PDB-5l3s: Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY

ID or keywords:

Entry

Database: PDB / ID: 5l3s

Title

Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY

Components

(Signal recognition particle ...) x 2

Keywords

PROTEIN TRANSPORT / Co-translational protein targeting / Signal Recognition Particle / GTPase

Function / homology

Function and homology information

signal recognition particle / signal recognition particle binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Sulfolobus acidocaldarius (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Bange, G. / Wild, K. / Sinning, I.

Funding support

Germany, 1items

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.
Authors: Wild, K. / Bange, G. / Motiejunas, D. / Kribelbauer, J. / Hendricks, A. / Segnitz, B. / Wade, R.C. / Sinning, I.

History

Deposition	May 24, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2016	Group: Database references
Revision 1.2	Oct 16, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell / Item: _pdbx_audit_support.funding_organization
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5l3s.cif.gz	922.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5l3s.ent.gz	762.9 KB	Display	PDB format
PDBx/mmJSON format	5l3s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5l3s_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	5l3s_full_validation.pdf.gz	4 MB	Display
Data in XML	5l3s_validation.xml.gz	95.7 KB	Display
Data in CIF	5l3s_validation.cif.gz	132.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l3/5l3s ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l3s	HTTPS FTP

-
Related structure data

Related structure data	5l3qC 5l3rC 5l3vC 5l3wC C: citing same article (ref.)
Similar structure data	4n4k-d 1z59-d 5osg-d 2hkj-d 4luq-1 6hs0-d 3ihy-5 5k94-1 1hk2-d 6y32-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Signal recognition particle 54 kDa protein

B: Signal recognition particle receptor FtsY

C: Signal recognition particle 54 kDa protein

D: Signal recognition particle receptor FtsY

E: Signal recognition particle 54 kDa protein

F: Signal recognition particle receptor FtsY

G: Signal recognition particle 54 kDa protein

H: Signal recognition particle receptor FtsY

hetero molecules

275 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Signal recognition particle 54 kDa protein

B: Signal recognition particle receptor FtsY

hetero molecules

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

2

C: Signal recognition particle 54 kDa protein

D: Signal recognition particle receptor FtsY

hetero molecules

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

3

E: Signal recognition particle 54 kDa protein

F: Signal recognition particle receptor FtsY

hetero molecules

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

4

G: Signal recognition particle 54 kDa protein

H: Signal recognition particle receptor FtsY

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.196, 199.672, 124.869
Angle α, β, γ (deg.)	90.00, 92.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Signal recognition particle ... , 2 types, 8 molecules ACEGBDFH

#1: Protein	Signal recognition particle 54 kDa protein / SRP54 Mass: 33113.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: srp54, SSO0971 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE7
#2: Protein	Signal recognition particle receptor FtsY / SRP receptor / Docking protein / P41 Mass: 33440.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 Gene: ftsY, dpa, sso, Saci_1462 / Production host: Escherichia coli (E. coli) / References: UniProt: P27414

#1: Protein

Signal recognition particle 54 kDa protein / SRP54

Mass: 33113.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: srp54, SSO0971 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q97ZE7

#2: Protein

Signal recognition particle receptor FtsY / SRP receptor / Docking protein / P41

Mass: 33440.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: ftsY, dpa, sso, Saci_1462 / Production host:

Escherichia coli (E. coli) / References: UniProt: P27414

-
Non-polymers , 6 types, 1261 molecules

#3: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER Mass: 522.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃ Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-G / GUANOSINE-5'-MONOPHOSPHATE Type: RNA linking / Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1214 / 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: 2.39 Å³/Da / Density % sol: 48.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 5.8, 1.26 M ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.9→37.87 Å / Num. obs: 191335 / % possible obs: 97.3 % / Redundancy: 11.7 % / Net I/σ(I): 11.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Resolution: 1.9→37.87 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.39

	R_factor	Num. reflection	% reflection
R_free	0.2162	3853	2.01 %
R_work	0.1732	-	-
obs	0.1741	191275	97.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.9→37.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17248	0	513	1214	18975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	18118
X-RAY DIFFRACTION	f_angle_d	1.016	24554
X-RAY DIFFRACTION	f_dihedral_angle_d	13.822	6805
X-RAY DIFFRACTION	f_chiral_restr	0.067	2819
X-RAY DIFFRACTION	f_plane_restr	0.004	3019

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 (%)
1.8976-1.9208	0.3412	108	0.298	5444	X-RAY DIFFRACTION	80
1.9208-1.9451	0.3059	141	0.2788	6338	X-RAY DIFFRACTION	93
1.9451-1.9707	0.3057	134	0.2652	6748	X-RAY DIFFRACTION	98
1.9707-1.9977	0.3319	142	0.2454	6751	X-RAY DIFFRACTION	99
1.9977-2.0262	0.2887	129	0.23	6777	X-RAY DIFFRACTION	99
2.0262-2.0565	0.2838	143	0.2283	6829	X-RAY DIFFRACTION	99
2.0565-2.0886	0.3169	152	0.2175	6679	X-RAY DIFFRACTION	98
2.0886-2.1228	0.2547	143	0.2072	6817	X-RAY DIFFRACTION	99
2.1228-2.1594	0.2489	124	0.1935	6749	X-RAY DIFFRACTION	98
2.1594-2.1987	0.2123	125	0.1811	6774	X-RAY DIFFRACTION	98
2.1987-2.241	0.2207	154	0.1786	6780	X-RAY DIFFRACTION	98
2.241-2.2867	0.2135	139	0.1778	6720	X-RAY DIFFRACTION	98
2.2867-2.3364	0.2311	144	0.173	6769	X-RAY DIFFRACTION	98
2.3364-2.3908	0.2277	152	0.1683	6639	X-RAY DIFFRACTION	98
2.3908-2.4505	0.2	146	0.1647	6811	X-RAY DIFFRACTION	98
2.4505-2.5168	0.2314	126	0.1653	6640	X-RAY DIFFRACTION	97
2.5168-2.5908	0.2242	118	0.168	6745	X-RAY DIFFRACTION	98
2.5908-2.6744	0.2392	152	0.1693	6749	X-RAY DIFFRACTION	98
2.6744-2.77	0.205	140	0.1714	6687	X-RAY DIFFRACTION	98
2.77-2.8809	0.2051	122	0.1732	6756	X-RAY DIFFRACTION	98
2.8809-3.0119	0.2316	139	0.1744	6765	X-RAY DIFFRACTION	98
3.0119-3.1706	0.2083	143	0.1721	6672	X-RAY DIFFRACTION	97
3.1706-3.3692	0.2179	128	0.1663	6706	X-RAY DIFFRACTION	97
3.3692-3.6291	0.1587	141	0.1514	6702	X-RAY DIFFRACTION	97
3.6291-3.994	0.1612	123	0.1467	6769	X-RAY DIFFRACTION	98
3.994-4.5711	0.1882	142	0.1423	6878	X-RAY DIFFRACTION	99
4.5711-5.7558	0.1962	143	0.1591	6911	X-RAY DIFFRACTION	100
5.7558-37.8807	0.2243	160	0.1738	6817	X-RAY DIFFRACTION	98

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	5.103	4.2969	-3.1621	7.442	-5.1633	3.6207	-0.1997	-0.2359	-0.6048	0.3348	0.1668	0.0653	0.4816	-0.234	0.0376	0.6808	-0.0761	0.0637	0.2752	0.0454	0.4064	-11.1945	-21.5759	59.8248
2	6.6092	3.6299	-3.5114	3.4235	-5.0181	8.9601	0.2939	-0.0303	0.1797	1.1024	0.0648	0.6131	-0.8008	-0.2062	-0.3187	0.8849	0.0094	0.1525	0.3966	0.0522	0.5287	-16.0578	-16.6372	67.9352
3	1.1684	0.4177	0.092	1.7751	0.3493	1.3897	0.0343	-0.1339	-0.12	0.3979	-0.0192	-0.0468	0.1744	0.0215	-0.0069	0.3449	0.0171	-0.001	0.1638	0.0146	0.1408	5.0384	8.5504	57.1306
4	2.1485	1.5642	0.6881	5.451	0.4495	0.3552	0.1221	0.3266	-0.5053	0.0401	-0.0159	-0.0326	0.7492	0.0083	-0.0072	0.7134	-0.064	-0.0288	0.2801	-0.0925	0.4025	-6.2508	-29.6632	37.5672
5	3.9112	-2.1276	1.6489	9.2275	-7.0923	7.6286	0.0979	0.3242	-0.4093	-1.1099	-0.0019	0.2496	0.409	0.2293	-0.1024	0.4396	-0.1065	0.037	0.2769	-0.166	0.3493	-2.0508	-23.4574	29.8567
6	1.1984	-0.083	0.2308	1.891	-0.2683	1.4335	-0.0344	0.2306	-0.0225	-0.3839	0.0398	0.03	0.099	-0.0715	-0.0038	0.2793	-0.0161	0.0108	0.1864	-0.0219	0.1245	-2.4617	9.7925	29.9805
7	3.6476	2.5069	0.9042	5.3404	1.0033	1.1651	0.0586	0.2086	-0.4109	-0.2113	0.0571	-0.257	0.4558	0.0464	-0.0752	0.4255	-0.0188	0.022	0.2009	-0.0579	0.2011	2.1707	-7.8623	31.9857
8	1.3436	0.0492	-0.3053	1.749	0.3223	0.6482	0.1358	-0.3877	-0.7582	0.3956	-0.0338	0.4111	0.7905	-0.4678	0.0596	0.8979	-0.2818	-0.0873	0.4795	0.2429	0.6887	-11.762	-5.6426	118.5638
9	5.0313	0.5022	-2.1394	2.3812	-0.7208	4.0555	-0.0268	-0.4026	-0.0914	0.2694	-0.0297	0.0106	-0.0891	0.2824	0.0517	0.3176	-0.0082	-0.0101	0.1465	0.0283	0.152	3.415	19.7362	115.7709
10	3.2315	-0.9278	-0.4535	3.3679	1.4003	2.4656	0.108	-0.2141	-0.0535	0.2213	-0.0213	-0.1989	0.1056	0.2394	-0.0904	0.3082	-0.0495	-0.0099	0.2008	0.0431	0.1614	7.1252	21.2744	116.4857
11	7.3992	5.0606	6.5391	7.3313	5.6542	8.4947	0.1841	0.3035	-0.7878	-0.1239	0.1915	-0.8789	0.3411	0.9014	-0.3374	0.3959	0.1184	-0.0299	0.324	0.0594	0.4476	13.4902	6.5957	111.19
12	2.9841	-0.7191	1.205	2.2527	-1.0244	2.7802	0.2725	-0.247	-0.6371	0.1535	-0.104	-0.0521	0.6174	0.0231	-0.1513	0.543	-0.0547	-0.0314	0.2428	0.0903	0.332	-2.8351	2.3632	114.5348
13	3.3278	0.7501	-0.5493	7.2251	-1.5148	4.7726	0.2448	-0.3737	-0.6125	1.1083	-0.265	0.5883	0.1051	-0.7432	0.0209	0.3758	-0.1415	0.0562	0.4792	0.0781	0.371	-15.3631	7.2745	117.7602
14	1.0793	-0.7088	-0.0155	8.5694	3.2583	1.3869	-0.2137	0.2864	-0.8336	0.0684	0.3895	0.1817	1.2501	-0.2132	-0.1521	1.1263	-0.2116	-0.0492	0.5536	-0.1799	0.9694	-11.345	-16.6629	89.9671
15	2.8491	0.6956	-0.0931	0.3959	-0.5541	3.9527	0.0056	0.3831	-0.0331	-0.3506	0.0054	0.0316	-0.2693	-0.1903	-0.0199	0.4685	0.046	0.0196	0.2413	-0.0183	0.1651	-4.4652	21.5952	89.1288
16	2.5794	0.1006	-0.3473	1.4252	0.1997	2.7663	0.142	0.3	-0.3573	-0.3083	-0.0757	0.0713	0.1969	-0.3753	-0.0559	0.4229	0.0065	-0.0195	0.2928	-0.068	0.2094	-10.3088	11.5312	91.4218
17	4.3173	2.4008	0.9124	4.2235	2.8338	2.1646	-0.1626	-0.2447	1.5283	0.7821	0.0142	-0.2681	-1.1627	0.6748	0.0901	1.1836	-0.266	-0.1586	0.5183	-0.0598	0.9211	28.2777	78.583	122.1703
18	3.0375	3.7568	0.1045	7.209	0.4342	0.0859	0.0538	-0.726	0.6465	0.6089	-0.3754	-0.2627	-0.559	0.5267	0.21	0.9781	-0.3323	-0.2282	0.6529	-0.0481	0.6559	26.1715	64.1032	131.8041
19	1.7833	0.5342	-0.0909	2.5801	-2.1751	6.1535	0.1036	-0.1078	0.1098	0.0677	-0.1928	-0.091	0.2342	0.1552	0.0963	0.3101	-0.0438	0.0193	0.1536	-0.0193	0.1173	14.7404	44.5056	120.6243
20	5.8585	-0.489	3.8304	2.2786	-1.077	8.8915	-0.0282	-0.3082	0.0558	0.2725	0.1312	0.0924	0.0243	-0.391	-0.1176	0.2209	-0.0205	0.0446	0.0977	-0.0139	0.1444	9.2107	40.5984	117.2247
21	9.2652	-1.7574	3.8426	3.213	0.0847	4.4706	0.1104	0.1886	-0.3142	-0.1566	0.0491	0.0483	0.2032	-0.0745	-0.1659	0.2323	-0.021	0.0368	0.1348	0.0178	0.1399	8.0255	35.1458	113.9227
22	3.3102	-0.7518	0.5717	5.5411	-5.3431	8.5324	0.0913	-0.2869	0.0621	0.4808	-0.0256	0.285	-0.0982	-0.3036	-0.1081	0.2609	-0.0289	0.0643	0.1839	-0.0781	0.1424	3.2625	42.2349	120.8471
23	7.9607	4.41	-4.6273	9.1763	-5.1611	8.5202	0.164	0.3887	0.9709	-0.0205	0.0614	1.1688	-0.6288	-1.2475	-0.2457	0.3355	0.1012	0.0591	0.329	-0.0353	0.4964	-1.0614	54.2455	115.1164
24	7.3613	1.9906	-2.4257	3.5431	-1.1816	4.1212	0.0222	0.0064	0.8367	0.3833	-0.0508	0.3758	-0.3912	-0.1675	0.0138	0.4349	-0.0506	0.0081	0.1731	-0.0483	0.2454	10.8881	58.9846	117.7314
25	5.7129	-1.2609	-0.3422	3.1957	0.3084	2.399	0.0224	-0.1763	0.5085	0.4976	-0.141	0.1584	-0.2289	0.0405	0.0871	0.4122	-0.0866	0.0085	0.2495	-0.0402	0.26	19.2814	57.1139	120.4157
26	2.7329	2.1833	0.2295	4.3778	3.4764	5.8413	0.1368	-0.0817	0.1157	0.8588	-0.1319	-0.6458	0.0352	0.3573	0.0059	0.3668	-0.0514	-0.1121	0.3216	0.015	0.2931	27.9386	52.5946	121.5282
27	3.0133	2.7513	-0.5964	8.6037	-0.8008	5.1226	0.1104	0.1673	0.3516	-0.0181	0.1962	0.2786	-0.2826	-0.3773	-0.3207	0.4536	-0.0739	0.0204	0.4387	0.2125	0.5746	24.4955	83.7062	97.0566
28	2.3873	0.4264	-0.7637	1.5285	-0.0303	4.0796	-0.0685	0.6202	0.0412	-0.5927	0.0146	-0.0124	0.2742	0.4775	0.062	0.4459	-0.0122	0.0068	0.4253	0.0612	0.1751	17.0886	43.1647	90.925
29	1.4569	-0.3494	0.2504	2.7121	-0.4021	2.1411	-0.0132	0.4076	0.1578	-0.3599	-0.0689	-0.1182	-0.0607	0.6211	0.0747	0.3621	-0.0578	0.0255	0.475	0.1031	0.2268	25.6955	50.4619	95.0629
30	1.8825	0.8393	-1.6935	7.3265	-2.5346	2.3123	0.0232	0.5565	0.8327	-0.2435	0.1185	0.2278	-0.6319	0.4396	-0.0923	0.5074	-0.1266	-0.1158	0.4659	0.2508	0.5354	11.5846	63.3237	94.1029
31	5.2266	4.1679	3.3631	5.6871	3.8934	3.2074	-0.3151	0.0696	0.4163	-0.1278	0.1226	0.4871	-0.6629	0.2653	0.1869	0.7062	-0.0748	0.0105	0.2701	-0.052	0.4771	31.4054	75.7218	54.6761
32	2.204	4.0609	-1.0545	7.0866	-2.0026	0.4993	0.5935	-0.7971	0.0802	0.9874	-0.8218	-0.3949	-0.0905	0.2777	0.1908	0.8279	-0.1952	-0.0133	0.5794	-0.1541	0.5722	29.4916	64.4769	66.8691
33	1.6373	0.8654	-0.5452	2.2765	-0.1648	1.2467	0.112	-0.1691	0.2975	0.2506	-0.056	0.22	-0.1673	-0.0748	-0.0409	0.3156	-0.0044	0.0251	0.1775	-0.0583	0.2189	13.547	44.5008	53.3879
34	2.9306	2.5028	0.0329	6.9436	1.6474	2.7503	0.1474	-0.2969	0.3102	0.9035	-0.2728	-0.4163	-0.1381	0.2303	0.1158	0.3645	-0.0497	-0.1129	0.2632	-0.0318	0.2943	31.0973	50.1412	58.0409
35	1.1243	-0.1409	0.01	1.7369	-0.6404	0.6246	-0.0345	0.2143	0.6708	-0.3839	0.1313	-0.0917	-0.7042	0.1356	-0.0627	0.8231	-0.139	0.0384	0.3494	0.0864	0.6124	29.7904	66.4984	27.5547
36	3.6687	-0.0711	0.2471	1.7308	-0.1816	1.7731	-0.0488	0.1263	-0.0375	-0.1418	0.0059	-0.0622	0.1662	0.0362	0.036	0.2907	-0.0139	0.0145	0.1254	-0	0.1399	27.4376	33.0343	31.7481
37	2.6703	-0.1215	-0.3448	3.2023	-0.2178	2.4263	-0.0349	0.1707	0.4608	-0.2344	0.1053	-0.1268	-0.3721	0.2674	-0.0777	0.3492	-0.0852	0.0067	0.202	0.0247	0.2597	30.9006	52.1813	32.3286
38	1.2183	1.0026	-1.2748	3.0562	-1.2811	1.435	-0.0311	0.6036	0.8396	-0.0933	0.0669	0.2362	-0.6746	0.0654	-0.0597	0.5872	-0.094	-0.1094	0.314	0.2145	0.536	18.1064	56.6141	27.7181
39	8.7455	-6.699	5.5844	5.1765	-4.4208	4.0466	-0.4718	0.2922	0.7412	-0.49	0.194	0.7834	-1.2144	-1.2437	0.2054	0.9225	0.2098	-0.0592	0.8879	0.2942	0.9783	1.7183	40.6817	103.1594
40	2.6268	-0.2941	1.2873	1.4103	-0.6169	0.7965	-0.3324	0.1544	-0.1595	-0.6392	0.2715	-0.8496	0.4262	1.2869	0.057	1.1272	-0.1353	0.1696	1.3284	-0.0633	1.157	16.4078	16.9773	40.9009
41	1.3245	-2.7201	-1.1927	5.6212	2.4734	1.0914	-0.4474	0.7405	-0.4932	-1.0211	-0.0884	-1.2116	1.0059	1.4409	0.4102	0.6486	0.3053	0.1774	0.9405	0.0321	1.0405	10.7391	22.4914	101.6084
42	3.2698	-3.7187	4.1024	4.242	-4.67	5.148	-0.4353	1.2169	0.7082	-1.1003	-0.1862	1.1355	-1.1047	-1.154	0.4896	0.525	0.0604	-0.1562	0.9718	0.0574	0.6097	7.9822	34.2303	38.2116

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 292 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 86 through 137 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 138 through 157 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 158 through 328 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 329 through 368 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 16 through 122 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 123 through 138 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 139 through 192 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 193 through 209 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 210 through 271 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 272 through 292 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 92 through 156 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 157 through 239 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 240 through 368 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 16 through 57 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 58 through 96 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 97 through 122 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 123 through 138 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 139 through 162 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 163 through 192 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 193 through 209 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 210 through 236 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 237 through 271 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 272 through 292 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 85 through 157 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 158 through 239 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 240 through 346 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 347 through 368 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 16 through 57 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 58 through 96 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 97 through 271 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 272 through 292 )
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 90 through 185 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 186 through 284 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 285 through 346 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 347 through 368 )
39	X-RAY DIFFRACTION	39	chain 'O' and (resid 1 through 1 )
40	X-RAY DIFFRACTION	40	chain 'P' and (resid 2 through 2 )
41	X-RAY DIFFRACTION	41	chain 'Q' and (resid 3 through 3 )
42	X-RAY DIFFRACTION	42	chain 'R' and (resid 4 through 4 )

-
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

-
Signal recognition particle ... , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 6 types, 1261 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

-Signal recognition particle ... , 2 types, 8 molecules ACEGBDFH

-Non-polymers , 6 types, 1261 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

-
Signal recognition particle ... , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 6 types, 1261 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