PDB-6uu9: E. coli mutant sigma-S transcription initiation complex with an 8...

ID or keywords:

Entry

Database: PDB / ID: 6uu9

Title

E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP for 30 minutes)

Components

(DNA-directed RNA polymerase subunit ...) x 4
(Synthetic DNA 50-mer (promoter ...) x 2
RNA 8-mer
RNA polymerase sigma factor RpoS

Keywords

TRANSCRIPTION / TRANSFERASE/DNA/RNA / Transcription initiation / RNA polymerase / DNA promoter / transcription bubble / de novo RNA synthesis / DNA scrunching / sigma-S factor / TRANSFERASE-DNA-RNA complex

Function / homology

Function and homology information

RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...
Similarity search - Function

RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 ...RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology

Biological species

Escherichia coli (E. coli)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 5.4 Å

Authors

Zuo, Y. / De, S. / Steitz, T.A.

Funding support

United States, 2items

Citation

Journal: Iscience / Year: 2020
Title: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Authors: Zuo, Y. / De, S. / Feng, Y. / Steitz, T.A.

History

Deposition	Oct 30, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 16, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6uu9.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb6uu9.ent.gz		Display	PDB format
PDBx/mmJSON format	6uu9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6uu9_validation.pdf.gz	334 KB	Display	wwPDB validaton report
Full document	6uu9_full_validation.pdf.gz	334 KB	Display
Data in XML	6uu9_validation.xml.gz	1.5 KB	Display
Data in CIF	6uu9_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/6uu9 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/6uu9	HTTPS FTP

-
Related structure data

Related structure data	6utvC 6utwC 6utxC 6utyC 6utzC 6uu0C 6uu1C 6uu2C 6uu3C 6uu4C 6uu5C 6uu6C 6uu7C 6uu8C 6uuaC 6uubC 6uucC 5iplS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6uu5-d 5ipn-d 6uu8-d 6utz-d 6uu3-d 6uu7-d 6uu2-d 6utx-d 6uua-d 6uu0-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	#253 - Jan 2021 Expressome similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (23) #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) #227 - Nov 2018 Telomerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (2) #84 - Dec 2006 Transposase 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) #87 - Mar 2007 Zinc Fingers 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) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#253 - Jan 2021
Expressome
similarity (11)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (23)
#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)
#227 - Nov 2018
Telomerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (2)
#84 - Dec 2006
Transposase
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)
#87 - Mar 2007
Zinc Fingers
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)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

AAA: DNA-directed RNA polymerase subunit alpha

BBB: DNA-directed RNA polymerase subunit alpha

CCC: DNA-directed RNA polymerase subunit beta

DDD: DNA-directed RNA polymerase subunit beta'

EEE: DNA-directed RNA polymerase subunit omega

FFF: RNA polymerase sigma factor RpoS

111: Synthetic DNA 50-mer (promoter non-template strand)

222: Synthetic DNA 50-mer (promoter template strand)

333: RNA 8-mer

hetero molecules

443 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	132.184, 153.474, 230.825
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABBBCCCDDDEEE

#1: Protein	DNA-directed RNA polymerase subunit alpha Mass: 26899.572 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA_1, NCTC9962_06804 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A377D9Q8, DNA-directed RNA polymerase
#2: Protein	DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V4, DNA-directed RNA polymerase
#3: Protein	DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta' Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: Protein	DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega Mass: 10118.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase

-
Synthetic DNA 50-mer (promoter ... , 2 types, 2 molecules 111222

#6: DNA chain	Synthetic DNA 50-mer (promoter non-template strand) Mass: 15313.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain	Synthetic DNA 50-mer (promoter template strand) Mass: 15562.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 2 molecules FFF333

#5: Protein	RNA polymerase sigma factor RpoS / Sigma S / Sigma-38 Mass: 38705.496 Da / Num. of mol.: 1 / Mutation: I219G, S221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoS, NCTC9075_01674 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A377K1M2
#8: RNA chain	RNA 8-mer Mass: 2694.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 6 molecules

#9: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical	ChemComp-2DA / 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE Type: DNA linking / Mass: 315.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₅P
#12: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₇P₂

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.52 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, sodium chloride, HEPES / Temp details: Room temperature

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 5.395→49 Å / Num. obs: 16580 / % possible obs: 99 % / Redundancy: 5.9 % / CC_1/2: 0.995 / Net I/σ(I): 6.93
Reflection shell	Resolution: 5.4→5.72 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.47 / Num. unique obs: 2511 / CC_1/2: 0.157 / % possible all: 95.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IPL

5ipl

Resolution: 5.4→48.988 Å / Cor.coef. F_o:F_c: 0.858 / Cor.coef. F_o:F_c free: 0.834 / SU B: 1079.238 / SU ML: 4.413 / Cross valid method: FREE R-VALUE / ESU R Free: 2.712
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3622	771	4.679 %	0
R_work	0.3142	-	-	-
all	0.317	-	-	-
obs	-	16477	98.323 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 279.166 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.093 Å²	0 Å²	0 Å²
2-	-	0.844 Å²	0 Å²
3-	-	-	-0.751 Å²

Refinement step

Cycle: LAST / Resolution: 5.4→48.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27525	1407	33	0	28965

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	29530
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	27598
X-RAY DIFFRACTION	r_angle_refined_deg	1.383	1.622	40177
X-RAY DIFFRACTION	r_angle_other_deg	0.715	1.619	63965
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.546	5	3503
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.506	21.715	1580
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.424	15	5160
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.444	15	263
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	3874
X-RAY DIFFRACTION	r_gen_planes_refined	0.048	0.02	32140
X-RAY DIFFRACTION	r_gen_planes_other	0.043	0.02	6060
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.3	6709
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.232	0.3	28961
X-RAY DIFFRACTION	r_nbtor_refined	0.155	0.5	2959
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.262	0.5	962
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.219	0.5	51
X-RAY DIFFRACTION	r_metal_ion_refined	0.113	0.5	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.325	0.3	42
X-RAY DIFFRACTION	r_nbd_other	0.346	0.3	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.347	0.5	7
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.225	0.5	1
X-RAY DIFFRACTION	r_mcbond_it	5.505	19.324	14033
X-RAY DIFFRACTION	r_mcbond_other	5.505	19.324	14032
X-RAY DIFFRACTION	r_mcangle_it	10.054	32.593	17529
X-RAY DIFFRACTION	r_mcangle_other	10.053	32.594	17530
X-RAY DIFFRACTION	r_scbond_it	3.665	19.533	15497
X-RAY DIFFRACTION	r_scbond_other	3.639	19.524	15490
X-RAY DIFFRACTION	r_scangle_it	7.073	32.884	22648
X-RAY DIFFRACTION	r_scangle_other	7.022	32.869	22636
X-RAY DIFFRACTION	r_lrange_it	27.793	267.895	107027
X-RAY DIFFRACTION	r_lrange_other	27.786	267.876	107021
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.131	0.05	6329

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 (%)
5.4-5.534	0.439	46	0.373	1046	X-RAY DIFFRACTION	89.6552
5.534-5.684	0.428	54	0.404	1109	X-RAY DIFFRACTION	99.9141
5.684-5.846	0.438	41	0.402	1074	X-RAY DIFFRACTION	99.8209
5.846-6.023	0.426	60	0.399	1066	X-RAY DIFFRACTION	100
6.023-6.218	0.455	54	0.389	1021	X-RAY DIFFRACTION	99.9071
6.218-6.433	0.378	37	0.411	1007	X-RAY DIFFRACTION	100
6.433-6.671	0.397	40	0.402	973	X-RAY DIFFRACTION	99.9014
6.671-6.939	0.418	52	0.4	932	X-RAY DIFFRACTION	100
6.939-7.241	0.353	50	0.363	868	X-RAY DIFFRACTION	99.1361
7.241-7.586	0.474	47	0.332	844	X-RAY DIFFRACTION	99.3311
7.586-7.986	0.369	34	0.31	822	X-RAY DIFFRACTION	99.8833
7.986-8.457	0.32	43	0.242	776	X-RAY DIFFRACTION	99.514
8.457-9.023	0.286	50	0.198	724	X-RAY DIFFRACTION	99.1037
9.023-9.719	0.237	29	0.184	678	X-RAY DIFFRACTION	99.1585
9.719-10.607	0.276	29	0.187	642	X-RAY DIFFRACTION	99.2604
10.607-11.793	0.219	21	0.203	590	X-RAY DIFFRACTION	98.8673
11.793-13.493	0.304	25	0.225	513	X-RAY DIFFRACTION	97.8182
13.493-16.232	0.359	29	0.315	433	X-RAY DIFFRACTION	96.0499
16.232-21.834	0.524	19	0.445	364	X-RAY DIFFRACTION	95.99
21.834-48.988	0.469	11	0.536	224	X-RAY DIFFRACTION	89.0152

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	4.5784	-0.1731	-0.1076	0.4689	-0.1424	2.7744	0.0021	-0.9927	0.208	0.0877	0.0299	0.0463	-0.2364	0.2353	-0.0321	0.9885	0.0982	0.02	0.2536	-0.1717	2.0032	41.068	-4.853	4.505
2	3.7624	0.0139	-0.5976	6.3478	1.6225	1.9945	0.0987	0.6354	-0.0351	-0.3133	0.0478	0.2771	-0.0534	-0.9466	-0.1464	1.4831	0.0216	-0.0988	0.6253	0.3228	1.8901	17.34	-1.948	-40.324
3	5.0954	0.0753	0.6203	4.6285	1.7919	3.3454	0.3476	0.1831	0.3447	0.1463	-0.4304	0.0825	0.2485	-0.3816	0.0829	1.8009	-0.1785	0.1517	0.1639	0.3642	1.7653	54.002	1.361	-58.064
4	5.0877	5.3687	-3.6592	6.2558	-2.6943	7.0875	-0.557	0.4403	0.5491	-0.7259	0.5866	-0.0299	-0.2918	-0.5169	-0.0296	1.5695	0.5073	0.2098	0.3289	-0.2315	2.1066	71.592	-30.384	-29.408
5	17.3091	-6.0045	3.6016	9.0874	-1.5514	1.0403	0.1495	0.7677	0.9721	-0.8073	0.1852	-1.0575	-0.0823	-0.1606	-0.3347	2.2738	0.3533	0.3435	0.5733	0.1285	2.742	49.88	31.981	-19.173
6	13.8356	-2.2871	0.3752	8.0809	-1.1092	0.1899	0.2669	1.2547	-0.1485	0.3812	-0.2646	0.5391	0.0853	-0.0954	-0.0023	2.0115	-0.1792	0.0181	0.6957	-0.5454	2.6657	33.791	31.009	10.201
7	9.9331	-0.1701	5.9331	10.8999	6.0737	13.085	0.2224	-0.3833	-0.6798	0.6351	0.5933	-0.2899	1.1284	1.1259	-0.8158	0.9622	-0.0646	0.0658	1.5257	0.2224	1.8714	-29.165	-2.84	3.083
8	4.0064	0.5826	2.6698	0.1679	0.0044	4.4235	0.3362	0.5645	-0.2684	-0.0372	-0.1327	-0.1129	0.3516	0.8317	-0.2035	2.0869	-0.0002	0.2521	1.24	-0.4771	4.141	86.166	2.065	-52.501
9	2.4643	1.0273	-0.0621	1.7243	0.9922	10.1147	-0.9536	-1.852	1.3728	0.3105	-0.5456	0.4033	1.6279	-0.5466	1.4992	2.5218	-0.1094	0.4029	3.22	-0.2357	3.0583	76.554	21.662	-30.189
10	0.5159	0.3116	0.002	0.555	-0.2706	0.2024	0.2746	0.5882	0.1507	1.1332	-0.0851	0.3691	-0.7051	0.3551	-0.1895	3.1759	-0.1911	0.3529	2.6866	0.5975	3.9542	34.249	48.101	-44.291
11	8.4726	1.8586	-4.5846	3.2341	1.5328	5.0208	0.1242	-1.032	0.5661	-0.3855	-0.044	-0.1859	-0.4839	1.0904	-0.0801	1.5548	0.2194	-0.2165	0.8531	0.2111	2.2178	78.555	3.05	-16.312
12	12.662	4.9356	-6.6781	7.9073	-5.3036	8.3973	0.1834	0.2379	-1.775	0.4264	-0.307	-0.4859	0.0243	0.1541	0.1237	1.5225	0.0364	0.1048	0.411	-0.0487	2.0456	73.758	-62.668	-30.229
13	1.6452	-1.1104	0.6698	3.125	-1.7713	3.2978	0.1538	-1.4404	0.7057	0.631	-0.7197	-1.2988	1.4888	0.2041	0.5659	3.1154	-0.6706	-0.3135	2.5327	0.3065	2.768	72.557	26.623	14.143
14	8.009	4.9286	0.046	4.1258	-1.949	8.606	0.0384	0.2158	0.5074	0.0915	0.6719	-0.4444	0.0021	-0.7079	-0.7103	1.3567	0.6055	0.1869	0.5222	-0.3763	2.4712	-0.419	17.87	6.692
15	37.2864	-8.3814	8.9225	3.3064	-3.891	6.9209	-1.8988	3.2505	-1.8202	1.2986	-0.5924	-0.4039	-0.4697	1.8108	2.4912	3.3818	0.3222	-0.2201	1.5404	0.0823	3.1929	29.052	-48.642	-53.236
16	14.246	-4.5029	0.716	2.6837	1.2933	4.116	-0.2772	0.8834	-3.0991	-1.1387	0.1095	0.5297	-0.3645	0.4616	0.1676	1.8483	-0.291	0.7665	0.4432	-0.2954	3.0043	23.347	-29.082	-3.212
17	4.8342	0.472	-4.3623	1.6507	1.5865	6.5993	0.1595	1.6191	0.0413	0.5906	0.3979	-0.4436	0.5708	-1.3468	-0.5573	0.9374	0.229	0.1753	0.8639	0.1526	2.1499	-4.04	-7.137	-12.039
18	19.1865	-2.8865	0.6604	0.9449	0.0059	5.9865	0.0477	-0.3653	1.6259	0.769	-0.6096	-0.5906	0.2501	-0.2477	0.5619	2.7479	-0.3085	-0.0971	1.4888	0.0539	2.4126	28.491	-53.033	-29.378
19	11.4838	1.9781	1.1623	2.5345	7.139	24.8379	-1.2869	0.4824	3.0801	-0.2611	0.8453	-0.038	0.4876	1.6844	0.4416	2.2133	-0.2333	0.5228	0.8465	0.0139	3.4498	43.62	2.657	-24.149
20	29.4226	-5.0568	-1.591	9.9545	-1.9249	16.959	-0.535	0.949	0.9703	0.027	0.1912	-0.4492	-0.4832	-1.872	0.3437	3.2245	-0.5064	1.1652	1.9687	-0.2434	3.8072	79.82	31.026	-52.367
21	3.684	-2.573	-11.1941	4.9858	8.7666	34.3247	-0.7052	-0.5719	-0.7276	0.0022	-0.8243	-1.9339	1.8042	1.2889	1.5295	2.0805	0.3011	-0.1821	2.4941	0.4731	2.9894	47.163	-19.155	-40.681

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	CCC	1 - 28
2	X-RAY DIFFRACTION	1	ALL	CCC	146 - 152
3	X-RAY DIFFRACTION	1	ALL	CCC	445 - 455
4	X-RAY DIFFRACTION	1	ALL	CCC	517 - 832
5	X-RAY DIFFRACTION	1	ALL	CCC	1056 - 1241
6	X-RAY DIFFRACTION	1	ALL	DDD	767 - 790
7	X-RAY DIFFRACTION	1	ALL	DDD	1504
8	X-RAY DIFFRACTION	1	ALL	333	101
9	X-RAY DIFFRACTION	2	ALL	CCC	1242 - 1321
10	X-RAY DIFFRACTION	2	ALL	DDD	343 - 500
11	X-RAY DIFFRACTION	2	ALL	DDD	791 - 943
12	X-RAY DIFFRACTION	2	ALL	DDD	1129 - 1153
13	X-RAY DIFFRACTION	2	ALL	DDD	1213 - 1317
14	X-RAY DIFFRACTION	2	ALL	DDD	1345 - 1407
15	X-RAY DIFFRACTION	2	ALL	DDD	1502 - 1503
16	X-RAY DIFFRACTION	2	ALL	EEE	2 - 91
17	X-RAY DIFFRACTION	3	ALL	CCC	1322 - 1342
18	X-RAY DIFFRACTION	3	ALL	DDD	1 - 342
19	X-RAY DIFFRACTION	3	ALL	DDD	1318 - 1344
20	X-RAY DIFFRACTION	3	ALL	DDD	1501
21	X-RAY DIFFRACTION	3	ALL	FFF	218 - 226
22	X-RAY DIFFRACTION	3	ALL	FFF	232 - 241
23	X-RAY DIFFRACTION	4	ALL	CCC	153 - 226
24	X-RAY DIFFRACTION	4	ALL	CCC	337 - 444
25	X-RAY DIFFRACTION	4	ALL	111	45 - 54
26	X-RAY DIFFRACTION	5	ALL	CCC	833 - 891
27	X-RAY DIFFRACTION	5	ALL	CCC	912 - 936
28	X-RAY DIFFRACTION	5	ALL	CCC	1040 - 1055
29	X-RAY DIFFRACTION	6	ALL	AAA	52 - 178
30	X-RAY DIFFRACTION	7	ALL	BBB	52 - 178
31	X-RAY DIFFRACTION	8	ALL	FFF	53 - 166
32	X-RAY DIFFRACTION	8	ALL	111	37 - 44
33	X-RAY DIFFRACTION	9	ALL	FFF	167 - 217
34	X-RAY DIFFRACTION	9	ALL	222	22 - 26
35	X-RAY DIFFRACTION	10	ALL	FFF	242 - 329
36	X-RAY DIFFRACTION	10	ALL	CCC	892 - 911
37	X-RAY DIFFRACTION	11	ALL	CCC	29 - 145
38	X-RAY DIFFRACTION	11	ALL	CCC	456 - 516
39	X-RAY DIFFRACTION	12	ALL	CCC	227 - 336
40	X-RAY DIFFRACTION	13	ALL	CCC	937 - 1039
41	X-RAY DIFFRACTION	14	ALL	AAA	1 - 51
42	X-RAY DIFFRACTION	14	ALL	AAA	179 - 235
43	X-RAY DIFFRACTION	14	ALL	BBB	1 - 51
44	X-RAY DIFFRACTION	14	ALL	BBB	179 - 235
45	X-RAY DIFFRACTION	15	ALL	DDD	1154 - 1212
46	X-RAY DIFFRACTION	16	ALL	DDD	637 - 766
47	X-RAY DIFFRACTION	17	ALL	DDD	501 - 636
48	X-RAY DIFFRACTION	18	ALL	DDD	944 - 1128
49	X-RAY DIFFRACTION	19	ALL	FFF	227 - 231
50	X-RAY DIFFRACTION	19	ALL	222	9 - 21
51	X-RAY DIFFRACTION	19	ALL	333	14 - 21
52	X-RAY DIFFRACTION	20	ALL	111	20 - 36
53	X-RAY DIFFRACTION	20	ALL	222	27 - 43
54	X-RAY DIFFRACTION	21	ALL	111	55 - 59
55	X-RAY DIFFRACTION	21	ALL	222	3 - 8

-
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-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABBBCCCDDDEEE

-
Synthetic DNA 50-mer (promoter ... , 2 types, 2 molecules 111222

-
Protein / RNA chain , 2 types, 2 molecules FFF333

-
Non-polymers , 4 types, 6 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-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABBBCCCDDDEEE

-Synthetic DNA 50-mer (promoter ... , 2 types, 2 molecules 111222

-Protein / RNA chain , 2 types, 2 molecules FFF333

-Non-polymers , 4 types, 6 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-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABBBCCCDDDEEE

-
Synthetic DNA 50-mer (promoter ... , 2 types, 2 molecules 111222

-
Protein / RNA chain , 2 types, 2 molecules FFF333

-
Non-polymers , 4 types, 6 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