[English] 日本語

Yorodumi

- PDB-7ucq: Pfs230 D1 domain in complex with 230AS-18 -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7ucq

Title

Pfs230 D1 domain in complex with 230AS-18

Components

230AS-18
Gametocyte surface protein P230

Keywords

CELL INVASION / antibody / Plasmodium falciparum / Pfs230 / transmission blocking

Function / homology

Function and homology information

cell surface / plasma membrane
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Tang, W.K. / Tolia, N.H.

Funding support

United States, 1items

Citation

Journal: Immunity / Year: 2023
Title: A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine.
Authors: Tang, W.K. / Coelho, C.H. / Miura, K. / Nguemwo Tentokam, B.C. / Salinas, N.D. / Narum, D.L. / Healy, S.A. / Sagara, I. / Long, C.A. / Duffy, P.E. / Tolia, N.H.

History

Deposition	Mar 17, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7ucq.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7ucq.ent.gz	788 KB	Display	PDB format
PDBx/mmJSON format	7ucq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uc/7ucq ftp://data.pdbj.org/pub/pdb/validation_reports/uc/7ucq	HTTPS FTP

-
Related structure data

Related structure data	7u9eC 7u9wC 7ua2C 7ua8C 7ubsC 7uc8C 7ufwC 7ui1C 7jumS 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

-
Assembly

Deposited unit

A: Gametocyte surface protein P230

H: 230AS-18

B: Gametocyte surface protein P230

I: 230AS-18

C: Gametocyte surface protein P230

J: 230AS-18

D: Gametocyte surface protein P230

K: 230AS-18

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

A: Gametocyte surface protein P230

H: 230AS-18

defined by author
Evidence: gel filtration
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

B: Gametocyte surface protein P230

I: 230AS-18

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

C: Gametocyte surface protein P230

J: 230AS-18

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

D: Gametocyte surface protein P230

K: 230AS-18

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

Unit cell

Length a, b, c (Å)	75.220, 145.730, 78.270
Angle α, β, γ (deg.)	90.000, 90.916, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	chain "B"
d_3	ens_1	chain "C"
d_4	ens_1	chain "D"
d_1	ens_2	chain "H"
d_2	ens_2	chain "I"
d_3	ens_2	chain "J"
d_4	ens_2	chain "K"

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	LEU	ASN	A	1 - 176
d_2	1	ens_1	LEU	ASN	C	1 - 176
d_3	1	ens_1	LEU	ASN	E	1 - 176
d_4	1	ens_1	LEU	ASN	G	1 - 176
d_1	1	ens_2	THR	LYS	B	1 - 233
d_2	1	ens_2	THR	LYS	D	1 - 233
d_3	1	ens_2	THR	LYS	F	1 - 233
d_4	1	ens_2	THR	LYS	H	1 - 233

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.999647811426, -0.0264804234174, 0.00174364181097), (-0.0264847292775, -0.999646105675, 0.00249449892518), (0.00167696935828, -0.00253980027248, -0.999995368583)	31.9304384248, -103.60471191, -39.1937751459
2	given	(0.432456007441, -0.898809257389, -0.0715801680623), (-0.901349902818, -0.428880053385, -0.0602515767339), (0.0234553686409, 0.0905749338431, -0.995613392357)	-2.14261798608, -1.66713005885, -30.9882343718
3	given	(-0.416643148405, 0.90752256724, 0.0530214752483), (0.908683902013, 0.414057192994, 0.0533873313813), (0.0264962848236, 0.0704232268507, -0.997165240073)	119.626798208, -31.3901636332, 7.24302207807
4	given	(0.999736808192, -0.021205762928, 0.0087538542692), (-0.0212384097357, -0.99976776416, 0.00365345018375), (0.00867434711203, -0.00383840656932, -0.999955010157)	32.2095345434, -103.727091198, -39.4928046064
5	given	(0.490491088771, -0.871307959651, -0.0155219613969), (-0.871421172303, -0.490534199167, -0.00115754481411), (-0.00660547489316, 0.0140939312131, -0.999878857064)	-2.58591485207, -3.99188645425, -32.325462742
6	given	(-0.521713659936, 0.852651522266, 0.0282884890493), (0.853116377941, 0.521529185154, 0.0141334610851), (-0.00270235553402, 0.0315069930254, -0.999499878272)	121.294119241, -26.2657006857, 7.14881447067

-
Components

#1: Protein	Gametocyte surface protein P230 Mass: 21468.346 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874
#2: Antibody	230AS-18 Mass: 27600.471 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, pH 4.6, 20% PEG 10000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→41.27 Å / Num. obs: 57254 / % possible obs: 97.7 % / Observed criterion σ(F): 6 / Redundancy: 3.4 % / B_iso Wilson estimate: 47.4 Å² / CC_1/2: 0.99 / Net I/σ(I): 8.21
Reflection shell	Resolution: 2.5→2.56 Å / Num. unique obs: 3779 / CC_1/2: 0.53

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JUM

7jum

Resolution: 2.5→41.27 Å / SU ML: 0.3562 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2484	2863	5 %
R_work	0.2036	54382	-
obs	0.2058	57245	97.73 %

Solvent computation

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

Displacement parameters

B_iso mean: 61.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→41.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12776	0	0	114	12890

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0046	13048
X-RAY DIFFRACTION	f_angle_d	0.7585	17672
X-RAY DIFFRACTION	f_chiral_restr	0.0507	1948
X-RAY DIFFRACTION	f_plane_restr	0.0048	2268
X-RAY DIFFRACTION	f_dihedral_angle_d	11.2684	4820

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	0.657860499312
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.815159728138
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.02926894882
ens_2	d_2	B	X-RAY DIFFRACTION	Torsion NCS	0.584501986882
ens_2	d_3	B	X-RAY DIFFRACTION	Torsion NCS	0.550265943501
ens_2	d_4	B	X-RAY DIFFRACTION	Torsion NCS	0.528722690148

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 (%)
2.5-2.54	0.3603	120	0.3558	2285	X-RAY DIFFRACTION	82.82
2.54-2.58	0.3584	143	0.313	2708	X-RAY DIFFRACTION	97.01
2.58-2.63	0.3357	141	0.2776	2689	X-RAY DIFFRACTION	97.69
2.63-2.69	0.3665	146	0.2664	2759	X-RAY DIFFRACTION	98.47
2.69-2.75	0.306	142	0.2641	2705	X-RAY DIFFRACTION	98.48
2.75-2.81	0.2781	144	0.248	2743	X-RAY DIFFRACTION	98.3
2.81-2.88	0.311	145	0.2529	2754	X-RAY DIFFRACTION	98.77
2.88-2.96	0.2917	143	0.2595	2708	X-RAY DIFFRACTION	98.79
2.96-3.05	0.3091	144	0.2626	2738	X-RAY DIFFRACTION	98.56
3.05-3.14	0.3212	145	0.2425	2758	X-RAY DIFFRACTION	98.57
3.14-3.26	0.281	145	0.232	2749	X-RAY DIFFRACTION	98.91
3.26-3.39	0.2614	143	0.2178	2730	X-RAY DIFFRACTION	98.73
3.39-3.54	0.2444	145	0.2066	2739	X-RAY DIFFRACTION	98.7
3.54-3.73	0.2719	144	0.1901	2752	X-RAY DIFFRACTION	98.47
3.73-3.96	0.2157	145	0.1863	2748	X-RAY DIFFRACTION	98.6
3.96-4.27	0.1985	144	0.1601	2727	X-RAY DIFFRACTION	98.8
4.27-4.69	0.2058	145	0.1494	2760	X-RAY DIFFRACTION	98.41
4.69-5.37	0.1844	145	0.1567	2759	X-RAY DIFFRACTION	98.78
5.37-6.76	0.227	146	0.1898	2766	X-RAY DIFFRACTION	99.15
6.76-41.27	0.2203	148	0.1888	2805	X-RAY DIFFRACTION	98.6

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	7.08613306243	0.773903630455	-0.0608351090491	3.51260476968	-0.51424264465	2.43565339128	0.353585590904	-0.276305070159	-0.778998232632	0.296038124561	-0.132576848675	-0.295501939188	-0.0338474689924	-0.0862986457814	-0.096434140227	0.482022902707	-0.0321018081858	-0.0606982607161	0.281858644439	0.038022923804	0.564509194811	46.7526658929	-41.5662454643	-5.92565728232
2	8.26267643157	-1.46859072434	2.15525000639	3.00055088603	-1.19194973166	2.14583495078	0.0806445054252	0.627260016243	-0.0256839955542	-0.08339211916	-0.162992067436	-0.500122673781	-0.20189536956	0.389117366315	0.0135420589641	0.496661407953	-0.0179845479684	-0.0197519364516	0.375005838188	-0.0120001935336	0.373653303877	49.4994133135	-35.5752222609	-8.97556782155
3	8.086702669	1.27800595933	0.581958915854	4.03246746115	-0.493981315683	4.7068137468	-0.0169059154454	-0.842574474999	1.38147043912	0.664641392434	0.259471886473	0.0814928228278	-0.851617596585	-0.035510404849	0.081430034255	0.705309432737	-0.0204634636811	-0.0394506400171	0.526672848322	-0.0560111287101	0.42910085691	38.1540695945	-25.6304016965	-1.45384908903
4	6.10653707458	-1.51429411862	1.66795569838	2.71885007815	-1.25699170652	1.56311204088	0.222195582082	-0.353014958435	-0.763522168556	0.283066937499	-0.135554403241	-0.258082830621	0.0199658387891	0.09930902015	-0.150605325577	0.501968227564	-0.0355007042839	-0.130846507553	0.438289999721	0.0826747633375	0.471546304565	49.5299546805	-41.4921275616	0.209261672497
5	4.43050626128	-0.249244012128	2.63012728788	4.49934850197	-1.75655900363	5.81352299308	-0.0399069578887	-0.46376528049	-0.0866616791809	0.44852189894	0.267869512962	0.444047718337	-0.766989009908	-1.54708929983	-0.207468261558	0.351702383219	0.0806295314655	0.0743159243322	0.509737201491	-0.010102763676	0.362792538701	2.26411236786	-22.6317795122	-13.1570928878
6	5.62666362808	-0.23507536004	3.97663664196	0.62130929711	-1.39993276778	7.74475739949	-0.0412028386717	-0.260531685689	0.564217837865	0.578971087592	0.0605893073977	0.219432160032	-0.539930522756	-0.0857772454501	-0.152786310189	0.502475737607	0.0167189530227	0.111816715032	0.365593923346	-0.0476521430089	0.310796696988	10.5004884131	-20.1662761652	-6.51126505573
7	4.53816992556	2.1884559921	-0.726946889445	7.19708831423	-1.11521989708	0.286705413894	0.0103805104789	0.186211186028	-0.15605039446	-0.0805275990387	0.194969670668	-0.0365222254265	-0.189942931737	0.187989954446	-0.167276290996	0.50338715289	0.0587750671731	0.0229124912179	0.408508108926	0.0231773284716	0.150215299329	13.8146990487	-26.4102373529	-15.5356375468
8	5.17011959297	1.13611251287	1.64097931878	4.33563439625	-1.78985839983	1.63182629743	0.0618109642482	0.307487650443	0.0913306608199	-0.141628039305	0.0236710704211	0.293046510117	-0.33030570709	-0.14369076592	-0.0758216712489	0.450995292247	0.082582276614	0.0380935391232	0.419736100481	0.029125327043	0.235942003984	10.6303553227	-21.3020388671	-18.0887913402
9	3.12539491846	-0.329593694435	-0.244470820098	1.88876124166	-1.10842466759	0.495783890428	0.0703690974577	0.0419542541003	-0.475452473593	0.0874622735	-0.0756961336691	0.0297169104857	0.108730700834	-0.104616781122	0.0170270917817	0.50761459647	0.00565384885927	-0.0249208950833	0.413949424034	-0.0517900990956	0.320051667207	13.5116862085	-42.3366400976	-10.2587966866
10	8.60540043329	4.9071776941	-3.28010759887	3.47974502486	-2.53436188166	2.68462650234	-0.231517466002	0.359236875401	-0.161284997657	-0.343795165559	0.269345540727	0.301818104166	0.0787914359242	-0.287373157744	0.017279899478	0.383032380537	0.0627356451204	0.00175919761702	0.380909637133	-0.0149735645904	0.366627416339	13.770540261	-40.7708182493	-16.2257374571
11	6.40231612005	-0.228400534545	-2.49385792477	4.30501890708	1.0233549246	5.04801698153	0.844830873023	0.233502880233	1.29804503602	-0.429177740915	-0.0604635219277	-0.291006798756	-1.05357437934	0.170042446308	-0.788571808155	0.730361574537	0.0647307857463	0.189137600809	0.617540080907	-0.0490157167186	0.992860905141	72.9756992556	-58.6294006079	-35.9068068574
12	6.32946624867	1.6416224433	-0.641433041859	2.47229396407	1.41824199417	3.83883483992	0.111968339238	-0.0203252088989	0.212670053335	-0.299430393667	0.68336429357	-1.13499679982	0.169934390629	0.590065261669	-0.619823769732	0.556727213687	0.029315936845	0.167791944664	0.640883728808	-0.248612250491	0.864420507387	84.7032189446	-69.6368305771	-29.6224002415
13	7.70766580649	-1.56538523325	-1.10365406165	5.24853004065	0.774508674109	8.1866226488	0.2928919853	0.720682441775	-0.827117827323	-0.7490892706	-0.219292140938	-0.55549622616	0.772788517952	-0.10178885869	-0.0407016756578	0.765629336468	-0.0325915346269	0.147546998666	0.54273733648	-0.0330960121638	0.31230293724	70.8065371399	-78.9979522043	-37.6789086102
14	6.54866173117	0.912148425634	1.3701661343	0.189552080317	0.68383584326	4.28547063831	-0.207065029299	1.24233209997	0.64194904524	-1.72342599418	0.578711312566	-0.846850937897	-1.14228083981	0.533065833312	-0.61697508682	1.30295238358	-0.156532346953	0.476573926292	0.672798091423	-0.0281394839952	0.814073462097	78.1425601323	-60.0532929606	-41.2600245649
15	4.69139613221	3.53608726016	-0.632197010641	3.35307896171	-2.31027011425	5.02123149696	0.12311607963	0.912457450403	1.48103987071	-1.28006233164	-0.0828967524306	0.133489135276	-1.14095339064	0.2389491811	-1.23339214173	1.74996835818	-0.0897840872263	0.759344059155	0.736527150646	0.0524438563709	1.18917236178	81.2705159327	-54.7230613455	-42.9239682188
16	3.14789992258	1.9045735219	0.216592607219	3.05627511892	-1.87894257289	2.14274222436	0.452076503133	0.425888029778	0.386411320213	-1.08783818612	0.675126428092	-1.64390190362	-0.434419577985	1.10720947986	-0.504139623541	1.14436230476	-0.209796602992	0.642046393048	0.989368919173	-0.246485530227	1.1801177667	90.0069213839	-66.3481646273	-44.1494954366
17	8.98801640328	3.83293854761	-1.52770809418	1.38003660301	-0.935276575979	2.31416998296	0.368274042939	0.06569363027	1.04821338511	-0.163455933598	0.245437522244	-0.277403073166	-0.657763140169	0.62250862771	-0.496876840314	0.622248839274	-0.0750518858133	0.296272545092	0.612285506211	-0.153400699837	0.824393444509	78.1187722995	-64.9179003632	-32.4367641539
18	5.30078324278	-0.892609641866	-1.64352508186	1.86268582857	1.61858300704	1.77283741017	-0.037360705654	0.0580770478772	-0.241989394144	-0.0974372617902	-0.0942997161321	0.226238106703	0.155838686366	0.0673476100078	0.144006353007	0.38795616544	0.0141363532289	-0.0332219352376	0.298246476866	0.0061999702597	0.261357466239	38.8919330236	-82.6579589763	-29.4438816332
19	5.09716516309	-1.28959676358	-0.568466512002	5.24189764072	-0.221085308836	1.36509284905	0.0121966709594	-0.899881736569	0.346353251266	0.184050715419	0.238479003334	-0.0156689061203	0.0169053746723	0.202993865956	-0.0874445419975	0.50738701753	-0.00122560320053	0.0413267558147	0.447754266396	-0.0288129345384	0.218969566587	43.3123214502	-74.624556611	-21.8210449686
20	3.86846017644	-1.31134159467	-3.24958483476	5.57878529601	1.96595272139	8.64276673588	0.123178125291	-0.294921629033	0.0812534390524	0.280918478831	-0.156889717776	-0.654810582954	0.490220596351	0.0806116392534	0.00762269494277	0.48496707887	0.0134551740731	-0.0661443908814	0.456687819508	0.0652180124243	0.290762917637	52.6748931763	-83.3977843874	-22.7971196211
21	2.47362172484	-0.206851052475	-0.84243838131	4.15481177152	-0.112761813489	4.07766973018	-0.240181634796	-0.272735005229	-0.276031534217	0.166804374737	0.123382651682	0.0507341158131	0.505416720567	0.0602928765652	0.0388625100863	0.455864617464	0.0273778020795	-0.0147909676113	0.468036933863	0.01863415823	0.317650825851	43.6455990609	-87.2423429317	-24.5696689873
22	2.08055620311	0.205267180296	-0.529065745248	2.82053218776	-0.401364078809	0.957539863341	-0.0136639613411	-0.207777458747	-0.00328793652898	0.162707212246	0.0720215465638	0.10196746904	0.00268137673272	-0.0618814936198	-0.0479058144871	0.466922038025	0.0114239116081	0.0224488328669	0.45500553011	-0.0195695403605	0.264927211637	43.5197468136	-74.1198803408	-23.2583916502
23	2.42695106053	-1.02910137826	-0.888561785076	5.45252590635	-0.782158644871	3.03748069494	0.0906996597694	-0.370899529185	0.522552494613	-0.336138170436	-0.129560794392	0.521512868549	-0.300292827222	-0.0582933294175	-0.171219442125	0.806016360276	-0.00612449932824	0.0301894905937	0.50925718121	-0.087842872831	0.536489814892	43.8204904739	-50.1557749476	-26.534988982
24	5.89454297059	0.408037836607	-0.00109751738345	4.16137234375	0.361239147669	2.21052774894	-0.0399820460817	0.482207937823	0.578347922732	-0.369626306709	0.0196225892879	-0.0642493806731	-0.215712139822	0.13655275323	-0.0189346038689	0.557349006018	0.030195437542	0.0542251882042	0.379157324619	0.00258759483414	0.326779412524	49.5817949564	-60.7908519534	-31.0744633542
25	3.01985412233	-2.03027130475	0.487905937787	6.58061629097	0.471823404946	4.20885962265	0.0462451462758	-0.0163109021083	-0.0272941074943	-0.53221678414	-0.00991023376087	0.495977653685	-0.408704593553	-0.171510241538	0.0798638138392	0.767923332719	0.0671872586959	0.0100407608188	0.490455860154	-0.0717580277122	0.364557753311	41.0583710991	-57.3481239451	-30.6919914272
26	4.45806648943	-3.14094740621	-1.47511094621	5.29065062966	2.57851748519	1.1772537555	-0.106049675422	-0.00209819609574	-0.0381275113441	0.251441700551	-0.21049253068	0.154978987005	0.0829552617943	-0.279688670275	0.239837026358	0.586910460507	-0.0272239395822	0.00260479021334	0.519854661018	0.00763125879772	0.202330941555	46.6417613241	-63.3739648609	-23.0490065013
27	6.90595285026	-0.441813415296	-1.00497995099	6.9685362034	3.35630530569	7.21212585358	0.441922371415	0.645863080866	0.468255397326	-0.802706618469	-0.128767588396	0.0576501060651	-0.876294676806	1.40957106868	-0.262373169776	0.743608931883	0.0629806093993	-0.0435514074826	0.582325323577	0.0941510664638	0.467978308572	56.8096645038	-17.5259299355	-31.1540832669
28	3.09965420274	0.000823696129825	0.00609588119788	2.60927594924	0.0492511121601	7.12619177601	0.250266282223	-0.366764295821	-1.3840692623	0.357274118309	-0.0101063786113	-0.249125574018	0.507721044933	0.471294337135	-0.158762439697	0.775713601261	0.0702806742258	-0.154090093634	0.517478467716	0.027085373534	0.625373694219	54.6555111081	-36.759027007	-22.9398337826
29	3.54863196196	-2.64484345388	0.222918527232	5.8723312726	0.0416543027356	1.18373768639	0.00749664405261	-0.0668630645525	-0.666798127416	0.437583042651	-0.0381869448208	0.161868072238	0.673549813737	0.0125104136107	0.0653036738601	0.623746447873	0.0419886670386	-0.0647010643989	0.475292129712	-0.0465759415207	0.381075543272	51.8707623797	-30.4439448805	-24.0788749137
30	9.43774643394	-5.45818579934	2.95641234396	9.04408079197	-1.22650662755	2.50761993981	0.54318713192	0.642197737666	-1.89967400478	-0.676804847571	-0.161290178134	1.08754018172	0.455901054183	-0.933813090274	-0.369915164414	0.568571707783	0.0133567654292	-0.0762325771166	0.608490427792	-0.11235799895	0.412615220829	37.6659501122	-24.9897534382	-30.9429173939
31	5.39536893819	0.65055224062	0.196920485245	3.45876081355	1.43012212054	3.3081410263	0.243286840902	0.932179643287	-0.0133468173084	-0.250200862373	-0.322799892766	0.221320735816	-0.01867027141	0.277842860481	0.00375246765811	0.685925320872	0.186562500542	-0.0370499320581	0.710902686732	-0.00324912934458	0.25863148038	57.2356195195	-23.2330815232	-36.1321054724
32	6.29732951609	2.00894858942	0.939851370078	4.96904503612	2.39159631388	3.51405436156	0.228187074192	1.35136415495	-0.349736709195	-0.871036856322	0.00110038349393	0.298766212104	0.121224047705	0.668229143406	-0.328002572635	0.860227968911	0.242826457213	-0.114990026497	0.811853963792	-0.0782222046888	0.484657877004	61.7756790326	-30.5325248274	-39.5249808679
33	2.51561364759	-0.781383947989	-1.13423964436	2.96785297498	-0.757005435148	2.18161871523	0.154583279578	0.815780660998	-0.838659921893	-0.443363096596	0.548684906773	0.0395820242249	0.584085171554	0.466368088644	0.274155894239	0.925951859459	0.275732892698	-0.192833141027	0.78684542845	-0.468661105778	0.567861687231	55.9108780806	-36.3395385853	-37.1152182212
34	6.36033208537	-2.60528021074	-0.79400172225	2.05973963845	1.73385980239	2.46424473211	0.301611210228	0.692363602285	-0.2338700229	-0.224416006766	-0.286939656793	0.168147021715	0.060653936819	-0.267695027046	-0.0932241881208	0.558654565838	0.0381085210569	-0.047696836748	0.492160717451	0.040302439528	0.340547693249	46.9416066937	-20.7128252774	-26.6727197017
35	7.07183631038	-1.89654460463	1.31538329738	4.45234003242	0.192203982876	3.57985724663	0.178384618476	0.581137103622	-0.603720869912	0.0950558111615	-0.0962585924641	-0.740456603106	0.345876224916	0.478806647696	-0.457281076206	0.629902706291	0.161075064098	-0.101215066834	0.585403528871	-0.0491618200744	0.49259010186	64.2029354772	-31.5480498085	-27.3813477165
36	1.39770607125	0.70631882288	1.74673496949	4.33658371152	-1.30046483105	3.50087485166	-0.313326424685	-0.0549392786613	0.11741578153	-0.167447915598	-0.0990920541137	0.514819857712	-0.759233279636	-0.762400434795	0.396066615343	0.807445078781	0.129569102987	0.0680292170621	0.314096158514	0.0444996437994	0.46536512496	18.2511314426	4.97887577989	-19.672889861
37	3.77877482208	-0.14182454459	0.892112038774	4.77187404501	-0.751850742262	1.77798017626	0.0197200256562	0.177215061381	-0.0164453437271	-0.423214057867	0.0558797160346	0.497907707805	-0.302812253189	0.178882970859	-0.143458227089	0.468875769196	0.0135399735337	0.0371045950216	0.378592728577	0.0419414446436	0.247757809552	20.1757877893	-3.30552523793	-26.1935700373
38	5.26092675954	0.489255756494	-0.556318845487	4.17900716911	-2.61626848549	1.66628766626	0.198463953331	-0.458657003992	0.855533574541	0.890190766676	-0.470320235969	0.540172473183	-0.278135858947	-0.183615690087	0.10196608518	0.534885758052	-0.00299157741004	0.0364450879104	0.397655748403	-0.052122137616	0.32842856434	28.4767132511	4.4692823336	-15.0548595662
39	3.26333613992	0.845377962904	0.226087317719	4.00421529671	-0.492595877159	4.39276745341	-0.0178227086026	-0.261764205089	-0.286153695692	0.450242735086	-0.0315715717532	0.322227044774	0.0266700253823	0.011040126366	-0.019593934081	0.482464024608	0.0523267337597	0.0179472004534	0.362286380146	0.0420307619339	0.245333371396	22.2504667021	-7.275066594	-16.9621644686
40	2.97749725672	-0.364715063062	-1.01934917659	3.55701307186	-0.531412881516	0.374911605899	0.0626291455643	-0.303527526322	0.115523459703	0.548970761873	-0.00395850271864	0.240983431315	0.0259732262632	-0.0875210651012	-0.0480105251695	0.643664351655	0.0359951735713	-0.0102057333626	0.417065880511	-0.0253248149535	0.304538304591	27.5858325879	-1.56761712276	-17.9409744915
41	3.82893314452	-0.654248331442	0.119459951188	3.02685796747	-0.826131102371	0.25519733126	0.0539922424961	-0.580995759581	0.181072479454	0.362528878362	0.133167513558	0.187219040962	-0.47087531837	0.0359776381305	-0.254404354918	0.705777534067	0.00649619633227	0.0357659808187	0.423335036107	-0.0819216785723	0.375187357906	30.9003013499	4.82685492208	-15.4523356457
42	5.22508312606	-1.27558190264	0.65326305288	7.06915426609	-2.41245024662	2.65489046839	0.0138534000012	-0.128766699041	0.624419464508	0.467922084886	-0.0908377930694	-0.705017541207	-0.94186704301	0.576205312093	0.0559001518392	0.591964711441	-0.171212167213	-0.0400775347422	0.51847540299	-0.0637378396163	0.297157461783	46.8482697946	6.07935448106	-20.2631594733
43	6.80346807287	-0.0328380701378	-0.488694771389	5.15346394515	-0.00257061574172	2.45269204231	-0.00514942493452	0.266219353742	0.216615930431	-0.341995742026	0.0976909888605	-0.446589504496	-0.658357762404	0.283677027296	-0.103514650696	0.611568524989	-0.109221079459	0.0207907481896	0.424555761121	-0.00386569730761	0.345632523685	43.17793758	4.75691395009	-27.2102586219
44	2.84750062588	-1.24338210108	0.753315180003	3.67826942399	1.00503416737	0.831116240702	0.166991323575	-0.190207854208	0.565025071122	0.365351974266	-0.0918958488301	-0.376726915725	-0.835242502673	0.288119634816	-0.0255940577169	0.870614373406	-0.0999984487751	0.0576375992959	0.358607951237	-0.0783267127861	0.352745803168	40.952373825	7.78916656737	-20.3106612842
45	4.14379997486	-3.11995062382	4.75395050331	7.29291094038	-4.18897050347	5.79734946141	0.771072411179	-0.261014771924	-0.605324489297	-0.141181041781	0.299828838158	0.419433641954	0.292850450273	-0.782657145884	-0.83873202446	0.640186630009	0.0279341570091	0.11160076138	0.573275328821	-0.0747521921183	0.523991357952	61.0542476451	-14.7144134294	7.94353474293
46	6.78897774209	-2.67571665186	0.937084002974	3.33086454925	-0.519568921938	1.79999101862	-0.16348830603	-0.805656857291	0.837916825968	0.175155442055	0.0937720887762	-0.240543484461	-0.143242431732	0.0102943965973	0.120179518017	0.521578115536	0.000246862967941	0.00647710811161	0.493548049441	-0.108176756218	0.328207774849	68.7488414778	-1.32010588137	13.7250561889
47	9.17936761191	-0.425755429059	-0.637570999767	4.86050617616	-1.55935934087	2.68772326598	0.0273396301587	0.776640775634	0.144741661031	-0.656087191613	0.0172411936715	0.0946055895347	0.154516730431	-0.0556767648424	-0.0604216185288	0.580504755204	0.0289596390976	-0.00125036029459	0.502376869954	-0.0321659310634	0.304692186141	61.0615646611	-3.24728967003	0.718955989584
48	4.5707832638	-1.28147913175	1.05899338859	2.10538278294	-1.08947196087	0.646843415641	0.0628037452199	-0.0364789768694	0.19082822025	-0.0796593818381	0.00482445879989	0.105515573941	0.00707271849971	-0.0546572560994	-0.0744797567236	0.518294528622	-0.00546968376068	0.066210571817	0.495632239987	-0.0532155540722	0.321783989342	61.6527844847	-3.53427760212	10.3069091822
49	2.68081354734	-1.6050311225	-0.617449826931	4.86571284439	-0.387972779963	3.39990481281	0.00285961641458	0.0425123472132	-0.202979640086	-0.243205661877	-0.124771501758	-0.353569538333	0.683753548633	0.286338877189	-0.0545945827056	0.438860464667	-0.000403783135577	0.0371373513701	0.362706934674	-0.0157527841104	0.281924225255	99.5928099144	-32.1655681007	16.2851687119
50	3.27961415751	-0.913322559429	1.06259141592	4.50959347519	-0.714100524684	3.09361357737	0.047531447541	-0.266816562722	-0.155296006565	0.416038315419	0.0853392657271	-0.0161416010294	0.0666209931632	0.00406718355294	-0.147801297505	0.432885336439	0.0216914872619	0.0260993508737	0.366329873127	-0.00585746145867	0.211571537378	93.7322178031	-29.2041707027	21.8382199565
51	2.68839550581	-2.02274217054	1.05911778802	2.18055502047	-0.240296581027	2.77361453103	0.396767696495	-0.453321775488	-0.937165377653	0.920124138987	0.19260893756	0.352146859315	1.49111306322	-0.411774683546	-0.372810721652	0.756208744402	-0.151332303153	-0.000912002397964	0.666504303246	0.274324034364	0.704786246949	72.929593678	-43.4156006356	21.5520971776
52	4.8191437797	-1.24398266554	1.57034824042	6.10587245747	0.397244976708	2.4834711129	0.158371607302	-0.163271063944	-0.567563043972	0.0135519888714	-0.084720484659	0.616601287705	0.376038513713	-0.292832345526	-0.0650754760422	0.447141597994	-0.0810180190688	0.00444816703461	0.450968015695	0.0791690836107	0.377880355852	74.8289873808	-35.0494133055	14.5958202219
53	5.28394911387	-0.284136199088	1.65078180747	2.42415234173	-0.598775669756	2.0409457422	0.201455903741	-0.28963612882	-0.848456730559	-0.0218167741583	0.27432438134	0.254983653028	0.754944885308	-0.050933764972	-0.441510089443	0.571957172146	-0.0563903748014	-0.0344431757973	0.443679050729	0.0853899748113	0.360421195976	78.1205012423	-39.7639784886	18.3479304302

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 557 through 594 )	A	A	557 - 594	1 - 38
2	2	chain 'A' and (resid 595 through 625 )	A	A	595 - 625	39 - 69
3	3	chain 'A' and (resid 626 through 639 )	A	A	626 - 639	70 - 83
4	4	chain 'A' and (resid 640 through 732 )	A	A	640 - 732	84 - 176
5	5	chain 'H' and (resid -1 through 17 )	H	B	-1 - 17	1 - 19
6	6	chain 'H' and (resid 18 through 33 )	H	B	18 - 33	20 - 35
7	7	chain 'H' and (resid 34 through 57 )	H	B	34 - 57	36 - 59
8	8	chain 'H' and (resid 58 through 99 )	H	B	58 - 99	60 - 101
9	9	chain 'H' and (resid 100 through 233 )	H	B	100 - 233	102 - 215
10	10	chain 'H' and (resid 234 through 251 )	H	B	234 - 251	216 - 233
11	11	chain 'B' and (resid 557 through 579 )	B	C	557 - 579	1 - 23
12	12	chain 'B' and (resid 580 through 625 )	B	C	580 - 625	24 - 69
13	13	chain 'B' and (resid 626 through 639 )	B	C	626 - 639	70 - 83
14	14	chain 'B' and (resid 640 through 656 )	B	C	640 - 656	84 - 100
15	15	chain 'B' and (resid 657 through 666 )	B	C	657 - 666	101 - 110
16	16	chain 'B' and (resid 667 through 699 )	B	C	667 - 699	111 - 143
17	17	chain 'B' and (resid 700 through 732 )	B	C	700 - 732	144 - 176
18	18	chain 'I' and (resid -1 through 33 )	I	D	-1 - 33	1 - 35
19	19	chain 'I' and (resid 34 through 51 )	I	D	34 - 51	36 - 53
20	20	chain 'I' and (resid 52 through 64 )	I	D	52 - 64	54 - 66
21	21	chain 'I' and (resid 65 through 83 )	I	D	65 - 83	67 - 85
22	22	chain 'I' and (resid 84 through 150 )	I	D	84 - 150	86 - 132
23	23	chain 'I' and (resid 151 through 168 )	I	D	151 - 168	133 - 150
24	24	chain 'I' and (resid 169 through 218 )	I	D	169 - 218	151 - 200
25	25	chain 'I' and (resid 219 through 233 )	I	D	219 - 233	201 - 215
26	26	chain 'I' and (resid 234 through 251 )	I	D	234 - 251	216 - 233
27	27	chain 'C' and (resid 557 through 579 )	C	E	557 - 579	1 - 23
28	28	chain 'C' and (resid 580 through 594 )	C	E	580 - 594	24 - 38
29	29	chain 'C' and (resid 595 through 625 )	C	E	595 - 625	39 - 69
30	30	chain 'C' and (resid 626 through 639 )	C	E	626 - 639	70 - 83
31	31	chain 'C' and (resid 640 through 656 )	C	E	640 - 656	84 - 100
32	32	chain 'C' and (resid 657 through 676 )	C	E	657 - 676	101 - 120
33	33	chain 'C' and (resid 677 through 699 )	C	E	677 - 699	121 - 143
34	34	chain 'C' and (resid 700 through 719 )	C	E	700 - 719	144 - 163
35	35	chain 'C' and (resid 720 through 732 )	C	E	720 - 732	164 - 176
36	36	chain 'J' and (resid -1 through 17 )	J	F	-1 - 17	1 - 19
37	37	chain 'J' and (resid 18 through 33 )	J	F	18 - 33	20 - 35
38	38	chain 'J' and (resid 34 through 45 )	J	F	34 - 45	36 - 47
39	39	chain 'J' and (resid 46 through 83 )	J	F	46 - 83	48 - 85
40	40	chain 'J' and (resid 84 through 109 )	J	F	84 - 109	86 - 111
41	41	chain 'J' and (resid 110 through 150 )	J	F	110 - 150	112 - 132
42	42	chain 'J' and (resid 151 through 181 )	J	F	151 - 181	133 - 163
43	43	chain 'J' and (resid 182 through 218 )	J	F	182 - 218	164 - 200
44	44	chain 'J' and (resid 219 through 251 )	J	F	219 - 251	201 - 233
45	45	chain 'D' and (resid 557 through 579 )	D	G	557 - 579	1 - 23
46	46	chain 'D' and (resid 580 through 639 )	D	G	580 - 639	24 - 83
47	47	chain 'D' and (resid 640 through 686 )	D	G	640 - 686	84 - 130
48	48	chain 'D' and (resid 687 through 732 )	D	G	687 - 732	131 - 176
49	49	chain 'K' and (resid -1 through 33 )	K	H	-1 - 33	1 - 35
50	50	chain 'K' and (resid 34 through 122 )	K	H	34 - 122	36 - 124
51	51	chain 'K' and (resid 123 through 162 )	K	H	123 - 162	125 - 144
52	52	chain 'K' and (resid 163 through 218 )	K	H	163 - 218	145 - 200
53	53	chain 'K' and (resid 219 through 251 )	K	H	219 - 251	201 - 233

+
About Yorodumi

-
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