PDB-7s00: X-ray structure of the phage AR9 non-virion RNA polymerase core

ID or keywords:

Entry

Database: PDB / ID: 7s00

Title

X-ray structure of the phage AR9 non-virion RNA polymerase core

Components

(DNA-directed RNA polymerase) x 2
DNA-directed RNA polymerase beta subunit
DNA-directed RNA polymerase beta' subunit

Keywords

TRANSCRIPTION / DNA-dependent multisubunit RNA polymerase / deoxyuridine / template strand promoter / RNAP

Function / homology

Function and homology information

DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase ...
Similarity search - Function

Biological species

Bacillus phage AR9 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Leiman, P.G. / Sokolova, M.L. / Fraser, A.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2022
Title: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Authors: Alec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman /

Abstract: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template ...

History

Deposition	Aug 28, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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	7s00.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb7s00.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	7s00.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7s00_validation.pdf.gz	669.8 KB	Display	wwPDB validaton report
Full document	7s00_full_validation.pdf.gz	702.1 KB	Display
Data in XML	7s00_validation.xml.gz	125.1 KB	Display
Data in CIF	7s00_validation.cif.gz	172.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/7s00 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/7s00	HTTPS FTP

-
Related structure data

Related structure data	24763C 24765C 7s01SC 7um0C 7um1C 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	#48 - Dec 2003 Catabolite Activator Protein similarity (1)

Deposited unit

c: DNA-directed RNA polymerase beta subunit

C: DNA-directed RNA polymerase

D: DNA-directed RNA polymerase

d: DNA-directed RNA polymerase beta' subunit

e: DNA-directed RNA polymerase beta subunit

E: DNA-directed RNA polymerase

F: DNA-directed RNA polymerase

f: DNA-directed RNA polymerase beta' subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: electron microscopy, The molecule is a mixture of monomers (minor fraction) and dimers (major fraction) in cryo-EM.

Unit cell

Length a, b, c (Å)	112.858, 166.270, 307.215
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "C" and (resid 1 through 533 or resid 535 through 649))
d_2	ens_1	(chain "E" and (resid 1 through 533 or resid 535 through 649))
d_1	ens_2	chain "c"
d_2	ens_2	chain "e"
d_1	ens_3	chain "d"
d_2	ens_3	chain "f"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	MET	LYS	B	1 - 533
d_1	2	ens_1	GLU	VAL	B	535 - 640
d_2	1	ens_1	MET	LYS	G	1 - 533
d_2	2	ens_1	GLU	VAL	G	535 - 640
d_1	1	ens_2	MET	ASN	A	1 - 484
d_2	1	ens_2	MET	ASN	F	1 - 484
d_1	1	ens_3	MET	ASN	D	1 - 410
d_2	1	ens_3	MET	ASN	I	1 - 410

NCS ensembles :

ID
ens_1
ens_2
ens_3

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.444081826121, -0.60547856341, 0.660444578265), (-0.616937800461, -0.327908899131, -0.715446367125), (0.64975309316, -0.725169954646, -0.227924230409)	-120.450082957, 3.44472128951, 106.898493696
2	given	(-0.442299975599, -0.615238781168, 0.652573347396), (-0.618797745489, -0.317345004556, -0.718596895527), (0.649199570058, -0.721646305492, -0.240346682953)	-120.593234526, 3.64425722625, 106.669656329
3	given	(-0.427626319316, -0.617074031548, 0.660572002599), (-0.629143091678, -0.321553234736, -0.707659867044), (0.649087591333, -0.718208296263, -0.250723237768)	-119.771835613, 2.84344187099, 107.128657335

#1: Protein	DNA-directed RNA polymerase beta subunit Mass: 58112.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage AR9 (virus) / Gene: AR9_g105 / Details (production host): pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star (DE3) / References: UniProt: A0A172JI16
#2: Protein	DNA-directed RNA polymerase Mass: 76978.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage AR9 (virus) / Gene: AR9_g089 / Details (production host): pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star (DE3) References: UniProt: A0A172JHZ2, DNA-directed RNA polymerase
#3: Protein	DNA-directed RNA polymerase Mass: 73100.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage AR9 (virus) / Gene: AR9_g154 / Details (production host): pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star (DE3) References: UniProt: A0A172JI62, DNA-directed RNA polymerase
#4: Protein	DNA-directed RNA polymerase beta' subunit Mass: 51947.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage AR9 (virus) / Gene: AR9_g270 / Details (production host): pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star (DE3) / References: UniProt: A0A172JIH0
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: an 1.5 ul aliquot of AR9 nvRNAP core (4.5 mg/mL) was mixed with an equal volume of a solution containing 100 mM Tricine pH 8.8, 270 mM KNO3, 15 % PEG 6000, 5 mM MgCl2, and incubated as a ...Details: an 1.5 ul aliquot of AR9 nvRNAP core (4.5 mg/mL) was mixed with an equal volume of a solution containing 100 mM Tricine pH 8.8, 270 mM KNO3, 15 % PEG 6000, 5 mM MgCl2, and incubated as a hanging drop over the same solution

Crystal

Density Matthews: 2.77 Å³/Da / Density % sol: 55.6 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: an 1.5 ul aliquot of AR9 nvRNAP core (4.5 mg/mL) was mixed with an equal volume of a solution containing 100 mM Tricine pH 8.8, 270 mM KNO3, 15 % PEG 6000, 5 mM MgCl2, and incubated as a ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.9786 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 24, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection

Resolution: 3.3→50 Å / Num. obs: 87373 / % possible obs: 98.6 % / Observed criterion σ(I): 1.1 / Redundancy: 4.49 % / B_iso Wilson estimate: 107.48 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.139 / Net I/σ(I): 10.07

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
3.3-3.5	4.15	1.17	13885	0.421	1.42	98.7
3.5-3.74		2.39	13096	0.774	0.757	99.3

-
Processing

Software

Name	Version	Classification
Coot	0.9.5	model building
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7S01

7s01

Resolution: 3.3→49.42 Å / SU ML: 0.4787 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2577	4305	5 %
R_work	0.2189	81770	-
obs	0.2208	86075	98.56 %

Solvent computation

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

Displacement parameters

B_iso mean: 155.21 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→49.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33878	0	2	0	33880

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	34522
X-RAY DIFFRACTION	f_angle_d	0.5751	46556
X-RAY DIFFRACTION	f_chiral_restr	0.0431	5157
X-RAY DIFFRACTION	f_plane_restr	0.0044	6004
X-RAY DIFFRACTION	f_dihedral_angle_d	4.5481	4481

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	C	X-RAY DIFFRACTION	Torsion NCS	0.996727242028
ens_2	d_2	c	X-RAY DIFFRACTION	Torsion NCS	1.2167871195
ens_3	d_2	D	X-RAY DIFFRACTION	Torsion NCS	1.63811954204

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 (%)
3.3-3.34	0.4314	137	0.4	2592	X-RAY DIFFRACTION	95.49
3.34-3.38	0.3749	143	0.3485	2728	X-RAY DIFFRACTION	99.69
3.38-3.42	0.346	142	0.3275	2700	X-RAY DIFFRACTION	98.65
3.42-3.47	0.318	145	0.3062	2742	X-RAY DIFFRACTION	99.93
3.47-3.51	0.3332	142	0.2882	2706	X-RAY DIFFRACTION	99.62
3.51-3.56	0.2827	141	0.2798	2686	X-RAY DIFFRACTION	98.95
3.56-3.61	0.3082	144	0.2825	2732	X-RAY DIFFRACTION	99.93
3.61-3.66	0.2956	143	0.2741	2708	X-RAY DIFFRACTION	98.72
3.66-3.72	0.2918	144	0.2737	2730	X-RAY DIFFRACTION	99.86
3.72-3.78	0.3023	143	0.25	2726	X-RAY DIFFRACTION	98.83
3.78-3.85	0.2963	143	0.2394	2720	X-RAY DIFFRACTION	99.97
3.85-3.92	0.2733	143	0.2292	2706	X-RAY DIFFRACTION	98.89
3.92-3.99	0.245	144	0.2253	2748	X-RAY DIFFRACTION	99.86
3.99-4.07	0.274	143	0.2116	2711	X-RAY DIFFRACTION	98.96
4.07-4.16	0.2522	145	0.2082	2747	X-RAY DIFFRACTION	99.52
4.16-4.26	0.2398	142	0.1995	2714	X-RAY DIFFRACTION	99.17
4.26-4.37	0.2592	145	0.2029	2736	X-RAY DIFFRACTION	98.94
4.37-4.48	0.2142	143	0.1885	2751	X-RAY DIFFRACTION	99.52
4.48-4.62	0.2317	143	0.1865	2706	X-RAY DIFFRACTION	99.13
4.62-4.76	0.225	145	0.1921	2752	X-RAY DIFFRACTION	98.87
4.76-4.93	0.2418	142	0.1879	2704	X-RAY DIFFRACTION	98.79
4.93-5.13	0.2521	145	0.1996	2756	X-RAY DIFFRACTION	98.91
5.13-5.37	0.2886	145	0.218	2745	X-RAY DIFFRACTION	98.9
5.37-5.65	0.2732	144	0.2223	2742	X-RAY DIFFRACTION	98.57
5.65-6	0.2743	144	0.2263	2729	X-RAY DIFFRACTION	98.46
6-6.46	0.3012	144	0.2435	2744	X-RAY DIFFRACTION	98.3
6.46-7.11	0.2841	144	0.2393	2742	X-RAY DIFFRACTION	97.27
7.11-8.14	0.2604	146	0.2108	2762	X-RAY DIFFRACTION	97.55
8.14-10.24	0.1834	146	0.168	2781	X-RAY DIFFRACTION	97.21
10.24-49.42	0.2225	145	0.1933	2724	X-RAY DIFFRACTION	91.17

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	3.57658353517	0.0510594043634	-4.43413365626	2.72555252915	1.87720631959	8.20600633042	0.329758883012	-0.316979322861	-0.24219274383	0.422130731345	-0.200260222855	0.239253615211	1.09540649026	-1.12927811817	0.2452713058	0.241414729229	-0.0741029108971	-0.153070196778	0.621081482086	0.149689500523	0.875823834347	-77.3178127213	-37.0420450831	-3.67834495081
2	2.83960781636	-0.898877633743	0.926439761093	1.63722287137	-1.81444074304	3.02053259242	0.0966856705385	-0.114199263114	-0.0961207128289	0.474645328064	-0.099780938357	0.580694194438	-0.54458621953	-0.435142689494	-0.0910195646307	0.64396043598	-0.0467623655828	0.186937214303	1.56728090593	-0.142655354328	1.11726012151	-97.0192408793	-14.8856484118	13.0989763722
3	4.81159915985	2.81719845959	0.450639741147	1.97169963952	-0.373232637077	6.48765982075	-0.198672766949	-1.65612111011	-0.963132497326	1.23017943939	0.138212763535	-0.843159783187	1.01255779166	1.18257783556	0.0413048643029	1.74616324739	0.313505608685	0.0416989517703	1.8078886053	0.118343613034	0.805923422056	-80.8622947553	-25.8995282368	56.4169120348
4	3.39099100995	0.217090745213	1.15224159848	3.07106909756	1.7432111406	4.39686169692	-0.325269227052	-0.522594010644	1.19337976367	0.465470513496	0.0322852950984	0.904932704546	-0.140466508012	-0.203488733375	0.339561569833	1.04783250618	0.174233422751	0.402229843689	1.59929415317	-0.179318996775	1.10780346684	-91.9557928332	-20.5112513191	45.1665898907
5	0.455138014267	-0.693202869496	0.662286225603	1.76374250285	0.288510586608	3.24376071126	-0.265083675054	-0.683758721444	-0.129750995347	0.709106903204	0.249342947972	0.526459884283	-0.637835646346	-0.314920445356	0.115308288938	0.72090915602	0.146864415392	0.250898903379	1.65074832167	-0.0901528496093	0.93049459212	-92.0691647508	-12.7676220025	22.9943253375
6	2.70128716357	-1.82484527377	1.46707530534	5.58232112158	-1.32880293302	3.89171531814	-0.0563599338621	-1.68004871778	1.04027393912	1.17128255097	0.027301512146	-0.14246178705	-0.225641450352	-0.83994945699	0.00561086543033	0.358996028311	0.0851148849281	0.0480369456246	1.43148976422	-0.087018196501	1.08991056263	-74.742234822	-15.7851504803	9.36051013805
7	2.49667249657	-1.09157163354	0.96843596917	3.69256041259	-1.19414685072	4.92967123228	-0.0373822995268	-0.121363860493	0.356487853637	0.341703271717	0.0538977975429	0.144634254348	0.396805005902	-0.577457538231	0.141491717288	0.422013266879	0.073868384433	0.124223694907	1.3335706621	-0.0990623227659	0.647483850889	-72.9206847759	-29.0215511304	16.9488237321
8	3.61608013768	-0.846270346379	1.16461481603	1.46917889763	-0.698066782251	1.29466383978	0.217911687129	-0.0445085008626	0.145494746109	-0.107889528949	0.0380384629178	0.317820166026	0.0744481017132	-0.252425845693	-0.172812382088	0.321226047386	-0.00133142182053	0.0529133641656	0.807640677178	0.0700219825445	0.640557270285	-77.7597258072	-26.9905228476	-9.38043577662
9	4.42600997744	-1.07648156604	-0.264736226664	3.24404379864	0.136108098778	1.31096849816	0.195287370143	0.653076208307	1.22353332095	-0.730936579824	-0.0290493793347	0.0999302091694	-0.456701356111	0.178095607865	0.161755256438	0.489932230978	0.0530182826666	-0.0602112472694	0.822080039517	0.332769378238	0.938368795114	-69.5522353799	-5.12001750469	-21.1094420375
10	3.7853171528	-2.06681734567	-1.01540649836	2.08200450089	2.0404029226	2.83162951691	0.246601978171	-0.429806741689	2.66851151039	-0.507118832221	0.506671261204	-0.314847413719	-1.71673519622	-0.92452532817	0.0332244517762	1.0851111381	0.430018946708	0.123193009319	1.29926942557	0.33625321745	2.15053716453	-86.9129051603	11.4848701365	-22.0524403251
11	2.71158197459	0.349536055353	0.235136683509	1.6438805119	-0.258167077098	1.53881693381	0.021583771729	0.364743907752	0.162504473415	-0.239317060942	0.0794984655508	0.099705490252	0.0587234288512	0.000570437877262	-0.0346590729821	0.31003666478	-0.00536716153173	-0.0259273925682	0.743716868338	0.076586682092	0.478177016905	-67.4728115628	-25.9758678169	-15.882088756
12	2.35211407995	1.56178832386	0.428372859235	4.51097776043	1.60147317885	5.58525501384	0.432688852878	-0.385794862264	-0.566784863103	0.182536972259	0.440545935376	0.348337261506	-0.123092949658	-1.35431765817	0.019571239379	0.593887283464	0.18588345494	0.110332105414	1.23851286934	0.24462886878	1.36971415484	-60.1706531759	9.2592559976	-4.38551050124
13	1.53965629831	-0.537127737234	-2.13477187036	1.85969655316	1.68199537635	5.78225092203	0.452547939686	0.155266494163	1.08597454484	-0.0944358242849	0.376526715758	-0.462648495176	-1.62097930655	-0.105298653069	-0.785342968245	1.05171398591	0.1054267884	0.0128024817419	0.650855382517	0.0156467538794	2.02562609527	-55.8995230883	28.3100466902	-1.19847795958
14	3.24366510683	0.407515622382	-1.44620520424	3.39940440824	0.550714330908	1.55859817466	0.0648154303203	0.402871706208	0.598804344078	-0.0777815120632	0.0317151035267	-0.721973937616	-0.0171366756174	0.400372880065	-0.14832817806	0.360442832358	0.045603097576	0.00873494919989	1.28221097026	0.280900400122	1.0712071744	-21.2871849243	-9.54161864078	-15.3065717831
15	2.23769714842	0.520142437966	0.490464085728	1.96213891183	-0.118956403232	0.1112340332	-0.0309446691861	-0.0841117415692	0.0876983187214	0.468765293517	-0.193196593988	0.145154045977	-0.0854777036457	-0.375963951968	0.160953243601	0.470921245975	0.100074332754	-0.0407657442631	0.948144807304	0.0272586269977	0.494129950246	-42.9841461723	-26.1408841849	8.70480636092
16	5.85958058725	-0.498308260967	-0.711940595193	5.16162665149	-0.835884302994	7.14905273036	0.328751880316	-0.920155059787	0.125263299701	1.12427134422	0.0309098138735	-0.372555208014	-0.190364203978	0.602062939312	-0.258332801834	0.61595338262	-0.0399975576871	-0.108694913292	0.830636177699	-0.275463715092	0.690472957194	-29.3557388785	9.75533818715	20.9713338884
17	2.08487010122	-1.47648541595	-0.303919490368	3.8381663797	-0.559747325944	6.23120740642	0.239714292761	-0.552873104597	0.515346153744	0.00597865995556	-0.0276957911082	0.440531484115	-0.327366962325	-0.165036387432	-0.115102672858	1.1109831068	0.060100227556	0.0234593749086	1.66831755805	-0.00109462712399	1.87691284943	-74.3467311216	40.6228927602	21.4839077393
18	0.820755852722	-2.43069353139	-0.152876340057	7.50003156294	-0.929223364057	6.07584870355	0.566913676975	0.765749433216	1.47544146854	-0.221681889258	-0.177662831406	0.96450243408	-0.693240135086	0.175975133025	-0.337633297837	1.65275422765	-0.321209433516	0.153452087175	2.7102763007	-0.139349356075	2.60518056654	-83.1722258057	40.9737040462	22.2954203878
19	4.6994759886	-2.6659165709	0.755231575868	1.83615923847	-1.35507009696	2.04554893221	0.00231439781608	0.193457009561	0.542516635214	0.0270973656839	0.0165547319729	-0.103273986439	-0.422350142946	-0.0284411220635	-0.00216152881158	0.424148851881	-0.0968123448715	0.0288885528084	0.615880716264	0.198259487177	1.16037743765	-48.8334627288	7.15784303445	-10.956694276
20	1.72682131091	0.238672814341	0.986002516423	2.47233496459	0.658798138152	1.81093984253	0.452396083783	0.862773919454	-0.211006973583	-0.309667163238	-0.222616156313	-1.18845627911	-0.334140193774	1.09651446133	-0.245955705684	0.890038878679	0.0286850311676	0.198341227134	1.53900133176	0.00882922453892	1.33966071564	-60.6761710186	64.801592783	56.6789465035
21	4.29858094424	-3.45897172929	-2.3789731422	6.03935544399	2.2531675317	2.13444125969	-0.388007350266	-0.879584306947	-0.154658928055	0.262232040256	0.823391926184	-1.01197302238	0.265775452934	0.849637663205	-0.38336744903	0.876385019724	0.100851014788	-0.108116611814	1.36850886952	-0.283888457083	1.25302136926	-42.6854629345	34.1064632187	55.684785227
22	2.36596266711	-2.24028812487	0.671912347416	4.41309238807	-4.56459067976	6.47322985054	0.337834984277	-0.509512681018	-0.291283127363	0.155982283365	0.0417338775587	-0.443486180738	0.769424535437	1.26622254721	-0.352857525737	0.842198626479	0.0165393779993	0.0569273296519	1.24660825109	-0.219734508194	0.944657737485	-65.1663579367	47.9866777641	69.4662624459
23	2.4577603593	0.13920443529	-0.34642902091	1.95691454444	-1.69432028283	4.94752474733	0.508434361313	0.0793155545968	0.141640580795	0.569247948982	-0.264424254016	-0.264960654158	-0.513804794096	0.581882631575	-0.273649752424	1.23485236844	-0.070000891244	0.153303136961	0.796385313817	-0.123871706763	0.919242733703	-75.811390566	66.96151399	78.108810256
24	0.249326223369	0.194305419782	1.08605835239	1.24671906024	-0.939435172133	5.13476664658	0.0822911501186	0.0990841428569	0.470638644521	0.245134562727	-0.358329443977	0.292364295517	-0.520443017602	-0.188478608911	-0.185789482273	1.09842365684	0.440285937341	0.396719985584	1.31360680969	0.138489567042	1.28372250096	-102.911611218	63.6488340779	63.3085029608
25	8.7616218748	4.18762626344	-0.445556882693	2.80560642505	-1.79592049443	4.59330132294	-0.46583940261	0.728968842153	1.62124821102	0.699979638346	0.554167545581	0.211322957573	-1.59319031473	-1.46479261816	-0.288273502747	1.5705312581	0.520317948764	0.061954571845	0.977625599873	0.308377089827	1.27675812026	-91.1631828612	78.5095842098	50.9349769786
26	1.36128347356	0.204054263799	-1.21075212949	1.39472451426	-0.670816260738	4.14925143473	0.0842887254984	-0.0461803833613	0.333913220203	0.642043359396	-0.35234234263	0.0195817496865	-0.871784188769	0.179549656999	0.353403415842	1.25607771391	0.0143349091714	0.261866900598	0.966566433004	-0.101288910544	0.989340454552	-86.7876196431	63.1351914368	83.0179208623
27	1.37794859983	0.475462356707	0.690132693431	2.54659628757	1.2566889507	2.50981706403	0.21197528213	-0.0428816078318	0.162009169877	0.625047713148	-0.0780526474976	-0.105040549718	-0.115910403869	0.152518617933	-0.0974373707283	1.0440750179	-0.0107870444923	0.224252626218	1.16989926976	-0.0284028667656	0.759930610791	-90.8101357497	51.9999983125	85.91988521
28	8.97915926855	0.782885850523	-0.473379754364	7.5000259204	0.0520619573615	5.29975918214	0.472034284312	0.711690534319	0.241851503061	-0.0750818603149	-0.421337042571	2.24840510005	1.2864241361	0.582449580037	-0.217366546595	1.35924140813	0.125917360618	-0.517629537958	1.44218764751	-0.300429547389	1.65357400399	-114.617855425	29.8168543288	48.5081844338
29	1.53032024453	0.756991992858	0.905887650649	1.37453837768	0.242842385273	1.02687708369	-0.297991222714	0.046285411574	-0.240080084538	0.893726951408	-0.0902044942642	0.291559983143	1.00975419885	-0.13401881031	0.293094317588	1.81659064851	-0.0771353124887	0.428266282591	1.29156028239	-0.00834617995005	0.973477504111	-97.5398225615	32.2105802092	101.94319815
30	1.19262438587	-1.25434478579	1.19510607198	4.09354590196	-1.0909394097	2.97360003722	-0.0778883777171	0.76360580217	-0.51532886705	0.0379510836706	-0.341115517698	0.974840759082	1.00634176284	0.0468969947589	0.365191283077	1.39873097548	-0.178342405621	0.610871547505	1.32490319172	-0.251275547247	1.60152382224	-104.256118036	2.90526137711	79.0772964033
31	4.09286327434	0.705958653195	-1.55877717912	0.454899859701	0.22554044414	1.46207738021	0.0358935252716	-1.58914855253	0.868258766007	1.31654049182	-0.674743940179	-0.87673529923	-0.773005801439	1.66090512287	0.244717958812	2.40196535838	-0.0337484593981	0.0598413886766	1.97855652457	0.274042930443	2.01280688711	-75.9113120374	17.6305036482	79.5151962295
32	3.58063124859	4.22221158687	2.71686292825	8.65011270197	0.722145221747	4.18404269582	-0.913869606233	-1.05230779986	-3.15069993173	-0.840371057523	0.771098950477	1.89969912371	0.895826923325	-2.76459185864	-0.0095229406756	1.55063982917	0.266738872065	0.154809230353	1.8462783736	-0.0549614582987	2.8284183259	-69.2348012271	9.6030564333	72.4351596414
33	4.28840736176	1.88818574678	-1.1563863393	3.02288311928	-2.19295860103	1.93053888449	1.08259753727	0.606849193637	-0.144858355051	-0.629042463145	-1.24756182136	-2.97040059901	0.369953269426	-0.0188858634094	0.66595957955	2.41196025891	0.11530538067	0.116773237386	1.39272462605	-0.19546256911	2.54429212041	-62.3375765486	10.4252391311	68.6785812034
34	3.78035340266	-0.00359973029093	-0.741492776021	5.62650696847	-3.06894923742	3.965659564	-0.454681483568	-0.22313725123	-0.931399603279	-0.227864305711	-0.608572488334	0.418172869189	0.903742034362	1.87539260891	1.06522309724	1.41888630504	-0.0609272304633	0.547283148331	1.58462557685	-0.369734285706	1.33001785923	-94.6160742054	2.21777851785	70.2218965917
35	6.22108990578	0.316107892515	0.61161840049	5.95642356925	0.991747074788	3.26619179394	-0.323020537787	1.69583690897	0.193744167957	-0.546348861962	0.253132245175	0.0605154008849	-0.393306562245	0.890079957678	0.0659301297331	1.63893089338	-0.272296202864	-0.0881450598736	2.21401264826	0.0963613154506	1.11384929507	-98.9150965173	18.74148513	24.3452271296
36	0.490325256691	-1.10606254792	-1.11770337601	2.91115622935	4.2178130645	6.62042350907	-0.625975785733	-0.314150319433	-0.18293213189	-0.502654132726	-0.491457311118	0.46382465994	1.0138372	1.0516669169	0.893529850708	1.85572642201	-0.136903320905	0.349373720671	1.74910016032	0.0995318955339	1.72823024693	-97.0178231614	31.7858308716	30.253670677
37	1.41867760258	-1.3730761043	-0.831847247868	4.22332965286	-1.02543574981	1.99216133048	0.308067206394	0.760317036754	-0.336865416905	0.516429029664	-0.63548695764	1.12532511903	-0.261705437111	-0.849551342835	0.247577158477	1.09820412945	0.0024937487719	0.427763535602	1.39974275977	-0.264735254969	1.27671774898	-111.97543431	39.6894042857	75.006920606

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'c' and (resid 1 through 29 )	c	A	1 - 29	1 - 29
2	2	chain 'c' and (resid 30 through 143 )	c	A	30 - 143	30 - 143
3	3	chain 'c' and (resid 144 through 252 )	c	A	144 - 252	144 - 252
4	4	chain 'c' and (resid 253 through 325 )	c	A	253 - 325	253 - 325
5	5	chain 'c' and (resid 326 through 394 )	c	A	326 - 394	326 - 394
6	6	chain 'c' and (resid 395 through 432 )	c	A	395 - 432	395 - 432
7	7	chain 'c' and (resid 433 through 484 )	c	A	433 - 484	433 - 484
8	8	chain 'C' and (resid 1 through 159 )	C	B	1 - 159	1 - 159
9	9	chain 'C' and (resid 160 through 234 )	C	B	160 - 234	160 - 234
10	10	chain 'C' and (resid 235 through 282 )	C	B	235 - 282	235 - 282
11	11	chain 'C' and (resid 283 through 535 )	C	B	283 - 535	283 - 535
12	12	chain 'C' and (resid 536 through 587 )	C	B	536 - 587	536 - 578
13	13	chain 'C' and (resid 588 through 649 )	C	B	588 - 649	579 - 640
14	14	chain 'D' and (resid 1 through 141 )	D	C	1 - 141	1 - 141
15	15	chain 'D' and (resid 142 through 284 )	D	C	142 - 284	142 - 284
16	16	chain 'D' and (resid 285 through 596 )	D	C	285 - 596	285 - 481
17	17	chain 'd' and (resid 1 through 177 )	d	D	1 - 177	1 - 161
18	18	chain 'd' and (resid 178 through 230 )	d	D	178 - 230	162 - 214
19	19	chain 'd' and (resid 231 through 426 )	d	D	231 - 426	215 - 410
20	20	chain 'e' and (resid 1 through 102 )	e	F	1 - 102	1 - 102
21	21	chain 'e' and (resid 103 through 382 )	e	F	103 - 382	103 - 382
22	22	chain 'e' and (resid 383 through 484 )	e	F	383 - 484	383 - 484
23	23	chain 'E' and (resid 1 through 159 )	E	G	1 - 159	1 - 159
24	24	chain 'E' and (resid 160 through 256 )	E	G	160 - 256	160 - 256
25	25	chain 'E' and (resid 257 through 311 )	E	G	257 - 311	257 - 311
26	26	chain 'E' and (resid 312 through 452 )	E	G	312 - 452	312 - 452
27	27	chain 'E' and (resid 453 through 601 )	E	G	453 - 601	453 - 592
28	28	chain 'E' and (resid 602 through 649 )	E	G	602 - 649	593 - 640
29	29	chain 'F' and (resid 1 through 269 )	F	H	1 - 269	1 - 269
30	30	chain 'F' and (resid 270 through 372 )	F	H	270 - 372	270 - 372
31	31	chain 'F' and (resid 373 through 432 )	F	H	373 - 432	373 - 432
32	32	chain 'F' and (resid 433 through 470 )	F	H	433 - 470	433 - 470
33	33	chain 'F' and (resid 471 through 512 )	F	H	471 - 512	471 - 512
34	34	chain 'F' and (resid 513 through 596 )	F	H	513 - 596	513 - 596
35	35	chain 'f' and (resid 1 through 160 )	f	I	1 - 160	1 - 144
36	36	chain 'f' and (resid 161 through 256 )	f	I	161 - 256	145 - 240
37	37	chain 'f' and (resid 257 through 426 )	f	I	257 - 426	241 - 410

-
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