PDB-7l6v: Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12

ID or keywords:

Entry

Database: PDB / ID: 7l6v

Title

Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12

Components

BoNT/A
JPU-A5
JPU-C1
JPU-D12
JPU-H7
Single-domain antibody VHH ciA-F12

Keywords

ANTITOXIN / neurotoxin / enzyme inhibitor

Function / homology

Function and homology information

bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Lam, K. / Jin, R.

Funding support

United States, 1items

Citation

Journal: Plos Pathog. / Year: 2022
Title: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
Authors: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.

History

Deposition	Dec 24, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 19, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2	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	7l6v.cif.gz	480.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7l6v.ent.gz	346.8 KB	Display	PDB format
PDBx/mmJSON format	7l6v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7l6v_validation.pdf.gz	479.9 KB	Display	wwPDB validaton report
Full document	7l6v_full_validation.pdf.gz	491.6 KB	Display
Data in XML	7l6v_validation.xml.gz	42.4 KB	Display
Data in CIF	7l6v_validation.cif.gz	61.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/7l6v ftp://data.pdbj.org/pub/pdb/validation_reports/l6/7l6v	HTTPS FTP

-
Related structure data

Related structure data	7lzpC 7m1hC 7na9C 7t5fC 3v0aS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5m6u-d 5k7g-d 5t8f-d 6chv-d 5vlr-d 5dxu-d 4w9n-d 5e6m-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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: BoNT/A

B: JPU-C1

C: JPU-A5

D: JPU-H7

E: Single-domain antibody VHH ciA-F12

F: JPU-D12

hetero molecules

116 kDa, 6 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)	115.899, 157.645, 173.001
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222
Space group name Hall	I22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1/2 #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

-
Protein , 2 types, 2 molecules AC

#1: Protein	BoNT/A / BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / ...BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / Neurotoxin type A / Peptidase M27 Mass: 48551.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) Gene: a, A, boNT, bont, bonta, botA, ACP52_06670, GJ703_01514 Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4, bontoxilysin
#3: Protein	JPU-A5 Mass: 13674.280 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

#1: Protein

BoNT/A / BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / ...

Mass: 48551.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium botulinum (bacteria)
Gene: a, A, boNT, bont, bonta, botA, ACP52_06670, GJ703_01514
Production host:

Escherichia coli (E. coli) / References: UniProt: Q7B8V4, bontoxilysin

#3: Protein

JPU-A5

Mass: 13674.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vicugna pacos (alpaca) / Production host:

Escherichia coli (E. coli)

-
Antibody , 4 types, 4 molecules BDEF

#2: Antibody	JPU-C1 Mass: 13297.776 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Antibody	JPU-H7 Mass: 13326.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#5: Antibody	Single-domain antibody VHH ciA-F12 Mass: 13201.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#6: Antibody	JPU-D12 Mass: 13747.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 523 molecules

#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.41 Å³/Da / Density % sol: 63.95 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20 % isopropanol, 0.1 M Na citrate pH 5.6, 20 % PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.01→116.52 Å / Num. obs: 103244 / % possible obs: 98.6 % / Redundancy: 2.8 % / B_iso Wilson estimate: 34.82 Å² / CC_1/2: 0.995 / R_pim(I) all: 0.089 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.01→2.04 Å / Num. unique obs: 5017 / CC_1/2: 0.352

-
Processing

Software

Name	Version	Classification
PDB_EXTRACT		data extraction
PHENIX	1.19_4092	refinement
XDS		data reduction
Coot		model building
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3V0A

3v0a

Resolution: 2.01→116.52 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2344	5109	4.98 %
R_work	0.1968	97538	-
obs	0.1986	102647	97.67 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→116.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7965	0	9	520	8494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	8143
X-RAY DIFFRACTION	f_angle_d	0.7986	11026
X-RAY DIFFRACTION	f_chiral_restr	0.0529	1194
X-RAY DIFFRACTION	f_plane_restr	0.0045	1435
X-RAY DIFFRACTION	f_dihedral_angle_d	13.0762	2928

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 (%)
2.01-2.03	0.3257	149	0.333	2983	X-RAY DIFFRACTION	90.31
2.03-2.06	0.3417	171	0.3294	3056	X-RAY DIFFRACTION	93.84
2.06-2.08	0.3872	148	0.3192	3213	X-RAY DIFFRACTION	96.22
2.08-2.11	0.3016	168	0.296	3241	X-RAY DIFFRACTION	98.3
2.11-2.14	0.3215	172	0.2866	3256	X-RAY DIFFRACTION	98.65
2.14-2.17	0.3409	172	0.286	3228	X-RAY DIFFRACTION	98.98
2.17-2.2	0.3061	167	0.2735	3275	X-RAY DIFFRACTION	98.99
2.2-2.23	0.3	199	0.2699	3267	X-RAY DIFFRACTION	98.92
2.23-2.26	0.3325	204	0.2742	3231	X-RAY DIFFRACTION	98.91
2.26-2.3	0.322	180	0.2528	3257	X-RAY DIFFRACTION	99.02
2.3-2.34	0.2724	170	0.2466	3285	X-RAY DIFFRACTION	99.34
2.34-2.38	0.3058	164	0.2445	3274	X-RAY DIFFRACTION	98.76
2.38-2.43	0.28	174	0.2403	3245	X-RAY DIFFRACTION	98.47
2.43-2.48	0.279	167	0.2312	3243	X-RAY DIFFRACTION	97.82
2.48-2.53	0.2743	173	0.2219	3275	X-RAY DIFFRACTION	99.14
2.53-2.59	0.2472	166	0.2122	3300	X-RAY DIFFRACTION	99.34
2.59-2.66	0.2684	190	0.2073	3297	X-RAY DIFFRACTION	99.29
2.66-2.73	0.2588	169	0.206	3290	X-RAY DIFFRACTION	99.2
2.73-2.81	0.2748	181	0.1995	3275	X-RAY DIFFRACTION	99.25
2.81-2.9	0.2279	171	0.1993	3317	X-RAY DIFFRACTION	98.92
2.9-3	0.2517	181	0.1988	3232	X-RAY DIFFRACTION	98.41
3-3.12	0.2326	154	0.1961	3335	X-RAY DIFFRACTION	98.78
3.12-3.26	0.2449	163	0.1848	3210	X-RAY DIFFRACTION	95.74
3.26-3.44	0.2219	157	0.1768	3309	X-RAY DIFFRACTION	98.72
3.44-3.65	0.2123	156	0.1793	3292	X-RAY DIFFRACTION	98.43
3.65-3.93	0.1989	178	0.1643	3289	X-RAY DIFFRACTION	97.94
3.93-4.33	0.1862	161	0.1546	3285	X-RAY DIFFRACTION	97.26
4.33-4.96	0.166	171	0.1457	3185	X-RAY DIFFRACTION	94.51
4.96-6.24	0.185	166	0.1728	3312	X-RAY DIFFRACTION	96.83
6.25-116.52	0.2103	167	0.1811	3281	X-RAY DIFFRACTION	92.22

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	1.23552034229	-0.658972783145	-0.507667453322	2.51396600884	-0.132395123586	1.76174951519	0.0379535570431	-0.0835359719743	-0.0654070114483	0.150572242982	-0.0339046947498	0.39200140906	0.037303238303	-0.135596627172	-0.00913733611979	0.238774552995	0.0137033773368	0.0477169815188	0.288423658324	0.0398600632014	0.317171063767	-72.3371682538	32.3895826775	38.6394019007
2	0.94268763088	-0.10471177253	-0.0897422645131	1.20719659764	-0.152376016628	0.599268578697	0.00817634036033	0.0563323905792	-0.14507717375	-0.0399575455982	0.0329959209363	0.255728132442	0.03894479207	-0.0958208064195	-0.0417093398824	0.254855416302	-7.52102774978E-5	-0.00288435831117	0.277008762862	0.0194029931409	0.300246314392	-69.1598708837	28.5071259718	28.3601931879
3	1.57656017756	-0.738111175257	0.333254710886	1.58882285895	-0.492248925206	0.921308625572	0.0914673989846	0.249931516932	-0.11365173062	-0.24145541888	-0.0462230730729	0.135497620772	0.0656147467739	-0.023264601317	-0.0296730256386	0.262435606143	-0.0152394987073	-0.0156754414003	0.252177118424	-0.0138582562291	0.210863875202	-63.7382251452	31.416163944	17.9966386707
4	1.48789297338	-0.293719845971	1.65661476916	0.972681993803	-0.597640744097	3.46338006489	-0.113914978859	0.815309876362	-0.368206892378	-0.343289116074	0.214905344414	0.701597109348	0.270204684697	-0.737274817905	-0.0630053628531	0.476558672454	-0.112852601834	-0.186578965726	1.01305007892	0.0930841390553	1.57787275382	-102.363188636	18.0655481841	14.4098233801
5	2.72587810658	-0.198755770078	-0.332781451225	2.33641825653	-0.199009515847	1.68667237128	0.211703963025	0.663137002736	-0.637479978697	-0.48524242704	0.117624424449	1.0017814227	0.223334046445	-0.733651484172	-0.270632680461	0.416498267911	-0.0264159210932	-0.202272888943	0.763892364143	0.0433530778749	0.995867560966	-95.7232811809	25.1834812255	15.1766589896
6	0.0429080438322	-0.283669228029	0.00046913195893	7.49515911732	-1.65235835912	1.57694048178	0.4163326764	0.495962919615	-0.41175724936	-0.325429349645	-0.0241432977667	0.705092777812	-0.0156775950937	-0.0602238913216	-0.425413808786	0.519006968314	0.0319519493196	-0.220205851391	0.684699763762	0.158931192134	1.07990144754	-86.0777151341	3.86016768479	12.3335651822
7	3.19405678312	1.46106201633	-1.41760106117	4.05454689239	-2.67513926219	3.99025763299	-0.0211065710176	-0.100369305974	-0.523876212493	0.15998156783	-0.0861295002299	0.454001529554	0.0675253113906	-0.554858661897	0.191731068831	0.596172388	-0.140012439193	-0.143747207088	0.537518457408	0.0641901327447	1.08986045147	-88.3959624111	-12.5324422095	21.9532234835
8	5.37246536991	-0.322060439474	-0.290207840913	4.16286252998	0.570259185538	3.83409186178	0.260292869797	-0.102888669933	-0.495387955822	-0.113430687683	-0.2797191839	0.906619910664	-0.357486839559	-0.413611037701	-0.0362354409184	0.412533007777	-0.00441179218451	-0.104992042623	0.362221156764	0.0259606654757	0.76772791806	-80.6067433447	0.336732679451	20.8667589936
9	4.00961982919	1.44507360614	0.330214050027	2.35218973954	-0.354684577074	2.66013550811	-0.017149279037	-0.173248993982	0.508326443131	0.221002435379	0.0117389124127	0.904406750962	-0.178516884967	-0.377414173351	-0.0960186944587	0.361538470409	0.0201418577121	-0.00151394158629	0.343319693172	-0.035567293921	0.753894380295	-79.3490018571	-2.12295637415	29.2966113075
10	2.00425257312	1.11649608447	0.449465355569	7.39176176563	-2.69705094719	4.38973741279	0.485965344876	-0.699881302592	0.629693858323	1.11993000646	0.249531451411	0.893146924651	-0.0668540950372	-0.685004839795	-0.713059802335	0.655310694466	-0.0417050947445	0.0802928879981	0.652095077551	0.0760224765269	0.789299962868	-80.2304183615	-9.81286297248	35.687775316
11	1.36657917238	-0.201301828723	0.819038513195	2.38606505303	-0.595430625122	1.02146049992	-0.0182811150422	-0.191907737338	-0.128168323152	0.11406897592	0.17149319032	0.866217604043	-0.0625985409122	-0.276354803643	-0.173466614265	0.419754238931	0.0318062904117	-0.0206552975951	0.406235729363	0.034902997376	0.785794216048	-79.9832230124	-2.88542606596	23.0886849911
12	4.6053594873	5.11215229472	-1.42053066097	7.64123148758	-1.61759985451	2.00330081879	-0.491232914645	-0.0643677782361	-0.161126247073	-0.35470892064	0.402170327814	1.21695069548	0.281015591299	-0.650252563851	0.119482574733	0.385744586423	-0.00593438561243	-0.0713490240988	0.603440186054	0.121079567135	1.03632730814	-90.6220746224	-3.23725848728	23.9889842916
13	4.70212725328	1.27242169691	-2.58830881908	1.93825135162	-0.24984602234	1.55033822774	0.0514568439183	-0.910229703406	-0.387568563649	0.378835838955	-0.424318052194	-0.1979211956	-0.1652076235	0.799853089708	0.337855360003	0.39264615335	-0.0629721740822	-0.0312054520544	0.483541350175	0.0241563524654	0.385956004312	-45.3429096325	47.7106495497	23.6279169627
14	0.0270848893662	-0.220614677511	-0.050291528791	5.27926945448	-3.46828225074	5.26585331701	-0.189706012388	0.456742966204	0.420151141778	0.0526046811243	-0.122235154378	-0.395679162095	-0.467564646148	0.451623195407	0.25527380538	0.486881353668	-0.130171492159	-0.0302320048736	0.63312272154	0.247651899112	0.607427092572	-30.8020195411	65.971956035	7.30110552158
15	2.11235920972	0.802399439459	0.376969291518	2.55983513881	-0.391024741718	1.31047587226	-0.143075723428	0.242968156925	0.0278240595759	-0.207791212686	-0.0214693885019	0.0180020330221	-0.0679895914039	0.083723782214	0.146238303623	0.367605216318	-0.0241082992575	-0.00331232283303	0.340854838922	0.0226653237131	0.270031294111	-46.7986865079	52.0405585317	12.2457805782
16	3.29521278643	0.768444519041	0.861497372562	1.96623379829	0.827039131814	3.9588919983	-0.285545220161	-0.283518585294	0.802188883156	0.255429440787	0.103288988577	0.153291702728	-0.56397276046	-0.118099691844	0.114155208026	0.548547662455	0.00607193596697	-0.0248609667274	0.355442163052	-0.0217159012215	0.480587636003	-48.859384803	64.8533295382	13.541152598
17	3.51796024977	-0.675054429234	0.0410562229585	8.08214618571	-0.577786860676	5.66784135083	0.0868637314048	0.66970122323	0.0385522932919	0.0350385454876	-0.13507581221	0.51326211899	-0.343653649578	-0.647065683604	0.115787057181	0.496208845395	-0.0858474159281	-0.0536481866074	0.507681474548	0.032471032689	0.292587891101	-52.2190986156	52.0380362512	1.55513381052
18	9.91817593867	-2.92012303742	-3.3271660525	2.76085748503	-1.72434782356	4.97482802854	0.0288065800164	0.275690444474	0.188014809302	0.776441259106	-0.066528836531	0.0948010554982	-0.648498085658	-0.0916559927733	0.164975357197	0.64825773188	-0.0741939991419	-0.102962584942	0.450380481583	0.218729687939	0.538648641305	-45.5197882736	65.6624406177	0.905984599685
19	1.51791043829	0.454273301428	0.326740129416	4.96667319165	-0.725695940683	1.72047582233	-0.0229466353348	0.241779563779	-0.146295219103	-0.452173108286	-0.0763092616565	-0.390730442505	0.127586895926	0.432236544407	0.114829771083	0.403939226841	-0.0320199452009	-0.0157651157461	0.377315766545	0.0332109418026	0.292787843922	-42.9775760794	50.8632431495	6.11874440124
20	1.5001868493	0.696583038152	0.0920037479077	2.47850783252	-0.596463118826	0.744932215143	-0.0351103207762	0.195365822787	0.511778159549	-0.0521476809158	0.0153278319177	0.0119189429513	-0.402706885159	0.17069664174	0.0274387327669	0.389956324905	-0.0510452640935	-0.0183169901522	0.320546850421	0.0347410634613	0.250280280132	-48.173015641	57.8523614685	13.9644965878
21	3.0802493118	-0.0242555619464	0.0913217226601	4.31022886422	-0.00591016837241	4.25770427821	-0.0422180654176	-0.110218527673	0.677327158692	0.126296987419	-0.552946892114	-0.31708455024	-0.811838334901	0.692062328953	0.66705034677	0.537161635629	-0.189842033662	-0.0801304926302	0.4719594405	0.0493461022984	0.571764286063	-34.0677189358	66.8670706623	13.3193400777
22	7.0286505793	-0.869746107121	0.98042143039	6.28934325045	-0.0416051794429	8.79976975484	-0.254945977458	0.024945435694	0.970935387491	-0.00728448977243	0.379430421877	-0.184079723235	-1.11378734671	0.391582632973	-0.0728619470818	0.394962905463	-0.0465543518081	0.0172095152678	0.380880683292	-0.0754674602775	0.458318412023	-88.0756245578	45.8130164752	59.5624932248
23	1.40199849189	-0.222443741615	-0.0201543070771	2.6183024947	-0.0813200404492	1.78709300881	-0.0444112962851	-0.224608380169	-0.106376313792	0.320173247297	-0.0269988582725	-0.122196269935	-0.0390630038791	0.106689795435	0.0845176964307	0.241381635413	0.0243166367896	0.00988634542221	0.358843150032	-0.00417388887009	0.225442936735	-89.5692175014	34.155041307	61.6952865367
24	1.8217720335	1.7441949031	-0.758426379124	3.03240693479	0.955123657323	3.26443966779	0.234584763785	-0.901857824409	-0.311102701142	0.206209712724	0.288544543549	-0.492377683178	0.190117709521	0.60464751889	-0.617856207468	0.281008310985	0.0379677495495	-0.0216594560279	0.61853200359	-0.0235584076193	0.357264762336	-77.6361536323	33.278735789	62.9635936907
25	2.44316794455	-0.3867441855	0.822491760912	1.15254241414	-0.135512227864	2.23882208817	0.0228518475298	-0.281803870638	-0.133546936084	-0.114585322655	0.0263739882946	-0.139413355197	0.21774555037	-0.12048860053	-0.0346378117963	0.34354512451	-0.000775869532984	0.0760329361274	0.359735730462	-0.00635213773008	0.349348109035	-83.4280145966	30.0104422173	52.4819544146
26	2.23316092617	-1.29314486955	1.35503063336	4.92142736039	-1.66287523936	3.15864983198	-0.124595353111	-0.0709940900969	-0.192376374776	-0.0465612981938	0.138499059785	-0.108206768306	0.199921946935	-0.099563189455	-0.0515777567049	0.318878666643	0.0198587339037	0.0321571878713	0.327586154606	0.0403210629743	0.307166501807	-90.2177722039	29.6663886749	57.5623945749
27	0.941228655507	0.939982090868	-0.432234299793	2.90602724285	-1.13407423123	1.48924422603	-0.143041931032	-0.362082033272	-0.25435581267	0.0555156206458	-0.023072841878	-0.667710398298	0.147063535883	0.329079464638	0.199585053156	0.353840657672	0.0714068166582	-0.0356735468113	0.476188886289	0.00892394497361	0.436733211966	-82.0252336365	28.2498289847	65.9379483481
28	4.08738809833	2.50386553109	2.29297128975	2.01387913592	0.165318055044	4.48215876648	-0.0232694833352	-0.10548556763	-0.166972873606	-0.0232927496617	0.0977092243862	-0.0815721686987	-0.314767913649	0.111531052125	-0.133392986049	0.354862277701	0.0175395466702	0.077236324519	0.361060115439	-0.00374387952784	0.397315602792	-75.9987321963	38.0753956063	53.9050650731
29	2.25537195988	0.507930109028	-0.815663232896	2.27036426966	-0.374195187194	2.06322928938	-0.0195269405473	-0.356838721168	-0.0232232680948	0.273509716472	-0.050674366996	-0.288816941909	-0.0171781371051	0.366547019312	-0.0287321460865	0.375810403193	0.043455020742	-0.0335493950878	0.542656468579	-0.00467932789925	0.356144940992	-82.2536271225	34.7020543081	68.2021714442
30	6.12398012099	0.0130050670456	-0.111335649639	7.0870772897	1.76759886518	3.67053023901	-0.126551964425	-1.06983788648	-0.0420545044739	0.704141302887	0.294259759838	0.0316375128135	0.530030370565	0.476158476467	-0.156751416973	0.715445219432	-0.00846199411713	-0.00534870098648	0.586761567313	0.0239132744731	0.529282701491	-63.1471638389	59.1356472509	39.1897737719
31	1.34315481144	-1.31553204159	0.9499589138	2.83069133016	-2.00126024278	4.57392207915	0.399820142346	-0.0241402901434	0.753329271757	-0.561392729618	-0.22619090946	-0.484783789999	-0.945901571165	0.13484804126	-0.194139997335	0.825207006553	-0.046514586608	0.0814424430076	0.318757866047	-0.0248748462578	0.715254667359	-62.9925652763	82.1240486626	30.3038087612
32	2.26059979182	-1.67824815642	1.24620606281	2.80946333455	-2.70785333468	2.71965163544	0.400255111988	0.120407003767	0.134044091689	-0.235149915974	-0.314886415641	-0.305929441447	0.296855678638	0.384487236947	-0.0679997852976	0.541853235629	0.0392303180837	0.0425008693235	0.405273433712	-0.09722533244	0.684865379992	-60.8914403103	66.6828722465	31.6304101704
33	1.60903477195	-0.324911412264	0.0750234491127	4.0642788483	-0.0368419928021	1.48097953223	0.0697229341389	-0.116298619863	0.531599101588	0.528353461009	0.194086543939	0.0399896887062	-0.304991550293	0.00269057078073	-0.202630234774	0.481772310546	0.0244397036246	0.120205877047	0.344768497256	-0.0101899248296	0.471564820026	-67.9322606722	59.4048162937	30.1999246177
34	2.83788680938	-3.44136347117	-2.62529768781	6.82351232427	5.69520676483	7.97998666019	0.0682168417834	-0.694053285542	0.88363118292	0.33627833333	0.10040337236	1.37947990527	-0.389633835158	-0.243267631305	-0.212130949766	0.674120509313	0.0701193156513	0.291746415126	0.490212641367	-0.0169687805656	0.905838609075	-76.3531283411	70.1161421652	30.6712044693
35	3.12473040903	-1.81526833933	0.276457744476	7.49247837064	-1.40813998457	2.93682231869	0.124354742513	0.294881266495	0.958103680103	-0.751455462704	0.211650741366	-0.0487345916427	-0.157577268122	-0.620462836153	-0.289037056638	0.571349102114	0.0404590179485	0.0537278981413	0.389999508048	0.114656162031	0.570111535067	-70.7162448329	64.4329647936	19.8193443544
36	1.04561081769	0.276158801233	-0.358649506905	3.08633922487	0.809630727975	2.36354946277	0.39132864886	0.0942245943382	0.261691373252	-0.460460661425	0.0317538830058	0.0675687986481	-0.498500103126	-0.187420874603	-0.450711699585	0.579918051905	0.0103782890597	0.0949649254714	0.367652057736	0.0816681162163	0.609140820757	-64.5592763555	70.2576910503	25.1900144897
37	1.18419489115	0.392775278074	-0.170586137102	2.15009114221	-0.246949187504	0.411151047032	0.150552497568	-0.10004311523	0.735933632927	0.273257641079	0.0352958287439	0.283743799994	-0.351339823914	-0.107411920432	-0.20617693282	0.484505807331	0.0871375414507	0.0910887298689	0.380703105824	0.00478286393312	0.540754193367	-74.407405268	60.9846057728	29.7694355317
38	2.04375650213	2.27091653715	0.343510883862	7.04001885787	-0.160998780321	1.44601036797	0.320965185609	-0.307239973175	0.446249488726	1.04889948404	-0.279517889698	0.0493308533073	-0.498420313093	-0.140058784893	-0.034281420268	0.722339016963	0.0559195035911	0.14376078535	0.385616539163	-0.100101558716	0.626193770241	-69.723777235	69.4250159304	35.9788536008

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 'A' and (resid 0 through 61 )	A	A	0 - 61	1 - 62
2	2	chain 'A' and (resid 62 through 216 )	A	A	62 - 216	63 - 217
3	3	chain 'A' and (resid 217 through 420 )	A	A	217 - 420	218 - 418
4	4	chain 'B' and (resid 1 through 25 )	B	D	1 - 25	1 - 25
5	5	chain 'B' and (resid 26 through 115 )	B	D	26 - 115	26 - 115
6	6	chain 'C' and (resid -3 through 7 )	C	E	-3 - 7	1 - 11
7	7	chain 'C' and (resid 8 through 25 )	C	E	8 - 25	12 - 29
8	8	chain 'C' and (resid 26 through 40 )	C	E	26 - 40	30 - 44
9	9	chain 'C' and (resid 41 through 59 )	C	E	41 - 59	45 - 63
10	10	chain 'C' and (resid 60 through 66 )	C	E	60 - 66	64 - 70
11	11	chain 'C' and (resid 67 through 108 )	C	E	67 - 108	71 - 112
12	12	chain 'C' and (resid 109 through 122 )	C	E	109 - 122	113 - 126
13	13	chain 'D' and (resid -4 through 8 )	D	F	-4 - 8	1 - 13
14	14	chain 'D' and (resid 9 through 17 )	D	F	9 - 17	14 - 22
15	15	chain 'D' and (resid 18 through 39 )	D	F	18 - 39	23 - 44
16	16	chain 'D' and (resid 40 through 51 )	D	F	40 - 51	45 - 56
17	17	chain 'D' and (resid 52 through 59 )	D	F	52 - 59	57 - 64
18	18	chain 'D' and (resid 60 through 66 )	D	F	60 - 66	65 - 71
19	19	chain 'D' and (resid 67 through 82 )	D	F	67 - 82	72 - 87
20	20	chain 'D' and (resid 83 through 110 )	D	F	83 - 110	88 - 115
21	21	chain 'D' and (resid 111 through 117 )	D	F	111 - 117	116 - 122
22	22	chain 'E' and (resid -1 through 7 )	E	G	-1 - 7	1 - 9
23	23	chain 'E' and (resid 8 through 33 )	E	G	8 - 33	10 - 35
24	24	chain 'E' and (resid 34 through 44 )	E	G	34 - 44	36 - 46
25	25	chain 'E' and (resid 45 through 59 )	E	G	45 - 59	47 - 61
26	26	chain 'E' and (resid 60 through 81 )	E	G	60 - 81	62 - 83
27	27	chain 'E' and (resid 82 through 97 )	E	G	82 - 97	84 - 99
28	28	chain 'E' and (resid 98 through 107 )	E	G	98 - 107	100 - 109
29	29	chain 'E' and (resid 108 through 120 )	E	G	108 - 120	110 - 122
30	30	chain 'F' and (resid 0 through 7 )	F	H	0 - 7	1 - 8
31	31	chain 'F' and (resid 8 through 17 )	F	H	8 - 17	9 - 18
32	32	chain 'F' and (resid 18 through 25 )	F	H	18 - 25	19 - 26
33	33	chain 'F' and (resid 26 through 39 )	F	H	26 - 39	27 - 40
34	34	chain 'F' and (resid 40 through 51 )	F	H	40 - 51	41 - 52
35	35	chain 'F' and (resid 52 through 63 )	F	H	52 - 63	53 - 64
36	36	chain 'F' and (resid 64 through 90 )	F	H	64 - 90	65 - 91
37	37	chain 'F' and (resid 91 through 111 )	F	H	91 - 111	92 - 112
38	38	chain 'F' and (resid 112 through 125 )	F	H	112 - 125	113 - 126

-
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

-
Protein , 2 types, 2 molecules AC

-
Antibody , 4 types, 4 molecules BDEF

-
Non-polymers , 3 types, 523 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

-Protein , 2 types, 2 molecules AC

-Antibody , 4 types, 4 molecules BDEF

-Non-polymers , 3 types, 523 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

-
Protein , 2 types, 2 molecules AC

-
Antibody , 4 types, 4 molecules BDEF

-
Non-polymers , 3 types, 523 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