PDB-6ylb: Crystal structure of the SAM-SAH riboswitch with SAM

ID or keywords:

Entry

Database: PDB / ID: 6ylb

Title

Crystal structure of the SAM-SAH riboswitch with SAM

Components

Chains: A,C,F,I,M,O
Chains: B,D,G,J,N,P

Keywords

RNA / Pseudoknot / SAM / Riboswitch

Function / homology

S-ADENOSYLMETHIONINE / RNA / RNA (> 10)

Function and homology information

Biological species

Roseobacter sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Huang, L. / Lilley, D.M.J.

Funding support

United Kingdom,

China, 2items

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.

History

Deposition	Apr 7, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6ylb.cif.gz	365.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6ylb.ent.gz	251 KB	Display	PDB format
PDBx/mmJSON format	6ylb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6ylb_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	6ylb_full_validation.pdf.gz	2.5 MB	Display
Data in XML	6ylb_validation.xml.gz	12.2 KB	Display
Data in CIF	6ylb_validation.cif.gz	16.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/6ylb ftp://data.pdbj.org/pub/pdb/validation_reports/yl/6ylb	HTTPS FTP

-
Related structure data

Related structure data	6yl5SC 6ymiC 6ymjC 6ymkC 6ymlC 6ymmC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ymk-d 6ymi-d 6ymj-d 6yl5-d 6hx7-d 3luo-2 3efh-2 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	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)

Deposited unit

A: Chains: A,C,F,I,M,O

B: Chains: B,D,G,J,N,P

C: Chains: A,C,F,I,M,O

D: Chains: B,D,G,J,N,P

F: Chains: A,C,F,I,M,O

G: Chains: B,D,G,J,N,P

I: Chains: A,C,F,I,M,O

J: Chains: B,D,G,J,N,P

M: Chains: A,C,F,I,M,O

N: Chains: B,D,G,J,N,P

O: Chains: A,C,F,I,M,O

P: Chains: B,D,G,J,N,P

hetero molecules

71.3 kDa, 12 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)	87.113, 147.937, 74.839
Angle α, β, γ (deg.)	90.000, 91.707, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: RNA chain	Chains: A,C,F,I,M,O Mass: 8389.874 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain	Chains: B,D,G,J,N,P Mass: 2895.791 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.66 Å³/Da / Density % sol: 66.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9119 Å / Relative weight: 1
Reflection	Resolution: 2.12→75.04 Å / Num. obs: 98596 / % possible obs: 99.9 % / Redundancy: 3.3 % / B_iso Wilson estimate: 57.35 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.056 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.12→2.16 Å / Redundancy: 3.2 % / R_merge(I) obs: 1.15 / Num. unique obs: 2658 / CC_1/2: 0.36 / R_pim(I) all: 0.76 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YL5

6yl5

Resolution: 2.12→37.46 Å / SU ML: 0.4024 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2627	4850	4.92 %
R_work	0.2248	93746	-
obs	0.2266	98596	93.04 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 83.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→37.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	4452	193	95	4740

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	5179
X-RAY DIFFRACTION	f_angle_d	1.2232	8038
X-RAY DIFFRACTION	f_chiral_restr	0.053	1068
X-RAY DIFFRACTION	f_plane_restr	0.009	219
X-RAY DIFFRACTION	f_dihedral_angle_d	15.1243	2566

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 (%)
2.12-2.14	0.4601	89	0.3939	1983	X-RAY DIFFRACTION	58.53
2.14-2.17	0.3777	91	0.3689	2114	X-RAY DIFFRACTION	62.25
2.17-2.2	0.3485	125	0.3683	2391	X-RAY DIFFRACTION	71.15
2.2-2.22	0.3817	167	0.3573	2847	X-RAY DIFFRACTION	86.48
2.22-2.25	0.3719	181	0.3619	3250	X-RAY DIFFRACTION	96.4
2.25-2.28	0.3251	162	0.3534	3289	X-RAY DIFFRACTION	97.62
2.28-2.32	0.3955	193	0.348	3233	X-RAY DIFFRACTION	97.58
2.32-2.35	0.3353	173	0.3396	3267	X-RAY DIFFRACTION	97.09
2.35-2.39	0.3857	219	0.3437	3223	X-RAY DIFFRACTION	97.15
2.39-2.43	0.3229	267	0.3402	3075	X-RAY DIFFRACTION	96.37
2.43-2.47	0.3493	216	0.3282	3237	X-RAY DIFFRACTION	96.7
2.47-2.51	0.3963	147	0.3311	3348	X-RAY DIFFRACTION	97.57
2.51-2.56	0.3334	163	0.3117	3234	X-RAY DIFFRACTION	97.5
2.56-2.61	0.361	209	0.3294	3206	X-RAY DIFFRACTION	97.24
2.61-2.67	0.3399	249	0.3225	3219	X-RAY DIFFRACTION	97.03
2.67-2.73	0.3593	142	0.3213	3248	X-RAY DIFFRACTION	96.8
2.73-2.8	0.3922	180	0.305	3245	X-RAY DIFFRACTION	96.64
2.8-2.88	0.4166	124	0.2951	3265	X-RAY DIFFRACTION	95.9
2.88-2.96	0.2576	94	0.2783	3281	X-RAY DIFFRACTION	95.23
2.96-3.06	0.2754	104	0.2594	3237	X-RAY DIFFRACTION	94.11
3.06-3.17	0.292	141	0.2579	3088	X-RAY DIFFRACTION	92.73
3.17-3.29	0.2935	146	0.2345	3276	X-RAY DIFFRACTION	96.86
3.29-3.44	0.2392	163	0.2127	3288	X-RAY DIFFRACTION	97.27
3.44-3.62	0.2151	120	0.2061	3248	X-RAY DIFFRACTION	95.76
3.62-3.85	0.2348	171	0.1895	3298	X-RAY DIFFRACTION	98.11
3.85-4.15	0.2498	115	0.1935	3383	X-RAY DIFFRACTION	98.7
4.15-4.56	0.2447	168	0.1855	3277	X-RAY DIFFRACTION	97.51
4.57-5.22	0.2838	147	0.1779	3188	X-RAY DIFFRACTION	95.01
5.22-6.58	0.1964	142	0.1696	3268	X-RAY DIFFRACTION	95.79
6.58-37.46	0.1657	242	0.1433	3240	X-RAY DIFFRACTION	98.33

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	4.19822513395	0.497675999689	0.0802686229149	1.04466518505	0.00480080860612	-0.320535276556	-0.0772445122157	0.0423938818831	0.499453671128	-0.37421514941	0.0840707824473	0.283059486604	-0.0271122038162	-0.101075264933	0.0470947814971	0.539554486358	-0.0462251286919	-0.0399253719619	0.509703556893	0.00474021276554	0.441691809245	34.2649220698	12.5991204856	25.1824110713
2	0.371170372085	0.36424535325	-0.264124738959	2.47731802793	-0.602863148941	1.69342274534	-0.0838281026832	0.21586516287	-0.0090231940171	-0.438768955096	0.260743093793	0.256963958798	0.0450691048721	-0.183305762907	-0.0814650939015	0.516791150814	-0.0125642735647	-0.078191367682	0.676426721774	0.0454588012452	0.550172694285	25.7176405933	11.8273525782	21.0552424369
3	0.754448116993	-0.19765361409	0.923931468203	0.330240055046	-0.322907826462	0.386749953117	0.0879542120023	-0.228140272117	0.0739600857499	0.503248510325	-0.00869553819163	0.290834133276	-0.295186161324	0.0153003154163	-0.144901019409	0.519618197205	-0.047769852719	0.0785742377667	0.573678350279	0.00770074231228	0.605509076048	45.4752104332	22.9924494936	27.5443765552
4	2.94321145725	-0.283046917289	2.18097417039	0.987635676638	-0.741261987579	1.66075683097	-0.575699652192	0.316931662948	0.880264922469	-0.315137450248	-0.0276204460214	-1.1466662045	-0.235133165222	0.28936765999	0.664487639691	0.542074212292	-0.172472307964	-0.0906992115673	1.02217795807	-0.0680158623276	0.981896537115	-4.57092207106	3.99150702993	11.6439210722
5	2.62679261238	1.01502036116	-0.137920797535	5.4446109803	4.1701574636	3.65097415774	-0.10786697719	-0.0348455495477	-0.48204886853	-0.567015987424	0.189527371859	0.119351210774	-0.309897272287	0.938772078016	-0.11169475618	0.551426472562	-0.107208949934	0.0702165880766	0.663742320778	-0.026718242918	0.358410774971	-18.2225710902	-2.15628477111	7.45269327746
6	1.36577320121	-0.517157922404	-0.972217427864	1.37703408874	0.0639201675827	2.51051873295	-0.747704506122	0.546550012517	0.135969194622	0.175133658667	0.412316570029	-1.01143847666	-0.359208246959	0.0722006210843	0.417206027113	0.673835450063	-0.309279637893	-0.158023340426	0.883663631092	0.00515569405639	0.948143600287	0.196051301158	6.76618849164	12.7119763762
7	1.88563434654	1.01741063094	0.989073623734	4.0732183815	-0.372535947518	4.64236790946	0.128722732808	-0.774463956941	0.0698426774186	-0.609404323466	0.166152976322	-0.689505194083	0.813840162126	-0.134716207123	-0.148452747446	0.658685929162	0.0202211116487	0.0396665646411	0.709034882512	-0.161622985788	0.618218583107	-14.3698871627	-10.6979333001	11.1503954807
8	1.08323578205	0.663207288367	0.8623549106	0.981125092241	-0.674378213481	1.06869190189	-0.206459237067	0.39364364176	-0.316698294112	0.175774301552	0.125924175134	0.123630050829	0.0132158837086	0.0455154150644	0.00443830856599	0.501656555377	0.0407793113693	0.0397466443996	0.569215896839	-0.0769265243695	0.363985596574	-4.99860267377	56.7723418981	23.0523928497
9	2.27399235022	-2.3338604277	1.8483870566	2.88262225553	-2.65139662974	4.69080234576	-0.265717129314	-0.311357648691	0.235790346366	-0.294835499702	-0.203226386957	-0.157593350562	0.293195857249	-0.172840841541	0.616251189454	0.420158632256	0.0272568716021	0.006131025966	0.605638345016	0.107023326387	0.400644959301	-11.7669803244	70.1813126953	29.8217347782
10	2.40600129671	0.958420213123	0.0367201959743	0.471162996132	0.0677748424622	0.897181653433	0.0547614496369	0.464495796852	-0.299915318896	-0.411994241131	0.16904718581	0.0500440928766	0.206213218335	0.00602980744938	-0.193971611118	0.587769864959	0.0617290142811	-0.0113029959894	0.480396761575	-0.0379195670663	0.404860630363	-1.96721860339	53.7010887929	21.2925512913
11	1.2123318777	0.118188252606	-0.169884976533	1.05304723037	1.29137137391	1.15139499063	0.216525261946	-0.41937771074	-0.0977701389708	0.322498839659	0.0511971995772	-0.551916764738	0.240542099975	-0.41617954861	0.0615236589485	0.52689488709	0.0467203882178	-0.0266451946465	0.569283159258	0.0307051824169	0.493967544876	-21.7099052965	65.4404490328	26.951169484
12	0.995257524624	0.189642936813	0.52221954777	1.78367944042	1.32708778009	2.82817092084	-0.334986773808	0.337281202619	0.162185385917	0.192390829465	-0.510244383354	0.704724230926	-0.0410320564071	-0.311157104273	0.77634169496	0.753968554376	0.166858783466	0.0736531805073	0.623886386274	0.0901604364272	1.09123758964	20.6434162977	32.2869564601	10.0182232249
13	4.81958566523	-0.69497745262	-3.57887306123	2.0420227819	-0.298072822139	3.19412212474	0.0302556762167	0.95603464994	1.15912283839	0.0805006776334	0.200893512648	0.424052069766	-0.145727440236	-0.526257716414	0.145527193495	0.653690182744	0.102838851219	-0.0476385961635	0.64472077818	0.223347327517	0.648546947213	32.6976380122	23.5789964428	6.19185091486
14	0.279166840087	0.52219885857	-0.187141067604	1.1435867349	0.413885147814	0.927949938331	-0.117489237612	-0.0907053113958	0.907085339179	0.14760442335	-0.377329026609	0.61760851606	0.0906089994	-0.282824966635	0.585739181212	0.641416710689	0.190900461605	0.0453992207391	0.759980846065	-0.142603154927	1.36704420897	15.8131453296	35.387207864	10.7016017454
15	2.66981943515	1.83359491435	0.965120899526	1.34475535006	0.526761428138	4.44261518917	-0.292329367915	-0.0776129175624	0.357534966586	0.292304274047	0.311503315189	0.814792993439	-0.24845467007	0.806959174233	-0.0704279073111	0.583106193082	-0.0461171936532	0.0373825629313	0.529455808723	0.0993083753758	0.661713756164	38.2135499285	31.3495130075	9.69439878344
16	0.801114679319	0.0964234070437	-0.0541614354371	2.96117805031	0.725731017911	0.58565007151	0.196613634587	0.0889474212213	0.0354895531421	-0.363744223216	-0.252274766064	-0.21466818076	-0.114331979532	-0.00751284129493	0.147634181023	0.517620788829	0.000505115178156	0.0391648686147	0.525334132207	0.0141766031471	0.358066827981	-29.6422346382	1.66892273446	25.7078279808
17	1.8178812229	-1.20295845172	-0.479551417828	1.7292317829	0.498193338967	1.25160073229	0.347885081938	0.495069941448	0.244137412177	-0.300129293923	-0.467695065994	0.208173487785	-0.207516297066	0.237476552696	0.0348077082189	0.616012680675	-0.13961062988	0.0777956239117	0.511176603395	0.00737637696649	0.480613798089	-25.8786140558	9.52647085986	21.8887320141
18	1.53055512584	0.171992565954	-0.395898902928	1.22209749139	-0.575620552871	1.09672862475	-0.0321308323454	-0.544513695959	0.533225169342	-0.2145262316	0.0851379708195	0.328456673485	0.294079767248	0.391073616795	0.135332626486	0.578348937954	-0.0440719135191	-0.0260810195955	0.520374833403	-0.0556658534651	0.372027902254	-26.3139885029	-13.3632646397	28.1165111683
19	1.89254629592	0.565176684152	-0.820407958833	0.414070430485	-0.474809643527	2.57299270475	-0.24287331302	0.0872741729303	-1.13800874271	-0.0344741035709	-0.396359430613	0.0812641569276	0.276534449811	0.0826108572052	0.906313362546	0.770795513851	-0.0834312321623	-0.00251162607377	0.495172706074	0.0437948151101	1.07686223865	-17.3036072311	38.9395649763	10.1636318157
20	1.90631615105	-0.555142577067	-1.04022498297	2.41830918599	-1.37562398906	1.49664165613	-0.18090399307	-0.415205681409	-1.02927278565	-0.204016044172	-0.0560771637309	0.653619566355	0.542403122241	-0.112829889118	0.278782755713	0.828607572212	-0.0565305600909	-0.0561270610042	0.443771112425	0.0689029787806	0.971387750898	-16.8411263363	39.7240542669	9.40188368658
21	2.85954347644	-1.17283208896	-1.18712702836	4.69239379576	-1.3794485567	5.93479027053	0.628680949964	-0.341900704048	-1.1666952339	0.0128214880203	-1.00825774115	0.917265247858	-0.659675217282	-0.473890932945	0.223561610979	0.525345181045	-0.00225116302177	-0.21491374123	0.581639727305	-0.0296104475397	0.722689010848	-24.8928260682	54.621001475	9.19635835963

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 32 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 43 through 51 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 7 through 17 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 18 through 22 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 23 through 32 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 43 through 51 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 7 through 17 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 18 through 22 )
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 23 through 32 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 43 through 51 )
12	X-RAY DIFFRACTION	12	chain 'I' and (resid 7 through 17 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 18 through 22 )
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 23 through 32 )
15	X-RAY DIFFRACTION	15	chain 'J' and (resid 43 through 51 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 7 through 22 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 23 through 32 )
18	X-RAY DIFFRACTION	18	chain 'N' and (resid 43 through 51 )
19	X-RAY DIFFRACTION	19	chain 'O' and (resid 7 through 17 )
20	X-RAY DIFFRACTION	20	chain 'O' and (resid 18 through 32 )
21	X-RAY DIFFRACTION	21	chain 'P' and (resid 43 through 51 )

-
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