PDB-7vn7: Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 7vn7

Title

Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning GACACGTGTC

Components

DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

Keywords

TRANSCRIPTION / Transcription factor-DNA complex

Function / homology

Function and homology information

plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / DNA-binding transcription factor activity ...
Similarity search - Function

Biological species

Serratia sp. (bacteria)

Arabidopsis thaliana (thale cress)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Nosaki, S. / Tanokura, M. / Miyakawa, T.

Funding support

Japan, 2items

Citation

Journal: Nat.Plants / Year: 2022
Title: Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout.
Authors: Nosaki, S. / Mitsuda, N. / Sakamoto, S. / Kusubayashi, K. / Yamagami, A. / Xu, Y. / Bui, T.B.C. / Terada, T. / Miura, K. / Nakano, T. / Tanokura, M. / Miyakawa, T.

History

Deposition	Oct 10, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 7, 2022	Provider: repository / Type: Initial release
Revision 1.1	Dec 28, 2022	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 11, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Nov 29, 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	7vn7.cif.gz	852.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7vn7.ent.gz	621.8 KB	Display	PDB format
PDBx/mmJSON format	7vn7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7vn7_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	7vn7_full_validation.pdf.gz	2 MB	Display
Data in XML	7vn7_validation.xml.gz	66 KB	Display
Data in CIF	7vn7_validation.cif.gz	91.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vn/7vn7 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/7vn7	HTTPS FTP

-
Related structure data

Related structure data	7vn2C 7vn3C 7vn4C 7vn5C 7vn6C 7vn8C 5zd4S 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (6) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #90 - Jun 2007 Fatty Acid Synthase similarity (3) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (5) #74 - Feb 2006 alpha-Amylase similarity (1) #208 - Apr 2017 Glucose Transporters similarity (1) #138 - Jun 2011 Glucansucrase similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (6)
#205 - Jan 2017
Nuclear Pore Complex
similarity (6)
#90 - Jun 2007
Fatty Acid Synthase
similarity (3)
#243 - Mar 2020
Voltage-gated Sodium Channels
similarity (5)
#74 - Feb 2006
alpha-Amylase
similarity (1)
#208 - Apr 2017
Glucose Transporters
similarity (1)
#138 - Jun 2011
Glucansucrase
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)

Deposited unit

C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

G: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

H: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

E: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

F: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

hetero molecules

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

1

C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

G: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

H: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
107 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

E: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

F: DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

hetero molecules

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

Unit cell

Length a, b, c (Å)	102.437, 93.211, 112.240
Angle α, β, γ (deg.)	90.000, 100.363, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein

Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 / Protein BIN2 SUBSTRATE 2

Mass: 48419.836 Da / Num. of mol.: 4 / Mutation: D82A,K83A,E172A,N173A,K239A,E359A,K362A,D363A
Source method: isolated from a genetically manipulated source
Details: The fused Maltose binding protein is derived from Escherichia coli O157:H7
Source: (gene. exp.)

Serratia sp. (strain FS14) (bacteria), (gene. exp.)

Arabidopsis thaliana (thale cress)
Strain: FS14 / Gene: malE, JW3994, BZR1, BIS2, At1g75080, F9E10_7 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0, UniProt: Q8S307

#2: DNA chain

DNA (5'-D(*TP*TP*GP*AP*CP*AP*CP*GP*TP*GP*TP*CP*AP*AP*A)-3')

Mass: 4593.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#3: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.52 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium cacodylate pH 6.5, 200 mM ammonium acetate and 10 mM calcium chloride and 10% (w/v) polyethylene glycol (PEG) 4000

-
Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.11→47.5 Å / Num. obs: 116947 / % possible obs: 98.1 % / Redundancy: 3.5 % / B_iso Wilson estimate: 34.72 Å² / CC_1/2: 0.999 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.11→2.15 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5754 / CC_1/2: 0.79

-
Processing

Software

Name	Version	Classification
PHENIX	1.18_3855	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZD4

5zd4

Resolution: 2.11→36.8 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2438	5846	5.01 %
R_work	0.2065	110949	-
obs	0.2083	116795	97.75 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.11→36.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13592	1220	140	299	15251

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15408
X-RAY DIFFRACTION	f_angle_d	0.8138	21140
X-RAY DIFFRACTION	f_chiral_restr	0.0527	2306
X-RAY DIFFRACTION	f_plane_restr	0.0048	2526
X-RAY DIFFRACTION	f_dihedral_angle_d	24.3881	5760

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 (%)
2.11-2.13	0.3487	189	0.2908	3671	X-RAY DIFFRACTION	97.87
2.13-2.16	0.3112	185	0.2697	3712	X-RAY DIFFRACTION	98.04
2.16-2.19	0.3076	221	0.262	3683	X-RAY DIFFRACTION	98.09
2.19-2.21	0.2896	192	0.2558	3674	X-RAY DIFFRACTION	97.87
2.21-2.24	0.2906	192	0.254	3679	X-RAY DIFFRACTION	98.17
2.24-2.27	0.2872	202	0.2537	3725	X-RAY DIFFRACTION	98.13
2.27-2.31	0.2949	192	0.2493	3658	X-RAY DIFFRACTION	98.04
2.31-2.34	0.3275	186	0.2559	3748	X-RAY DIFFRACTION	98.25
2.34-2.38	0.3112	200	0.2528	3666	X-RAY DIFFRACTION	98.32
2.38-2.42	0.2918	197	0.2475	3709	X-RAY DIFFRACTION	98.29
2.42-2.46	0.2948	193	0.2487	3698	X-RAY DIFFRACTION	98.33
2.46-2.5	0.3115	196	0.2463	3749	X-RAY DIFFRACTION	98.55
2.5-2.55	0.3028	200	0.2405	3710	X-RAY DIFFRACTION	98.56
2.55-2.6	0.2446	178	0.2356	3709	X-RAY DIFFRACTION	98.48
2.6-2.66	0.2672	192	0.2328	3739	X-RAY DIFFRACTION	98.47
2.66-2.72	0.2705	214	0.2304	3679	X-RAY DIFFRACTION	98.56
2.72-2.79	0.2932	194	0.239	3729	X-RAY DIFFRACTION	98.44
2.79-2.86	0.2988	192	0.2546	3738	X-RAY DIFFRACTION	98.5
2.86-2.95	0.3145	211	0.2554	3678	X-RAY DIFFRACTION	98.13
2.95-3.04	0.297	196	0.2451	3702	X-RAY DIFFRACTION	97.92
3.04-3.15	0.242	184	0.2273	3730	X-RAY DIFFRACTION	98.47
3.15-3.28	0.2445	178	0.221	3706	X-RAY DIFFRACTION	97.76
3.28-3.43	0.2399	197	0.2127	3691	X-RAY DIFFRACTION	97.15
3.43-3.61	0.2308	186	0.2024	3674	X-RAY DIFFRACTION	96.94
3.61-3.83	0.2342	221	0.1874	3642	X-RAY DIFFRACTION	96.62
3.83-4.13	0.2152	164	0.1677	3688	X-RAY DIFFRACTION	96.37
4.13-4.54	0.1592	186	0.1576	3698	X-RAY DIFFRACTION	97.17
4.54-5.2	0.1675	218	0.1512	3681	X-RAY DIFFRACTION	96.61
5.2-6.54	0.207	204	0.1789	3682	X-RAY DIFFRACTION	96.14
6.54-36.8	0.218	186	0.1511	3701	X-RAY DIFFRACTION	94.55

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	3.75441232423	-0.3555981289	-0.805764806996	1.8607156211	-0.00461458634376	1.99628144946	0.04674659458	-0.162955095546	0.104068448935	0.0175897065142	-0.0232947583099	-0.0426662933902	-0.155194634086	0.112745774364	-0.0161012917182	0.264910464501	-0.03266111067	0.0271278608268	0.206915969964	0.0271629375777	0.177931371236	-2.65020154	14.3921066075	11.241012434
2	2.51439038098	-1.2086744137	0.823706006748	3.84064142927	-0.910978277611	2.74345507856	0.252874738767	-0.229954772376	-0.4554212552	0.267881083157	0.0529539148922	-0.122135467598	0.838347583329	-0.059962361283	-0.245933726872	0.491906246486	-0.0678020739569	-0.108399955314	0.203841782245	0.00529186148288	0.35729155893	-6.6357851279	-36.75375137	28.2901646836
3	2.51062438316	0.755141995093	0.337598011526	1.82295262552	0.0623646459983	1.73623333885	-0.0772791512438	0.0614739820275	-0.0600399020432	0.395987311209	0.164352576938	-0.284407577673	-0.103841557844	0.20721151152	-0.0845461460704	0.409828648256	0.102201472329	-0.0480158840261	0.338466351691	-0.0634122599918	0.269859314127	-8.07455796064	14.341874857	44.7923443019
4	1.58079936926	1.34444722745	0.422121738241	2.60986539757	0.667700219745	2.39584820985	0.204471003703	0.116477513091	-0.348194126354	0.0756193980057	0.0676427131136	-0.139787530363	0.950248310823	-0.184661265776	-0.22273016771	0.494347259331	-0.0406189666764	-0.105086824277	0.208505477435	0.0258873265131	0.401352675473	-2.47553105636	-36.8115358845	26.002138742
5	0.542474805833	0.0113825837829	1.1431390082	1.93017716593	-0.867862056618	8.31643383877	0.205456933908	-0.0904478369159	-0.0834079735222	0.36854265712	0.037035346676	0.01792639574	0.240515391188	-0.67696211994	-0.213514952698	0.234219783269	-0.0614101237447	-0.00110674039596	0.210916285047	0.0135380559925	0.223269007694	-6.19913129989	-23.795036529	28.7497379438
6	1.48933553996	0.426908329536	0.53169855974	1.19288337018	-0.259660975228	6.92712329642	0.0889105277762	-0.0712617255971	-0.176055225403	0.104251798757	0.0824295434036	-0.164205034176	0.275170497095	0.276380884812	-0.18300160098	0.259156814889	-0.0294288327684	-0.00565105538973	0.156409299583	-0.0164055417194	0.231686642979	-3.24682415663	-23.7921841317	25.5843208158
7	6.14494829575	3.80113503486	1.13093914887	5.69963701472	2.08541501322	3.8935044824	-0.131410465642	0.708813909873	0.340899549882	-0.570930859364	0.118762608444	0.228271250772	-0.21911054858	0.281622255465	0.0207792112818	0.222779816203	0.0628545986996	0.00362189120405	0.349883216625	0.039208924575	0.209351953208	25.85534199	-11.4780800123	35.2454556615
8	4.0067385677	0.260915639306	-0.238834625288	0.972733426429	-0.129406579425	1.26691215276	0.10396737785	-0.270051628889	0.0495971558702	0.0771923168998	-0.127874440249	-0.14398088675	0.0062832019494	0.52353504966	0.0234290469703	0.262783791451	0.0122670330805	-0.00917032670293	0.403221625166	0.02114892489	0.171621293264	43.2637873656	-14.0285890209	46.2889530577
9	1.27467626002	-2.11829070774	0.765627857808	7.67349152854	-5.90837672116	5.30105799601	-0.0358812423433	0.112278744083	-0.0419900418845	-0.0758853645693	0.2136498008	0.273827670953	-0.460942919517	-0.702263839024	-0.147953019606	0.777273833884	-0.0911372694219	-0.128328546244	0.622445587739	-0.158261066199	0.419442850572	45.624537435	29.712882429	29.9801802907
10	3.3828138683	-0.162651529562	-0.338480140601	1.38182700681	-0.338634562488	2.60982693224	0.0444118726412	0.0857724145355	0.0515631944949	-0.0603989413926	0.0229959542121	0.198564127241	0.0697735030658	-0.821797120584	-0.0569574159865	0.227918768504	-0.0533125660016	-0.0024567933993	0.425030249702	0.018011915097	0.190557312078	52.4039236947	-14.4965843624	11.1134261749
11	0.766574059398	0.34715743455	-0.564136188234	3.3924453349	2.00434489845	2.03055084411	-0.0571611612928	-0.202336844744	-0.19036131306	0.662817880834	0.336526003197	-0.290047223805	-0.00681278465241	0.498982886478	-0.200243626591	0.916386997491	0.0409732250043	-0.174631571902	0.674437749572	0.0569939940628	0.588641033299	48.4725875852	34.2367604788	28.1149669285
12	0.152070045055	-0.516226801511	-0.988815686133	1.43375609228	3.29663813788	7.51394243931	0.328627707775	0.190173043215	0.00347203256971	0.262306805301	0.0197359040755	-0.0587783498267	1.69605509047	-0.119242994628	-0.308885225166	0.899706818975	0.0120552633034	-0.0814670506607	1.0160640848	0.000801832880758	0.381896951693	46.7989242765	23.7730232439	29.6082533795
13	0.392442094592	0.583687702335	-1.83493216415	0.769873434026	-2.85707585936	2.03828861518	0.187875668703	-0.13778759043	-0.00508102949235	-0.287573814611	0.112055096182	0.15761749354	1.86460749896	0.0853728542303	-0.264010631592	1.0108512584	0.149125813308	-0.102482830583	1.04967559611	0.0192013331025	0.36028290473	45.1815068823	23.7378685312	26.0003896631

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 -348 through 26 )	C	A	-348 - 26	1 - 375
2	2	chain 'C' and (resid 27 through 88 )	C	A	27 - 88	376 - 437
3	3	chain 'D' and (resid -347 through 26 )	D	C	-347 - 26	1 - 374
4	4	chain 'D' and (resid 27 through 88 )	D	C	27 - 88	375 - 436
5	5	chain 'G' and (resid -3 through 11 )	G	E	-3 - 11
6	6	chain 'H' and (resid -3 through 11 )	H	F	-3 - 11
7	7	chain 'A' and (resid -348 through -276 )	A	G	-348 - -276	1 - 73
8	8	chain 'A' and (resid -275 through 3 )	A	G	-275 - 3	74 - 352
9	9	chain 'A' and (resid 4 through 88 )	A	G	4 - 88	353 - 437
10	10	chain 'B' and (resid -346 through 20 )	B	I	-346 - 20	2 - 368
11	11	chain 'B' and (resid 21 through 88 )	B	I	21 - 88	369 - 436
12	12	chain 'E' and (resid -3 through 11 )	E	K	-3 - 11
13	13	chain 'F' and (resid -3 through 11 )	F	L	-3 - 11

-
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://pdbjlvh1.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