PDB-8dh1: T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair

ID or keywords:

Entry

Database: PDB / ID: 8dh1

Title

T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair

Components

Non-template strand DNA
RNA
T7 RNA polymerase
Template strand DNA

Keywords

Transferase/DNA/RNA / T7 RNA polymerase / elongation complex / unnatural base / Ds-Pa / synthetic DNA / transcription / Transferase-DNA-RNA complex

Function / homology

Function and homology information

DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Escherichia phage T7 (virus)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Model details

T7 RNA polymerase, elongation complex, unnatural base pair, synthetic DNA

Authors

Oh, J. / Wang, D.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Authors: Oh, J. / Kimoto, M. / Xu, H. / Chong, J. / Hirao, I. / Wang, D.

History

Deposition	Jun 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8dh1.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb8dh1.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	8dh1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8dh1_validation.pdf.gz	934.8 KB	Display	wwPDB validaton report
Full document	8dh1_full_validation.pdf.gz	996.4 KB	Display
Data in XML	8dh1_validation.xml.gz	107.6 KB	Display
Data in CIF	8dh1_validation.cif.gz	148.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/8dh1 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dh1	HTTPS FTP

-
Related structure data

Related structure data	8dh0SC 8dh2C 8dh3C 8dh4C 8dh5C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#181 - Jan 2015 Cascade and CRISPR similarity (2) #253 - Jan 2021 Expressome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #40 - Apr 2003 RNA Polymerase similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #227 - Nov 2018 Telomerase similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase 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) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids 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) #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 (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#181 - Jan 2015
Cascade and CRISPR
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (11)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (2)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#227 - Nov 2018
Telomerase
similarity (2)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
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)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
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)
#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 (2)

Deposited unit

B: T7 RNA polymerase

A: Template strand DNA

C: RNA

D: Non-template strand DNA

E: T7 RNA polymerase

F: Template strand DNA

G: RNA

H: Non-template strand DNA

I: T7 RNA polymerase

J: Template strand DNA

K: RNA

L: T7 RNA polymerase

M: Template strand DNA

N: RNA

O: Non-template strand DNA

hetero molecules

443 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: T7 RNA polymerase

A: Template strand DNA

C: RNA

D: Non-template strand DNA

hetero molecules

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

2

E: T7 RNA polymerase

F: Template strand DNA

G: RNA

H: Non-template strand DNA

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

3

I: T7 RNA polymerase

J: Template strand DNA

K: RNA

hetero molecules

defined by author
109 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

L: T7 RNA polymerase

M: Template strand DNA

N: RNA

O: Non-template strand DNA

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

Unit cell

Length a, b, c (Å)	78.866, 86.156, 201.676
Angle α, β, γ (deg.)	89.85, 85.09, 69.56
Int Tables number	1
Space group name H-M	P1

-
DNA chain , 2 types, 7 molecules AFJMDHO

#2: DNA chain	Template strand DNA Mass: 5616.727 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	Non-template strand DNA Mass: 2666.761 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 8 molecules BEILCGKN

#1: Protein	T7 RNA polymerase / DNA-directed RNA polymerase Mass: 98984.227 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P00573, DNA-directed RNA polymerase
#3: RNA chain	RNA Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 69 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-S8L / 1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-pyrrole-2-carbaldehyde Mass: 467.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆NO₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.51 % / Mosaicity: 0.14 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.65→39.34 Å / Num. obs: 130161 / % possible obs: 90.3 % / Redundancy: 3.9 % / CC_1/2: 0.994 / R_merge(I) obs: 0.121 / R_pim(I) all: 0.071 / R_rim(I) all: 0.14 / Χ²: 0.94 / Net I/σ(I): 8.1 / Num. measured all: 509307
Reflection shell	Resolution: 2.65→2.69 Å / % possible obs: 89.9 % / Redundancy: 3.9 % / R_merge(I) obs: 2.619 / Num. measured all: 25182 / Num. unique obs: 6486 / CC_1/2: 0.315 / R_pim(I) all: 1.533 / R_rim(I) all: 3.036 / Χ²: 0.92 / Net I/σ(I) obs: 0.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.19	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PDB_EXTRACT	3.27	data extraction
PHENIX	1.19	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8DH0

8dh0

Resolution: 2.65→39.34 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2715	6387	4.95 %
R_work	0.2297	-	-
obs	0.2318	128924	89.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.65→39.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24720	2302	2	63	27087

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	27839
X-RAY DIFFRACTION	f_angle_d	0.697	38143
X-RAY DIFFRACTION	f_dihedral_angle_d	13.774	4580
X-RAY DIFFRACTION	f_chiral_restr	0.045	4202
X-RAY DIFFRACTION	f_plane_restr	0.009	4514

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 (%)
2.65-2.68	0.4171	197	0.3782	3589	X-RAY DIFFRACTION	79
2.68-2.71	0.3854	233	0.3576	4033	X-RAY DIFFRACTION	88
2.71-2.74	0.406	244	0.3409	3988	X-RAY DIFFRACTION	89
2.74-2.78	0.3598	227	0.3435	4147	X-RAY DIFFRACTION	90
2.78-2.82	0.3852	208	0.3189	4123	X-RAY DIFFRACTION	91
2.82-2.85	0.3461	198	0.3226	4159	X-RAY DIFFRACTION	90
2.85-2.9	0.3552	221	0.3056	4039	X-RAY DIFFRACTION	90
2.9-2.94	0.3378	222	0.2959	4094	X-RAY DIFFRACTION	89
2.94-2.98	0.3566	207	0.2845	4045	X-RAY DIFFRACTION	90
2.98-3.03	0.3618	189	0.2781	4125	X-RAY DIFFRACTION	88
3.03-3.09	0.3299	201	0.298	3890	X-RAY DIFFRACTION	85
3.09-3.14	0.3342	198	0.3035	3615	X-RAY DIFFRACTION	79
3.14-3.2	0.4014	208	0.3151	4061	X-RAY DIFFRACTION	91
3.2-3.27	0.3925	217	0.298	4286	X-RAY DIFFRACTION	93
3.27-3.34	0.3308	220	0.2669	4180	X-RAY DIFFRACTION	93
3.34-3.42	0.2778	222	0.2561	4241	X-RAY DIFFRACTION	92
3.42-3.5	0.3	222	0.2399	4216	X-RAY DIFFRACTION	93
3.5-3.6	0.2962	216	0.2347	4204	X-RAY DIFFRACTION	91
3.6-3.7	0.291	205	0.2228	4139	X-RAY DIFFRACTION	92
3.7-3.82	0.2489	183	0.2181	4155	X-RAY DIFFRACTION	91
3.82-3.96	0.2609	231	0.21	4119	X-RAY DIFFRACTION	89
3.96-4.12	0.2427	170	0.2042	3723	X-RAY DIFFRACTION	81
4.12-4.3	0.233	217	0.1955	4184	X-RAY DIFFRACTION	92
4.3-4.53	0.2482	217	0.1868	4319	X-RAY DIFFRACTION	95
4.53-4.81	0.2278	215	0.1779	4231	X-RAY DIFFRACTION	93
4.81-5.18	0.2229	222	0.1866	4223	X-RAY DIFFRACTION	92
5.18-5.7	0.2482	235	0.2087	4097	X-RAY DIFFRACTION	90
5.7-6.53	0.2832	187	0.2313	3914	X-RAY DIFFRACTION	86
6.53-8.21	0.2421	224	0.2082	4284	X-RAY DIFFRACTION	95
8.21-39.34	0.1976	231	0.2019	4114	X-RAY DIFFRACTION	90

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	2.5567	-0.0399	-0.4256	1.3159	-0.3027	1.7712	0.1404	0.0186	1.2896	0.1676	0.0552	0.3201	-0.4254	-0.4621	-0.1743	0.7009	0.0221	0.1106	0.5896	-0.0426	1.1127	-2.0351	45.2709	-96.2395
2	2.7613	0.0546	-0.25	0.8829	-0.2287	1.4789	0.1848	-0.3512	-0.3432	-0.2079	-0.0476	0.2727	0.3733	-0.0576	-0.1291	0.8358	-0.0579	-0.1622	0.6023	0.0048	0.5082	8.4604	9.9241	-91.8304
3	8.2982	4.6475	-1.1517	6.0083	-1.7523	2.0666	0.3108	-0.53	1.698	-0.4007	0.1917	1.9879	0.2034	-0.9181	-0.7055	0.791	-0.1057	-0.1045	0.8429	0.0186	0.9465	0.2751	23.0829	-92.8794
4	4.3806	-6.2106	1.582	9.1518	-3.435	5.194	0.5344	-0.4986	0.5405	-0.3764	-0.5675	0.8175	0.1313	-0.3766	-0.0386	1.0223	-0.1993	-0.1493	0.6551	-0.1427	0.9776	3.3342	22.1989	-98.3779
5	1.7738	0.8219	-0.2146	1.0635	-1.1338	2.0541	0.073	0.1642	-0.3601	0.0092	0.326	0.0522	0.6273	-0.1522	-0.3047	1.1479	0.037	-0.2313	0.9467	-0.0893	0.7481	10.0494	-14.0843	53.4531
6	2.0561	-0.0493	1.0063	0.8577	0.1224	2.2103	0.1107	0.4068	0.1441	0.0027	-0.1645	0.0525	-0.2175	0.2281	0.0505	0.9587	0.0317	-0.0553	1.0449	-0.0749	0.453	22.0403	18.64	49.2529
7	3.8003	-3.6023	1.4939	6.9556	-1.481	3.2532	0.1313	-0.2052	-0.8775	0.6637	-0.2961	1.8724	-0.4868	-0.036	0.0973	1.0041	0.0613	0.1485	1.2673	-0.2471	0.9079	3.9124	11.2583	53.4271
8	5.1954	0.7936	-2.4496	3.3006	-3.9863	5.2496	0.2628	-0.1431	0.1111	0.912	-0.0605	1.6216	-0.4182	-0.4237	-0.012	0.9685	0.082	0.0657	1.3824	-0.2321	0.9397	12.5404	8.4478	58.8741
9	9.8298	0.3611	-3.204	2.9601	-3.8214	5.6985	-0.8161	0.5656	0.3653	0.2781	-0.3483	-0.344	0.2884	-1.1282	1.0509	2.9151	0.8251	0.6138	2.2938	0.1458	1.7184	-7.8383	25.8495	44.3783
10	2.1119	0.4285	0.0788	0.2821	-0.2006	0.9878	0.1182	1.2325	0.6793	-0.1447	-0.0799	-0.0883	-0.0378	0.2076	-0.0432	0.4776	0.0956	0.0762	1.0045	0.3714	0.8292	33.0752	53.1652	-56.5292
11	1.8647	-0.2035	0.3788	1.1763	-0.1819	0.9988	0.1337	0.3425	0.035	-0.0469	-0.0945	-0.133	0.1712	0.1397	-0.0479	0.2897	-0.0086	0.0209	0.4095	0.0205	0.3607	18.9655	30.75	-35.0979
12	2.5475	2.1501	0.063	1.8704	0.3257	3.7449	0.1797	0.5026	0.0999	-0.0617	-0.0822	-1.2602	0.5045	1.0054	-0.2533	0.3635	0.1007	0.0627	0.8757	0.1242	0.7678	35.2215	33.954	-45.861
13	8.3879	5.6877	-3.9059	3.8675	-2.6829	4.6745	0.124	0.6767	-0.4043	-0.2085	-0.3126	-0.6858	0.0741	0.8045	0.1086	0.3812	-0.0138	-0.0045	0.6326	0.1257	0.5277	26.7004	43.169	-40.0977
14	4.4003	1.1693	-3.904	0.7752	-1.2497	3.5572	-0.2943	1.2751	-0.193	-0.2333	0.3907	-0.2259	0.3354	-0.3282	-0.1505	2.4203	-0.0384	0.0404	3.0796	0.134	2.5211	43.5844	19.7423	-49.7479
15	1.9555	0.0499	0.4694	2.0063	0.021	1.0274	0.0223	-0.6755	-0.7291	0.2582	-0.0095	-0.3472	0.3314	0.1014	-0.0174	0.548	0.0056	0.0597	0.897	0.1287	0.7986	35.3699	56.243	7.5874
16	2.509	0.0529	-0.2847	1.278	-0.09	1.0658	-0.0103	-0.6346	0.0738	0.0228	-0.1198	-0.0026	-0.0744	0.0324	0.126	0.4111	0.0807	-0.0248	0.4982	-0.1247	0.406	36.483	81.7608	-5.8194
17	2.0219	1.9797	1.9909	8.6975	8.8599	9.0291	-0.3584	0.6306	-1.193	-0.4327	0.4172	-3.1058	-0.6341	1.7805	0.0263	1.9207	0.3547	-0.0647	2.8112	-0.0863	2.4468	72.9306	73.5607	2.4182
18	7.1279	3.6654	-0.9169	5.539	1.444	7.6818	-0.4864	-0.8384	-1.4621	-0.4757	0.2982	-0.6537	0.3623	2.6961	0.4001	0.8177	0.1283	-0.0551	1.1776	0.1113	0.622	50.0062	71.9199	-1.3149
19	7.0129	3.1158	-1.2196	1.7482	1.1292	8.0502	-0.1166	-0.7705	-1.6437	-0.2564	-0.2212	-1.1371	1.4357	0.7935	0.6948	0.6641	0.205	0.1104	0.7482	0.1636	0.6562	33.017	60.6896	3.3718
20	3.6836	-3.7728	-1.513	4.458	0.4193	2.776	-0.647	-1.3374	-0.0321	-0.1133	0.0715	-1.1875	0.4989	1.017	0.6181	0.7075	-0.0035	0.0562	0.9367	0.1308	0.7109	36.578	64.3095	-2.1265
21	3.2805	2.2793	-0.197	4.3896	3.8519	5.6879	-1.1167	-1.8419	-1.7251	0.4035	0.6133	-1.4647	-1.5917	-0.4558	0.4769	1.6715	0.3294	-0.1699	2.1137	0.165	2.0033	65.5024	75.1086	1.9813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid 6 through 263 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid 264 through 883 )
3	X-RAY DIFFRACTION	3	chain 'J' and (resid 7 through 18 )
4	X-RAY DIFFRACTION	4	chain 'K' and (resid 1 through 8 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 4 through 301 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 302 through 882 )
7	X-RAY DIFFRACTION	7	chain 'M' and (resid 5 through 18 )
8	X-RAY DIFFRACTION	8	chain 'N' and (resid 1 through 8 )
9	X-RAY DIFFRACTION	9	chain 'O' and (resid 2 through 6 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 331 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 332 through 883 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 3 through 18 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 8 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 3 through 8 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 18 through 407 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 408 through 883 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 2 through 6 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 7 through 12 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 13 through 18 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 1 through 8 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 2 through 9 )

-
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

-
DNA chain , 2 types, 7 molecules AFJMDHO

-
Protein / RNA chain , 2 types, 8 molecules BEILCGKN

-
Non-polymers , 4 types, 69 molecules

-
Details

-
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

-DNA chain , 2 types, 7 molecules AFJMDHO

-Protein / RNA chain , 2 types, 8 molecules BEILCGKN

-Non-polymers , 4 types, 69 molecules

-Details

-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

-
DNA chain , 2 types, 7 molecules AFJMDHO

-
Protein / RNA chain , 2 types, 8 molecules BEILCGKN

-
Non-polymers , 4 types, 69 molecules

-
Details

-
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