PDB-2q80: Crystal structure of human geranylgeranyl pyrophosphate synthase ...

ID or keywords:

Entry

Database: PDB / ID: 2q80

Title

Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP

Components

Geranylgeranyl pyrophosphate synthetase

Keywords

TRANSFERASE /

isoprenoid pathway / isopentenyl transferase /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase /

farnesyltranstransferase activity /

Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process /

dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase /

geranyltranstransferase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Kavanagh, K.L. / Dunford, J.E. / Bunkoczi, G. / Smee, C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding
Authors: Kavanagh, K.L. / Dunford, J.E. / Bunkoczi, G. / Russell, R.G. / Oppermann, U.

History

Deposition	Jun 8, 2007	Deposition site: RCSB / Processing site: PDBJ
Supersession	Jun 19, 2007	ID: 2FVI
Revision 1.0	Jun 19, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Dec 5, 2012	Group: Structure summary
Revision 1.4	Apr 3, 2024	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_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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	2q80.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2q80.ent.gz	280.8 KB	Display	PDB format
PDBx/mmJSON format	2q80.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q8/2q80 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/2q80	HTTPS FTP

-
Related structure data

Similar structure data	4plb-d 6fm4-d 6r4v-d 6z1a-d 6qx2-3 6qx2-2 6qx2-1 5cdn-1 5cdr-d 6qx1-d 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	#201 - Sep 2016 Isoprene Synthase similarity (8) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Geranylgeranyl pyrophosphate synthetase

B: Geranylgeranyl pyrophosphate synthetase

C: Geranylgeranyl pyrophosphate synthetase

D: Geranylgeranyl pyrophosphate synthetase

E: Geranylgeranyl pyrophosphate synthetase

F: Geranylgeranyl pyrophosphate synthetase

hetero molecules

213 kDa, 6 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)	141.248, 141.248, 211.705
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
3	1	E
4	1	B
5	1	C
6	1	F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 2

Dom-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	LYS	LYS	A	A	6 - 296	7 - 297
2	PHE	PHE	D	D	6 - 295	7 - 296
3	PHE	PHE	E	E	6 - 295	7 - 296
4	PHE	PHE	B	B	6 - 295	7 - 296
5	PHE	PHE	C	C	6 - 295	7 - 296
6	PHE	PHE	F	F	6 - 295	7 - 296

#1: Protein	Geranylgeranyl pyrophosphate synthetase Mass: 35002.910 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O95749, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase, geranylgeranyl diphosphate synthase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE / Geranylgeranyl pyrophosphate Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₀H₃₆O₇P₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.51 Å³/Da / Density % sol: 51.06 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2M MG FORMATE, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 / Wavelength: 1.008 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2005
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.008 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.08 Å / Num. all: 59513 / Num. obs: 59513 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Net I/σ(I): 12
Reflection shell	Resolution: 2.7→2.72 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.83 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: GGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)

Resolution: 2.7→47.08 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.905 / SU B: 29.353 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.69 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25329	2211	3.7 %	RANDOM
R_work	0.20246	-	-	-
all	0.20434	57186	-	-
obs	0.20434	57186	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.886 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→47.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13713	0	176	24	13913

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	14222
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9499
X-RAY DIFFRACTION	r_angle_refined_deg	1.389	1.976	19244
X-RAY DIFFRACTION	r_angle_other_deg	0.947	3.001	23066
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.521	5	1698
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.744	24.433	670
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.149	15	2427
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.695	15	69
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2153
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	15585
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2832
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	3505
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	9094
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	6992
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	7042
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	264
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.055	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.103	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.247	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.286	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.161	0.2	3
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	0.438	1.5	8744
X-RAY DIFFRACTION	r_mcbond_other	0.094	1.5	3432
X-RAY DIFFRACTION	r_mcangle_it	0.735	2	13732
X-RAY DIFFRACTION	r_scbond_it	1.167	3	6230
X-RAY DIFFRACTION	r_scangle_it	1.855	4.5	5510
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1673	tight positional	0.16	0.03
2	D	1673	tight positional	0.16	0
3	E	1673	tight positional	0.14	0
4	B	1673	tight positional	0.15	0
5	C	1673	tight positional	0.14	0
6	F	1673	tight positional	0.16	0
1	A	1982	medium positional	0.39	0.25
2	D	1982	medium positional	0.32	0
3	E	1982	medium positional	0.32	0
4	B	1982	medium positional	0.31	0
5	C	1982	medium positional	0.28	0
6	F	1982	medium positional	0.32	0
1	A	1673	tight thermal	0.38	0.5
2	D	1673	tight thermal	0.33	0
3	E	1673	tight thermal	0.32	0
4	B	1673	tight thermal	0.27	0
5	C	1673	tight thermal	0.3	0
6	F	1673	tight thermal	0.29	0
1	A	1982	medium thermal	0.53	2
2	D	1982	medium thermal	0.5	0
3	E	1982	medium thermal	0.45	0
4	B	1982	medium thermal	0.44	0
5	C	1982	medium thermal	0.4	0
6	F	1982	medium thermal	0.45	0

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	144	-
R_work	0.312	4187	-
obs	-	-	100 %

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	2.6177	-0.6893	0.711	1.0551	-0.5743	1.5634	-0.0501	0.2556	-0.0656	-0.1374	-0.068	-0.1512	-0.3288	0.1882	0.1182	-0.1747	-0.0417	0.0323	-0.098	0.0312	-0.2158	-11.065	-53.878	-38.438
2	1.994	0.1171	-0.476	0.8646	-0.0281	1.5494	-0.2251	-0.0178	-0.3365	0.0705	-0.0026	-0.0874	0.1925	0.1686	0.2276	-0.1848	0.0083	-0.0138	-0.1422	0.027	-0.2054	-14.631	-67.523	-30.252
3	6.2195	-0.5969	0.4062	0.4652	-0.6174	1.2602	-0.0431	-0.2851	0.0552	0.1492	0.0113	-0.0622	-0.1268	-0.0559	0.0318	-0.1434	-0.0342	-0.0358	-0.1883	-0.0093	-0.2335	-21.916	-56.864	-17.444
4	2.9682	-1.3277	-1.9798	1.268	1.2627	1.5315	-0.1792	0.1109	-0.4313	0.1326	-0.0629	0.045	0.3399	-0.2021	0.2422	-0.0602	-0.0566	0.0361	-0.0583	-0.0786	-0.1268	-22.925	-74.487	-50.075
5	3.5914	-2.7301	-0.8077	2.9805	0.3366	1.29	-0.018	0.1612	-0.0111	-0.1216	-0.0564	-0.1371	-0.1113	-0.0321	0.0745	-0.1386	-0.042	0.0399	-0.0434	-0.0699	-0.2476	-14.683	-63.172	-58.552
6	3.2621	-2.2632	-1.6699	2.7171	1.1935	0.8559	0.1051	0.8187	-0.3513	-0.2627	-0.3552	0.2492	-0.0491	-0.6285	0.25	-0.0468	0.0573	-0.0213	0.4059	-0.1456	-0.2132	-28.944	-62.039	-69.337
7	2.983	0.6682	-0.7298	1.2819	-0.2582	1.6022	-0.0077	0.4489	-0.2044	-0.1059	0.0026	0.2836	0.0267	-0.5375	0.0052	-0.1371	-0.0662	-0.0359	0.1281	-0.0872	-0.1144	-72.9	-64.427	-30.334
8	5.1709	-1.2394	-1.5881	0.5308	-0.0101	2.4459	-0.2422	0.1538	-0.5841	0.2661	0.022	0.1446	0.3433	-0.1753	0.2203	-0.1187	-0.1314	0.0291	-0.131	-0.0538	-0.0763	-63.127	-73.348	-20.724
9	5.4846	1.9475	-2.6251	2.1916	-1.3808	1.8249	-0.4724	0.5609	-0.787	-0.3051	0.1362	-0.0826	0.4959	-0.4376	0.3363	0.0159	-0.1585	0.055	0.0691	-0.2239	0.0552	-56.167	-81.003	-35.642
10	1.6038	0.1834	-1.2017	0.9743	0.1571	1.3575	-0.0053	-0.044	-0.1758	0.066	-0.016	-0.1301	0.1687	-0.1573	0.0212	-0.1424	-0.0103	-0.0326	-0.0815	0.0218	-0.2162	-58.66	-53.635	-11.137
11	1.2498	0.6345	-1.3399	1.7537	-0.4838	1.7585	0.1098	0.2303	0.0022	0.0834	-0.0409	0.2707	-0.0152	-0.4568	-0.0688	-0.196	0.0171	-0.02	0.0142	0	-0.2536	-71.807	-46.116	-17.536
12	2.002	-0.2413	-2.1604	0.6736	-0.4578	4.4592	0.2397	0.0166	0.3023	0.0183	-0.0801	-0.1202	-0.2548	0.0049	-0.1597	-0.1205	0.0419	0.0302	-0.0561	0.0344	-0.2069	-61.505	-31.337	-19.143
13	1.7638	0.7282	-0.8618	1.4347	-1.4977	1.727	0.2785	0.3072	0.5348	0.2255	-0.0066	0.3332	-0.4089	-0.3634	-0.2718	-0.0026	0.2653	0.154	0.1604	0.2161	-0.0364	-48.962	-17.162	-50.93
14	3.1257	-1.8745	0.4153	1.9015	-0.9324	1.0066	0.0604	0.5878	0.5212	-0.0725	0.1271	-0.0306	-0.1874	-0.1443	-0.1874	-0.1253	0.1693	0.091	0.2394	0.2505	-0.0982	-37.559	-19.798	-62
15	2.1655	-0.4875	-0.2011	4.9015	-1.0808	1.294	0.0766	0.2623	0.3997	0.2618	0.1527	0.0211	-0.4141	-0.1121	-0.2294	-0.0677	0.0942	0.0634	-0.0115	0.083	-0.1604	-26.114	-21.785	-48.423
16	0.6319	-1.0596	0.27	2.0843	-1.3159	2.5376	0.1386	0.7075	0.1981	-0.3303	0.0817	0.0556	0.1189	-0.154	-0.2204	-0.0746	0.2016	0.027	0.6974	0.1664	-0.1655	-52.735	-33.751	-70.785
17	0.6447	1.3174	-1.3281	2.8421	-2.324	3.7502	-0.0463	0.3487	0.4777	-0.0476	0.318	0.2529	-0.1803	-0.6679	-0.2717	-0.1151	0.2512	0.0279	0.5687	0.2635	-0.0821	-65.327	-27.562	-62.57
18	1.6765	-0.7073	0.4961	3.1707	-3.2969	5.9592	0.2109	0.7081	-0.0114	-0.5615	0.3122	0.4441	0.5023	-0.9328	-0.523	-0.0749	0.0071	-0.0776	0.7803	0.1123	-0.1275	-72.224	-43.993	-60.921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	6 - 106	7 - 107
2	X-RAY DIFFRACTION	2	A	A	107 - 168	108 - 169
3	X-RAY DIFFRACTION	3	A	A	169 - 296	170 - 297
4	X-RAY DIFFRACTION	4	B	B	6 - 106	7 - 107
5	X-RAY DIFFRACTION	5	B	B	107 - 168	108 - 169
6	X-RAY DIFFRACTION	6	B	B	169 - 295	170 - 296
7	X-RAY DIFFRACTION	7	C	C	6 - 106	7 - 107
8	X-RAY DIFFRACTION	8	C	C	107 - 168	108 - 169
9	X-RAY DIFFRACTION	9	C	C	169 - 295	170 - 296
10	X-RAY DIFFRACTION	10	D	D	6 - 106	7 - 107
11	X-RAY DIFFRACTION	11	D	D	107 - 168	108 - 169
12	X-RAY DIFFRACTION	12	D	D	169 - 295	170 - 296
13	X-RAY DIFFRACTION	13	E	E	6 - 106	7 - 107
14	X-RAY DIFFRACTION	14	E	E	107 - 168	108 - 169
15	X-RAY DIFFRACTION	15	E	E	169 - 295	170 - 296
16	X-RAY DIFFRACTION	16	F	F	6 - 106	7 - 107
17	X-RAY DIFFRACTION	17	F	F	107 - 168	108 - 169
18	X-RAY DIFFRACTION	18	F	F	169 - 295	170 - 296

-
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