684	30.8237
8	0.0304	0.0028	-0.0037	0.0444	0.0166	0.007	0.0459	0.0969	-0.0416	-0.0933	-0.0297	0.0242	-0.1796	-0.0835	-0.0001	0.3609	0.1528	-0.0833	0.3452	-0.0833	0.3164	18.7059	74.2332	22.7518
9	0.0222	0.0026	-0.0055	0.1362	-0.1074	0.0889	-0.0157	-0.046	0.0191	0.1265	-0.1249	0.106	0.0283	-0.1277	-0.0641	0.1394	0.0153	0.0405	0.1598	-0.0775	0.1507	29.5179	52.6769	24.288
10	0.135	0.0282	0.0352	0.0546	-0.0517	0.07	0.1013	-0.1182	0.0187	0.074	-0.0282	0.0213	-0.0753	-0.0554	0.1022	0.0907	-0.0275	0.0087	0.0417	-0.0151	0.0705	63.58	52.1811	67.1678
11	0.0031	-0.0023	-0.0007	0.0049	0.0012	-0.0002	0.0063	0.0186	-0.0443	-0.0116	0.0161	-0.0238	0.0104	-0.0099	0.0144	0.0837	-0.0588	-0.0359	0.0586	-0.0022	0.0907	53.5881	41.7647	51.9555
12	0.1433	0.0103	0.0077	0.0498	0.0126	0.1352	-0.0141	0.0959	0.1551	-0.0029	-0.0047	0.0767	-0.1649	-0.0184	-0.0654	0.0932	-0.0149	-0.031	0.0265	0.0145	0.0602	68.385	62.3711	55.3693
13	0.0066	-0.0034	-0.0326	0.1665	0.0439	0.1389	-0.0221	0.066	-0.0398	-0.1248	-0.134	-0.1338	-0.0424	0.0947	-0.2252	-0.0206	-0.1228	0.0437	0.0243	0.0441	0.0798	85.1854	59.1064	47.7678
14	0.0445	0.0214	-0.0484	0.2	-0.1269	0.3556	-0.0527	-0.0406	-0.0549	0.0771	-0.1186	-0.0486	0.0655	0.0015	-0.2603	0.07	-0.0299	-0.0072	0.0629	-0.0161	0.0643	75.973	51.896	62.6515
15	0.0027	0.0032	-0.0049	0.0129	-0.0144	0.0164	-0.0065	-0.0036	-0.0057	-0.0229	0.0051	0.0082	-0.0034	-0.0065	0.0005	0.6271	0.1983	-0.0321	0.5767	-0.0245	0.6338	20.3767	88.6153	45.8929
16	0.0028	-0.0015	0.0013	0.0029	-0.0006	0.0022	-0.0728	0.001	0.0426	0.0019	0.003	0.0159	-0.0356	-0.0179	-0	0.3125	0.07	-0.035	0.2055	0.0272	0.3946	34.7306	86.0166	39.4009
17	0.0023	0.0034	0.0011	0.0068	-0.0011	0.0065	0.0128	-0.045	-0.0338	0.0127	0.0228	0.0565	-0.0203	-0.1075	-0	0.3469	0.0585	-0.0925	0.2088	-0.0112	0.3798	29.9916	75.135	41.7932
18	0.0269	-0.0043	0.0301	0.0035	-0.0118	0.0534	-0.0507	0.0151	0.0355	-0.0133	-0.0436	-0.0045	-0.0133	0.0152	0.0074	0.4511	0.0671	-0.0446	0.1528	-0.0126	0.4279	33.1458	88.7473	33.3469
19	0.0067	-0.0015	-0.0033	0.0093	0.0053	0.0035	-0.0372	-0.0693	0.0301	0.0607	-0.0976	-0.0826	-0.0612	-0.0364	0	0.2762	0.0996	-0.0633	0.2248	-0.0468	0.3187	35.2983	82.7168	47.051
20	0.0037	0.0047	0.0033	0.0086	0.0063	0.0052	-0.0039	-0.0034	0.0017	0.0093	-0.0247	0.0341	-0.0045	-0.031	0.0067	0.4329	0.1589	-0.1552	0.2657	-0.154	0.4144	26.0257	91.6117	50.4832
21	0.0264	-0.0047	0.0306	0.0008	-0.0037	0.0298	-0.0448	-0.0185	0.0704	-0.0077	-0.0492	0.0182	-0.072	0.0174	-0.0285	0.1769	0.0601	-0.1014	0.1119	0.0167	0.2235	46.3593	74.8776	47.4158
22	0.0186	-0.0251	0.0055	0.0933	0.0451	0.0497	0.0459	0.0786	0.0568	-0.0764	0.0189	0.0354	-0.071	-0.0456	0.0952	0.1138	0.0144	-0.0446	0.0649	0.1425	0.2483	52.7471	70.6709	45.626

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 (resseq 1:66)	A	1 - 66
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 67:87)	A	67 - 87
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 88:204)	A	88 - 204
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 205:247)	A	205 - 247
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 248:310)	A	248 - 310
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 10:15)	B	10 - 15
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 16:52)	B	16 - 52
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 53:101)	B	53 - 101
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 102:153)	B	102 - 153
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 1:66)	C	1 - 66
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 67:87)	C	67 - 87
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 88:217)	C	88 - 217
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 218:265)	C	218 - 265
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 266:310)	C	266 - 310
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 10:14)	D	10 - 14
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 15:25)	D	15 - 25
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 26:41)	D	26 - 41
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 42:57)	D	42 - 57
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 58:81)	D	58 - 81
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 82:92)	D	82 - 92
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 93:114)	D	93 - 114
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 115:153)	D	115 - 153

-
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