PDB-7s58: Crystal Structure of the tick evasin EVA-P974 complexed to human ...

ID or keywords:

Entry

Database: PDB / ID: 7s58

Title

Crystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7

Components

C-C motif chemokine 7
Evasin P974

Keywords

IMMUNE SYSTEM / Inflammation / Chemokine / Evasin / Evasin-chemokine complex

Function / homology

Function and homology information

CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines ...
Similarity search - Function

Biological species

Amblyomma cajennense (Cayenne tick)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Bhusal, R.P. / Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.

Funding support

Australia, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.
Authors: Bhusal, R.P. / Aryal, P. / Devkota, S.R. / Pokhrel, R. / Gunzburg, M.J. / Foster, S.R. / Lim, H.D. / Payne, R.J. / Wilce, M.C.J. / Stone, M.J.

History

Deposition	Sep 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 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	7s58.cif.gz	302.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7s58.ent.gz	204.5 KB	Display	PDB format
PDBx/mmJSON format	7s58.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7s58_validation.pdf.gz	469.1 KB	Display	wwPDB validaton report
Full document	7s58_full_validation.pdf.gz	472.8 KB	Display
Data in XML	7s58_validation.xml.gz	23.7 KB	Display
Data in CIF	7s58_validation.cif.gz	34.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/7s58 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/7s58	HTTPS FTP

-
Related structure data

Related structure data	7s4nSC 7s59C 7s5aC 7so0C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vil-6 2yqd-d 3o99-d 4mjs-1 4dxf-1 7s59-2 7s58-3 4tse-2 4pwq-1 6vil-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7s4nSC

7s59C

7s5aC

7so0C

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (8)

Deposited unit

A: Evasin P974

B: Evasin P974

C: Evasin P974

D: Evasin P974

E: C-C motif chemokine 7

F: C-C motif chemokine 7

J: C-C motif chemokine 7

H: C-C motif chemokine 7

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

1

A: Evasin P974

H: C-C motif chemokine 7

defined by author
Evidence: surface plasmon resonance
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Evasin P974

E: C-C motif chemokine 7

defined by author
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Evasin P974

J: C-C motif chemokine 7

defined by author
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Evasin P974

F: C-C motif chemokine 7

defined by author
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.025, 64.415, 181.432
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 "A" and ((resid 2 through 3 and (name N...
d_2	ens_1	(chain "B" and ((resid 2 through 3 and (name N...
d_3	ens_1	(chain "C" and ((resid 2 through 3 and (name N...
d_4	ens_1	(chain "D" and ((resid 2 through 3 and (name N...
d_1	ens_2	(chain "E" and (resid 8 through 15 or (resid 16...
d_2	ens_2	(chain "F" and (resid 8 through 16 or (resid 17...
d_3	ens_2	(chain "H" and ((resid 8 and (name N or name...
d_4	ens_2	(chain "J" and (resid 8 through 15 or (resid 16...

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	TYR	GLY	A	1 - 83
d_2	1	ens_1	TYR	GLY	B	1 - 83
d_3	1	ens_1	TYR	GLY	C	2 - 84
d_4	1	ens_1	TYR	GLY	D	2 - 84
d_1	1	ens_2	SER	THR	E	2 - 25
d_1	2	ens_2	HIS	LYS	E	29 - 69
d_2	1	ens_2	SER	LYS	F	1 - 65
d_3	1	ens_2	SER	THR	H	2 - 25
d_3	2	ens_2	HIS	LYS	H	27 - 67
d_4	1	ens_2	SER	THR	G	1 - 24
d_4	2	ens_2	HIS	LYS	G	28 - 68

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.234394217857, 0.227674206836, 0.9451051826), (0.219989313265, -0.959391724254, 0.176556567371), (0.946923467174, 0.166529201567, -0.274961765234)	32.7190746737, 10.8363914317, -43.8173741102
2	given	(-0.233552461725, -0.205465436191, -0.950387921931), (-0.109583437012, -0.965630160954, 0.235690183481), (-0.966149428378, 0.159192797536, 0.203009692522)	-3.70948136896, 17.1867259689, -4.58976688846
3	given	(-0.999136663447, -0.00778136609618, 0.0408090443148), (-0.0165941708214, 0.975288021804, -0.22031320437), (-0.0380862344025, -0.22080019218, -0.974575145324)	31.0927156234, -5.04842864839, -42.1804496035
4	given	(-0.228039641342, -0.2365468617, -0.944480547283), (-0.0607261894982, -0.964695363161, 0.256271703871), (-0.971756271853, 0.115794812129, 0.205624195071)	-0.75811138682, 16.0822956698, -2.98452060056
5	given	(0.243112142659, 0.194454003719, 0.950307385286), (0.191646188139, -0.970017353902, 0.149459264351), (0.950877607615, 0.145787425954, -0.273089365905)	31.9151683091, 10.027131568, -44.2877042394
6	given	(-0.999715448893, -0.0234234831921, 0.00451239175435), (-0.0234755183454, 0.932512443894, -0.360374030726), (0.00423335358893, -0.360377416633, -0.932796974855)	29.4248352253, -7.32649653824, -41.473607414

#1: Protein	Evasin P974 Mass: 9702.080 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amblyomma cajennense (Cayenne tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023FDY8
#2: Protein	C-C motif chemokine 7 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small- ...Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7 Mass: 8974.482 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80098
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.8 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.82→48.88 Å / Num. obs: 61992 / % possible obs: 99.4 % / Redundancy: 13.4 % / B_iso Wilson estimate: 40.65 Å² / CC_1/2: 0.999 / Net I/σ(I): 18.5
Reflection shell	Resolution: 1.82→1.85 Å / Num. unique obs: 3397 / CC_1/2: 0.678

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7S4N

7s4n

Resolution: 1.82→30.77 Å / SU ML: 0.2626 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.244	3048	4.93 %
R_work	0.2236	58716	-
obs	0.2246	61764	99.06 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→30.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4499	0	0	217	4716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4600
X-RAY DIFFRACTION	f_angle_d	1.0045	6234
X-RAY DIFFRACTION	f_chiral_restr	0.0756	678
X-RAY DIFFRACTION	f_plane_restr	0.0062	809
X-RAY DIFFRACTION	f_dihedral_angle_d	11.3625	651

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.52201649749
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.440630027833
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.790296131393
ens_2	d_2	E	X-RAY DIFFRACTION	Torsion NCS	1.04176568618
ens_2	d_3	E	X-RAY DIFFRACTION	Torsion NCS	0.699051727234
ens_2	d_4	E	X-RAY DIFFRACTION	Torsion NCS	0.575997870306

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 (%)
1.82-1.84	0.4003	121	0.3446	2443	X-RAY DIFFRACTION	91.25
1.84-1.87	0.3286	119	0.3164	2608	X-RAY DIFFRACTION	98.52
1.87-1.91	0.3401	131	0.3225	2627	X-RAY DIFFRACTION	99.32
1.91-1.94	0.4143	145	0.3521	2550	X-RAY DIFFRACTION	96.08
1.94-1.98	0.3649	143	0.2976	2644	X-RAY DIFFRACTION	99.93
1.98-2.02	0.3575	138	0.2899	2660	X-RAY DIFFRACTION	99.26
2.02-2.06	0.3078	134	0.2765	2665	X-RAY DIFFRACTION	99.86
2.06-2.11	0.3175	150	0.2625	2629	X-RAY DIFFRACTION	99.39
2.11-2.16	0.3358	148	0.2686	2655	X-RAY DIFFRACTION	99.5
2.16-2.22	0.2955	120	0.255	2695	X-RAY DIFFRACTION	99.89
2.22-2.29	0.2837	123	0.2699	2624	X-RAY DIFFRACTION	98.99
2.29-2.36	0.3079	139	0.2509	2657	X-RAY DIFFRACTION	99.75
2.36-2.45	0.2858	154	0.2584	2669	X-RAY DIFFRACTION	99.75
2.45-2.54	0.3179	148	0.2662	2670	X-RAY DIFFRACTION	99.61
2.54-2.66	0.3083	146	0.2653	2671	X-RAY DIFFRACTION	99.93
2.66-2.8	0.2756	118	0.2529	2736	X-RAY DIFFRACTION	100
2.8-2.97	0.2913	143	0.2542	2686	X-RAY DIFFRACTION	100
2.97-3.2	0.2363	127	0.2324	2744	X-RAY DIFFRACTION	100
3.2-3.53	0.247	146	0.214	2703	X-RAY DIFFRACTION	99.96
3.53-4.04	0.2019	148	0.1893	2745	X-RAY DIFFRACTION	99.97
4.04-5.08	0.1683	153	0.163	2763	X-RAY DIFFRACTION	100
5.08-30.77	0.2216	154	0.2179	2872	X-RAY DIFFRACTION	98.5

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	7.93376328424	0.550428083899	-3.09683895262	0.771179119599	-0.0707023168366	7.92730643269	-0.395021683228	-0.648421306757	0.270031421632	0.288581907007	0.684691419534	-0.328761465866	0.799241200719	0.501629491568	-0.2909050979	0.265136965628	-0.0264000937907	-0.0411840695948	0.26531446151	0.0152816347227	0.37386235458	4.24328445746	-11.8552893023	-24.1417626725
2	8.60904797515	-1.05253925866	-7.1860611366	1.05442349078	0.841672958995	6.00569071671	-2.06096107174	-1.21601511347	-1.74250794892	0.260087268784	0.655493186942	0.00201720208367	3.33581151679	1.49425092217	0.761572397298	0.765678954116	0.139023192264	0.231215680115	0.461784325471	0.0716873767007	0.569168527326	2.15034271521	-19.4446844157	-21.1150446044
3	8.20659720227	-0.862300450794	-4.36071095737	3.46879338341	1.5010199324	5.48208355279	0.121655252645	-0.343577774048	1.06988049717	0.173621579492	0.221451971153	-0.0668836217978	-0.00291995927046	0.35388294013	-0.25229505708	0.263431834161	0.0127781600193	0.00579817684853	0.336909257081	0.0120848270911	0.503925176583	-5.54429900263	-5.95190512604	-18.4069507821
4	7.04309865774	0.936293163696	-1.37752952084	5.9856266188	0.570180477976	7.92676265798	0.629285388619	0.00128213274864	1.38830799557	0.058722174566	-0.530979858083	0.33668104014	-1.03146878321	-0.949807064902	-0.136976754115	0.523459099054	0.0238258944797	0.0762764284893	0.389238756268	0.00674526065521	0.651028952906	2.33170561872	26.1774621436	-32.9480864419
5	4.84473528186	-0.519627819922	-1.07293705264	4.194931552	0.785930906795	3.71954658043	0.318858005614	0.315383525352	0.155278546546	-0.380797385139	-0.164944296589	0.192377361362	0.231607755196	-0.122641122039	-0.19961684105	0.502832283712	0.0465960146289	-0.0858106524963	0.287589461358	0.0130052195212	0.320737082715	11.5237613693	18.5954989382	-39.8170483497
6	9.53879425372	3.90518644798	2.23459360194	3.17675982749	-2.01230374073	5.74919275253	0.816400656283	0.630679054642	-0.118609592189	1.08615367894	-0.586613200529	1.98676606739	0.226992447619	-0.94134607961	-0.288926151958	0.55874908658	0.163646179217	-0.11732569296	0.423576776545	-0.0921214851585	0.599832809244	2.97949588734	12.7621849013	-46.5707463428
7	6.47601899642	2.61056501555	0.324236928406	6.70153050627	0.820030937402	5.04300894654	0.146846027024	0.520565719859	-0.372392133153	-0.247954790874	0.160411731174	-0.18400683354	0.694840570246	0.360467364081	-0.230141319445	0.591579137109	0.133772885477	-0.10369647307	0.38322770604	-0.0484252296081	0.400880211028	13.3240696495	10.9215158369	-44.3339232624
8	5.99023649138	0.42228807785	-0.94043321028	5.4470203309	1.12739795858	3.69604453435	0.210556620592	0.229930654348	-0.702861184778	-0.495112753496	-0.0472710797377	-0.279395614647	0.609240419025	-0.0247732591358	-0.0755482130943	0.593914985227	0.0676702975943	-0.0565971701818	0.347917842848	-0.0246958118885	0.346261988241	15.8430404814	11.3546292828	-44.2340801241
9	4.53566935157	0.446911659184	-0.905512680929	3.60427351834	1.15129956766	5.06425478811	0.165158566573	-0.366380674062	0.837152206436	-0.197503924206	0.16360425369	0.275759504447	-1.52679288593	1.56840094529	-0.185689230739	0.642395905005	-0.26408904124	-0.0982336322376	0.717211131799	-0.0905193665576	0.560587249136	27.8674442245	29.576704449	-20.9520061298
10	5.87708443632	0.639599743623	-1.01428626675	6.40538907834	-1.28636298648	5.63631791093	-0.207850384356	-0.547937239395	-0.412993243719	-0.231338399472	-0.0608875283025	1.04663471345	0.893857990806	-0.209702689657	0.19442571657	0.636373375408	-0.144890574744	0.0609136436792	0.457834280328	0.0299963349248	0.467373906883	15.0220330383	16.7159082979	-10.896887384
11	5.43846237606	-1.09143428297	-1.33536067783	2.30476125781	0.407132793532	4.37474375554	-0.262366097535	-0.453073921754	0.69417785025	-0.0788245334039	0.132566202872	0.0363327003431	-0.416529267359	0.595877592524	0.121289547914	0.552977528364	-0.256937414861	-0.00134512377991	0.545800959958	-0.025439566763	0.484873970913	20.4512277515	31.1297351372	-13.9140160264
12	4.43610328459	0.571601057365	0.205704180895	3.68112035815	0.0737887399105	5.60194036997	0.403882161351	-0.327275758231	-0.551957599091	0.199065470993	-0.714811460885	-0.681471224609	1.11888747577	1.13569835368	0.340344572506	0.731302199582	-0.00481486486981	-0.0130267617595	0.623021264853	0.124238014446	0.40406601951	20.5351311932	16.8040448389	-4.02810419277
13	3.02575094699	-0.555236384741	-0.400554232411	2.88579414036	-0.0507253981835	4.6106240659	0.0758250320666	-0.748311088329	-0.151605974166	0.419678242768	0.0455823544274	0.508461010274	0.464493587578	0.0482753252702	-0.146101163494	0.723634773502	-0.172787461905	0.0738333204764	0.642698142861	-0.0185805653039	0.449880109179	12.3975082544	20.6136529075	-4.35270523789
14	8.2854087275	1.16659359831	-2.86664808152	7.56595546392	2.09663402536	5.83783928911	-0.448155350568	-0.034741314677	-0.914967011271	0.980066856329	0.865504002784	0.948636446813	1.38781962028	-0.599770701665	-0.489704886337	0.501061178058	-0.0479461506583	0.0135431442158	0.569869030723	0.184540460146	0.53185041937	23.0380378392	-18.9049205917	-9.22137599749
15	4.43905171991	0.341408560516	-2.68066493701	0.52454193739	-0.840616869048	2.71273407377	0.603548442763	1.81678909233	0.911388895041	-0.589279371115	-0.0294372508393	1.03403035844	-0.195792997067	-0.763162453366	-0.475943763297	0.240950575757	-0.0234526176127	0.0488904943366	0.874975834311	0.332469257732	0.608554405756	28.6838726891	-4.76898585857	-22.7292837259
16	9.05505853628	-2.31070139059	-0.787683189847	2.30476282446	0.168960244835	9.17289372686	-1.27278338271	0.195248275222	-0.548160970162	-0.135068377591	1.23999650647	-0.485350418408	1.1648815829	-0.353817262238	0.186310276639	0.459703506718	-0.109914683224	0.0177975995599	0.535249936098	0.100861613325	0.481251881197	29.4073121707	-20.152353302	-12.4766226313
17	6.5956484765	1.59225573111	-0.590056602597	6.09619333772	1.9019022197	3.66492204833	0.265939564088	1.10751041727	0.174856820757	0.145494089065	-0.711977789598	-0.280622290368	0.651836912465	-1.33418150358	0.271748758328	0.324782572977	-0.194359305814	0.00739189931784	0.935311736851	-0.00758053622866	0.395056874391	31.8938044327	-13.3466104463	-24.2164418505
18	8.78603996653	-4.95790268439	-1.94156318646	9.02085898985	1.17722385161	9.59376445163	0.227157380369	-1.5039266448	0.804187520596	0.122223963303	0.26317536504	-0.555381620581	0.163842202504	0.188306778008	-0.55425634689	0.333960296595	-0.0753041748622	-0.0225857021897	0.384830421582	0.0480110002342	0.494452474149	39.0617826809	-7.60124982037	-13.749135922
19	7.24514842816	1.21928001256	-2.27617447802	4.93951179794	0.0666794084747	4.72268492327	0.237776810068	1.01230266735	1.14830067506	-0.179230230992	-0.0595640753209	0.276091915752	-0.111936526572	-0.955342571579	-0.192653265443	0.257322208136	-0.0185559944213	0.0261220376966	0.571466906941	0.182170977786	0.511381683119	35.0907573658	-5.53220405077	-24.0523346127
20	5.87334525277	-0.512517964829	-3.23734053654	2.83144237695	0.0492239509313	5.15857656126	0.338411225119	-0.187975204173	0.443239388154	0.0625412270973	0.0242701342842	-0.165686978633	-0.286081076536	0.366342997886	-0.2925292817	0.427231593564	-0.0234019007797	-0.0169927523661	0.314999541479	0.00419808901733	0.438907675901	5.05586600403	22.4965668091	-28.1858711618
21	8.82153340953	-0.844024803459	-3.01940798505	8.15226657331	-0.30186770735	6.1874507841	-0.164609266651	0.928756471671	-0.451137277922	0.151998094565	0.224301950812	-0.146451486672	0.493832581475	-0.451032185565	-0.0441704559542	0.396412792319	-0.0697294437227	0.0109442785623	0.45044296622	-0.0323203096847	0.629449781707	-4.39411479398	18.3929341912	-22.7058930442
22	7.91771212544	0.691610572589	-2.04459708137	2.84712384627	-0.842685590434	6.8659127424	0.0545197027235	0.390601183206	-0.713657173434	0.191243639564	-0.0762435898929	0.000999526730291	0.331531628911	-0.122555386781	-0.0409931159759	0.435575071982	-0.04742924038	-0.00470031161449	0.257717046085	-0.0499866691822	0.496988236697	3.35870236577	18.7023188359	-26.001516122
23	4.70585938856	5.12913369313	-0.0435998533751	7.769929693	-1.34162134274	-0.0461877320927	0.416209710947	-0.872155239609	-0.194536867646	0.323846319457	-0.507391252837	0.933369914546	-0.211588619289	-0.0796244713348	0.0320175022357	0.457202854923	-0.0155437976206	0.102825155771	0.355729501829	-0.0130892313126	0.593262538776	-5.71052918364	15.2893557247	-15.6133243573
24	6.3223140422	-0.733188860826	-2.11831864394	2.86523889978	-0.919345849253	5.30645866746	-0.170826887548	1.38497023923	0.0387123218298	0.12561064366	0.522313529441	-0.163958746702	0.531912871494	-1.15320061179	-0.355794174191	0.360871179048	-0.109246310438	-0.0599976394874	0.694986761837	0.159668158555	0.459896450912	18.9964286196	-13.6686888087	-11.3279913089
25	7.35221685444	0.35176144588	-2.56594818799	7.753648935	-3.39182559688	9.28211938253	0.503936076301	-0.750111790442	0.934923618688	-0.123281473507	0.603193803824	0.500261350251	-0.0912459422376	0.451773358018	-0.960405950891	0.331447166736	-0.0719454225664	0.0189766983592	0.685858177489	-0.000529486790066	0.555267587312	17.6258359228	-8.73763729211	-0.606824222153
26	5.82043285006	-0.64627130136	-2.98562157365	3.16094792846	1.06167857527	4.76863501243	0.373469891995	0.834450892438	1.23579729204	-0.5228762585	0.662804673978	0.448551135096	0.152310715015	-0.95136461333	-0.454076350136	0.261427256171	-0.0272559617478	-0.00453270953986	0.764813229707	0.355952380973	0.53828959832	18.5818018999	-9.85428573383	-8.69102128621
27	4.31205974496	2.58677933773	0.873415629648	2.92558093046	1.83886955191	5.63549693795	0.297009429758	-0.286583013639	1.00617322706	1.65871105759	-0.51715386033	2.06594510051	-0.537441421751	-0.644301120683	-0.10169096714	0.623635697783	0.0428197154851	0.212526231885	0.563080179962	0.134239629292	0.687764028045	11.0437755039	-3.60312850521	0.363278457648
28	4.28481300308	-0.200783874166	-2.11517236801	4.39054608957	0.202123085842	4.71632879824	-0.000642197036669	0.0708430526004	-0.16399368947	0.0290895237411	-0.00085162093606	-0.00268341147282	-0.0177058743347	0.199166827418	-0.0709613114479	0.41465345824	-0.0279845026795	-0.0234714888629	0.432770198891	-0.0288234453739	0.392072295637	23.8270526638	23.9896795163	-23.7683213813
29	7.53541333123	-1.82515523654	-4.27568098023	5.85177262685	3.18954854814	7.96791628054	-0.516672148163	-1.89691053255	0.162383574449	0.808088473545	1.88934787399	0.417437521614	0.345032139952	1.03764249308	-0.853350884367	0.503219301595	0.14917940917	0.0317311477824	0.950287610518	0.152249321879	0.52665463194	33.5594551334	19.1976968803	-27.2836899469
30	6.32047764718	-1.12843688523	-1.97889191932	5.80906696053	0.612778121475	5.76768564489	0.133374834137	-0.850878378504	-0.352644843844	0.331111583799	-0.145756574766	0.12861075274	0.426212657549	0.903916774192	-0.0584104721907	0.451263855018	0.0041950614621	-0.0516507399031	0.520169429264	0.0327472072541	0.453625741628	25.5418216358	19.3981628472	-23.7909075239
31	7.96868618485	-5.14365654463	-1.27964013038	9.8953360733	-0.189772675427	3.20503356149	0.134156557675	0.555505037646	0.0719120484403	-0.167943758878	-0.677884416169	-0.849468415103	0.632271699908	0.918211969495	0.451219631345	0.573332148184	0.125433908181	0.0218944132856	0.570477788075	0.0559736538901	0.463167925045	31.3544615928	16.8602559867	-34.5040430903
32	3.67831087518	-4.36201653964	-1.00566208805	2.00091082675	-0.819521931263	4.64171877544	-0.0160471243412	1.35533088933	1.93456773837	0.335526086387	-0.535913916299	0.13923373424	-0.950197439251	0.222061282163	0.275115488246	0.467534701558	0.0729711928462	0.0179134219347	0.585557429852	0.449893728917	1.16736785402	42.2864677911	3.1064321074	-26.7563026076
33	7.55964469859	-0.98330087309	-7.39231876842	5.35749493827	2.90026853938	7.8296698063	-0.177871387912	-0.924918814803	0.511263805304	-0.11176139738	0.828111540592	-0.0591650521089	0.708589462415	1.0037823779	-0.574600306888	0.424207983931	0.119247728647	-0.117792821982	0.415730384066	-0.0813976719046	0.350479961281	10.6904365089	-14.6461722393	-28.7112914641
34	7.79365520293	-1.51042259207	-3.18507773924	8.85336640365	2.28466818811	9.79530846745	0.0500814143329	0.880614743964	0.644969061132	0.206741012686	0.264859350946	0.00510361242467	0.429283108639	-0.817126072101	-0.33976990849	0.413874287747	-0.00267367128388	-0.0541765191579	0.451140517635	0.15696806533	0.417314794491	12.7452039544	-13.2415322378	-39.7417036655
35	8.21581458356	-0.977935891008	-4.29450804125	7.13075328829	0.689426679436	7.95557036272	0.264400950319	-0.570819253645	1.01963095927	0.0603224355081	0.461822584223	-0.341808427501	0.291777799166	0.245608604313	-0.623103268871	0.260391497043	0.010392553736	-0.0545129733692	0.355792263991	-0.119193606101	0.454273572778	11.3635663741	-12.1591192548	-31.6898041202
36	3.89956546448	-1.62267266089	1.70873750749	3.72894031599	-2.72386619627	3.20463423025	0.0846901295924	0.255949419819	1.02498593584	-0.806466744347	-0.789316546729	-1.05077894459	-0.126560295196	1.37655129627	0.506340592583	0.576637378776	0.0444057255031	0.000400055375386	0.451336797058	-0.0812584955489	0.544641182705	18.7582527686	-9.12782754837	-42.6716399329

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 2 through 26 )	A	A	2 - 26	1 - 25
2	2	chain 'A' and (resid 27 through 41 )	A	A	27 - 41	26 - 40
3	3	chain 'A' and (resid 42 through 85 )	A	A	42 - 85	41 - 84
4	4	chain 'B' and (resid 2 through 12 )	B	B	2 - 12	1 - 11
5	5	chain 'B' and (resid 13 through 47 )	B	B	13 - 47	12 - 46
6	6	chain 'B' and (resid 48 through 53 )	B	B	48 - 53	47 - 52
7	7	chain 'B' and (resid 54 through 70 )	B	B	54 - 70	53 - 69
8	8	chain 'B' and (resid 71 through 85 )	B	B	71 - 85	70 - 84
9	9	chain 'C' and (resid 1 through 12 )	C	C	1 - 12	1 - 12
10	10	chain 'C' and (resid 13 through 26 )	C	C	13 - 26	13 - 26
11	11	chain 'C' and (resid 27 through 41 )	C	C	27 - 41	27 - 41
12	12	chain 'C' and (resid 42 through 59 )	C	C	42 - 59	42 - 59
13	13	chain 'C' and (resid 60 through 84 )	C	C	60 - 84	60 - 84
14	14	chain 'D' and (resid 1 through 12 )	D	D	1 - 12	1 - 12
15	15	chain 'D' and (resid 13 through 26 )	D	D	13 - 26	13 - 26
16	16	chain 'D' and (resid 27 through 36 )	D	D	27 - 36	27 - 36
17	17	chain 'D' and (resid 37 through 47 )	D	D	37 - 47	37 - 47
18	18	chain 'D' and (resid 48 through 53 )	D	D	48 - 53	48 - 53
19	19	chain 'D' and (resid 54 through 85 )	D	D	54 - 85	54 - 85
20	20	chain 'E' and (resid 7 through 21 )	E	E	7 - 21	1 - 15
21	21	chain 'E' and (resid 22 through 30 )	E	E	22 - 30	16 - 24
22	22	chain 'E' and (resid 31 through 57 )	E	E	31 - 57	25 - 51
23	23	chain 'E' and (resid 58 through 76 )	E	E	58 - 76	52 - 70
24	24	chain 'F' and (resid 8 through 21 )	F	F	8 - 21	1 - 14
25	25	chain 'F' and (resid 22 through 30 )	F	F	22 - 30	15 - 23
26	26	chain 'F' and (resid 31 through 57 )	F	F	31 - 57	24 - 47
27	27	chain 'F' and (resid 58 through 75 )	F	F	58 - 75	48 - 65
28	28	chain 'J' and (resid 8 through 21 )	J	G	8 - 21	1 - 14
29	29	chain 'J' and (resid 22 through 30 )	J	G	22 - 30	15 - 23
30	30	chain 'J' and (resid 31 through 57 )	J	G	31 - 57	24 - 50
31	31	chain 'J' and (resid 58 through 70 )	J	G	58 - 70	51 - 63
32	32	chain 'J' and (resid 71 through 76 )	J	G	71 - 76	64 - 69
33	33	chain 'H' and (resid 7 through 21 )	H	H	7 - 21	1 - 15
34	34	chain 'H' and (resid 22 through 30 )	H	H	22 - 30	16 - 24
35	35	chain 'H' and (resid 31 through 57 )	H	H	31 - 57	25 - 49
36	36	chain 'H' and (resid 58 through 75 )	H	H	58 - 75	50 - 67

-
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