PDB-7ui1: Pfs230 D1D2 domain in complex with 230AL-37

ID or keywords:

Entry

Database: PDB / ID: 7ui1

Title

Pfs230 D1D2 domain in complex with 230AL-37

Components

230AL-37
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: 3.3 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 28, 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	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7ui1.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb7ui1.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	7ui1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7ui1_validation.pdf.gz	497.3 KB	Display	wwPDB validaton report
Full document	7ui1_full_validation.pdf.gz	527.3 KB	Display
Data in XML	7ui1_validation.xml.gz	70.9 KB	Display
Data in CIF	7ui1_validation.cif.gz	95.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/7ui1 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7ui1	HTTPS FTP

-
Related structure data

Related structure data	7u9eC 7u9wC 7ua2C 7ua8C 7ubsC 7uc8C 7ucqC 7ufwC 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)

Deposited unit

A: Gametocyte surface protein P230

H: 230AL-37

B: Gametocyte surface protein P230

I: 230AL-37

C: Gametocyte surface protein P230

J: 230AL-37

D: Gametocyte surface protein P230

K: 230AL-37

hetero molecules

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

1

A: Gametocyte surface protein P230

hetero molecules

defined by author
Evidence: gel filtration
40.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: 230AL-37

hetero molecules

defined by author
27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Gametocyte surface protein P230

I: 230AL-37

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

4

C: Gametocyte surface protein P230

J: 230AL-37

hetero molecules

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

5

D: Gametocyte surface protein P230

K: 230AL-37

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.580, 155.140, 375.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

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	ASP	GLY	A	1 - 308
d_2	1	ens_1	ASP	GLY	C	1 - 308
d_3	1	ens_1	ASP	GLY	E	1 - 308
d_4	1	ens_1	ASP	GLY	G	1 - 308
d_1	1	ens_2	GLN	LYS	B	1 - 227
d_2	1	ens_2	GLN	LYS	D	1 - 227
d_3	1	ens_2	GLN	LYS	F	1 - 227
d_4	1	ens_2	GLN	LYS	H	1 - 227

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999603612699, 0.0230629594252, 0.0161467452205), (-0.0228687890103, -0.99966514551, 0.0121084821927), (0.0164205958438, 0.0117344260344, 0.999796312895)	3.37862202545, -158.901129554, 1.79766392546
2	given	(0.946641733384, -0.216576903133, -0.23867105741), (0.187741716872, 0.972499404618, -0.137833072093), (0.261958921134, 0.0856700241977, 0.961269041732)	25.2684313968, -71.4023138581, 9.96737462006
3	given	(-0.974637700808, 0.221592397848, -0.0312755715954), (-0.219830116586, -0.97417169827, -0.0516161034072), (-0.041905512817, -0.0434316877994, 0.998177146848)	-2.69726578108, -231.486434405, -2.90837866877
4	given	(-0.999894932678, 0.0144956223343, -2.32029131386E-5), (-0.0144862746509, -0.999190045034, 0.0375419998246), (0.000521010531309, 0.037538391511, 0.999295050378)	3.76099786983, -160.325462186, 2.85455417329
5	given	(0.967368930765, -0.172094973989, -0.185958790376), (0.150141453193, 0.980550817304, -0.126402684772), (0.204095310636, 0.0943579069927, 0.974392985178)	24.4862259956, -71.9104791701, 8.96174022712
6	given	(-0.976294459853, 0.182291528194, -0.11670015599), (-0.174146290983, -0.981733071, -0.0766371100806), (-0.128538698439, -0.054497486668, 0.990205951785)	0.583815854186, -229.959004478, -3.72821154891

#1: Protein	Gametocyte surface protein P230 Mass: 40738.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874
#2: Antibody	230AL-37 Mass: 27582.699 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: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.41 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.3→19.89 Å / Num. obs: 44493 / % possible obs: 98.7 % / Redundancy: 7.2 % / B_iso Wilson estimate: 65.24 Å² / CC_1/2: 0.98 / Net I/σ(I): 5.54
Reflection shell	Resolution: 3.3→3.39 Å / Num. unique obs: 3161 / CC_1/2: 0.45

-
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: 3.3→19.89 Å / SU ML: 0.4484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2995	1716	4.97 %
R_work	0.2639	32811	-
obs	0.2657	34527	77.23 %

Solvent computation

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

Displacement parameters

B_iso mean: 94.34 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17060	0	25	0	17085

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	17444
X-RAY DIFFRACTION	f_angle_d	0.5883	23594
X-RAY DIFFRACTION	f_chiral_restr	0.0473	2604
X-RAY DIFFRACTION	f_plane_restr	0.0056	2988
X-RAY DIFFRACTION	f_dihedral_angle_d	27.014	2316

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	1.22466359432
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.976399830654
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.04925273096
ens_2	d_2	B	X-RAY DIFFRACTION	Torsion NCS	0.671525493137
ens_2	d_3	B	X-RAY DIFFRACTION	Torsion NCS	0.820673939944
ens_2	d_4	B	X-RAY DIFFRACTION	Torsion NCS	0.787584624185

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.3-3.4	0.3691	37	0.3467	630	X-RAY DIFFRACTION	18.58
3.4-3.51	0.3784	71	0.3245	1319	X-RAY DIFFRACTION	38.03
3.51-3.63	0.3288	78	0.3188	1717	X-RAY DIFFRACTION	49.25
3.63-3.78	0.361	114	0.3131	2177	X-RAY DIFFRACTION	61.59
3.78-3.95	0.308	136	0.3122	2548	X-RAY DIFFRACTION	73.92
3.95-4.15	0.2918	157	0.2973	3061	X-RAY DIFFRACTION	86.2
4.15-4.41	0.3056	181	0.2638	3446	X-RAY DIFFRACTION	98.35
4.41-4.75	0.2814	185	0.2327	3512	X-RAY DIFFRACTION	99.95
4.75-5.22	0.2679	183	0.23	3484	X-RAY DIFFRACTION	98.18
5.22-5.95	0.2815	189	0.2532	3570	X-RAY DIFFRACTION	99.6
5.95-7.43	0.3094	189	0.2791	3621	X-RAY DIFFRACTION	99.69
7.43-19.89	0.2986	196	0.2383	3726	X-RAY DIFFRACTION	98.22

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	2.96944279946	1.11238897041	0.814454646447	0.517002687056	0.811714973123	4.46608304868	0.214959575179	0.41615875455	-0.370804299166	-0.918609487637	-0.440123913754	0.75247924918	0.533838872965	-0.872398738561	0.250733353494	1.30865492042	-0.0477103476547	-0.366051870726	0.773645831911	-0.218390292916	0.650330753159	-16.7491297895	-59.0764448806	44.419236751
2	3.09738145905	0.27585053921	-0.531942733725	1.63507437629	1.49611269064	1.71863812185	-0.0357072538825	1.88896734084	-0.474642615921	-1.52698002706	-0.370854363207	1.01424258723	-0.270497758603	-1.82017663832	0.464886514403	2.4825621988	-0.258642554855	-0.466994412732	2.20676009483	-0.332797875047	1.19369087604	-25.5884255546	-62.3827499407	13.2777166318
3	7.85711544925	-2.6910135459	-2.11229998733	2.85080705396	0.988354090455	4.21211899408	0.566051364406	0.63691238772	0.693540817435	0.433939794039	-0.473202820215	0.0339671981111	0.649721429594	-3.01445667509	-0.0123597540426	2.12560851108	0.202972057593	-0.41033840399	2.35569999041	-0.303594558833	1.15021131838	-27.8746810465	-50.4985049367	13.6404383123
4	1.85925560996	0.357601134037	0.835343425899	0.44480150214	0.103829907258	2.13056605349	-0.129251809006	0.31487354242	0.162576578481	-0.117806270649	0.0263226947089	-0.235707382488	-0.0889537771357	0.47070773884	-0.249140229017	0.218392569097	-0.422699217558	0.0805172497322	1.18414951871	-0.418966140783	0.884438086052	10.8642124472	-44.2310554468	76.450455238
5	1.04358878005	0.0578463545947	0.404930879857	0.560874031413	0.172072528244	0.961711530225	0.124686705142	-0.104207268611	0.00763520406987	-0.00144896203203	0.0703604036067	-0.19874293607	-0.125293509963	0.187628571413	0.237728580662	0.119980615537	-0.501423502028	0.0153232543012	0.239407033683	-0.250066521855	0.414703146661	0.790971781738	-47.3112204159	78.2310383661
6	5.15944283009	0.387122887596	2.47861328938	4.67687913567	2.83296091397	2.69732520726	-0.0547620056646	-0.415980267426	0.0222069608406	0.155295187207	0.14905707665	-0.0346603740085	0.0705836139748	0.00138085434206	-0.220333838498	0.280832546726	-0.278445867056	-0.025488332591	0.667453963248	-0.0182557146781	0.434588094107	4.86330407348	-44.8675348171	85.9897496023
7	3.55942182514	0.61982379114	1.93711959711	3.31421309444	1.11347414978	2.08566148129	-0.279360539824	-0.274201183825	0.0464410019988	-0.327921584894	0.499369251251	-0.742147319058	-0.328116183184	0.129270754674	-0.155258758113	0.384519052763	-0.197123684443	0.111047106803	0.505135525432	-0.160900563005	0.471015931316	5.85781680805	-56.354067948	76.7223694413
8	3.15979587366	0.958965321237	1.88516555326	2.51641541164	-0.123358325963	3.12520668316	0.102736187829	0.260191648126	-0.266924531696	-0.645275558305	0.226627494312	-0.592109346411	0.476696456432	0.581354283506	-0.257348661632	0.257454627635	-0.119032197558	0.0858905599567	0.303796529411	-0.122208905487	0.574928081924	7.05338739795	-69.1436775336	69.1857632745
9	6.92985780008	-5.75768402488	-1.83783639396	8.06347045012	1.10248785659	1.35190099866	-0.831005735732	-0.706659248693	-0.489789668732	-0.0866319087907	0.940663219631	0.146512736691	0.0984956624065	-0.0602971956261	-0.0973139843434	0.279124190005	-0.170092476983	0.0730149837506	0.41317664768	-0.0620723536455	0.240171595701	2.37882959294	-64.8418436498	76.4129320564
10	6.22720176965	-1.88254860659	-0.896629875012	2.46104985771	0.756253870633	3.4674985095	-0.269461514295	0.127615093992	0.228192396374	-0.625006807023	0.00329838051798	-0.68502302696	0.341090498421	0.676170563076	0.197846594179	1.10115418893	-0.0406710024319	0.430810077778	0.6371794466	-0.00251778548427	0.801344102806	19.9141316279	-96.0056662585	47.6539023987
11	3.6688592753	0.330678677041	-1.14025502729	0.0544893609542	-0.230273923358	4.67780115853	-0.175033564587	0.852526026005	0.492083084817	-1.21670160857	-0.0752984784694	-0.573504190868	-0.525107194173	0.498672992853	0.217536786992	1.47782390594	-0.095986648766	0.548193237134	0.878362337256	0.0467436228661	0.916153402909	19.8693550191	-98.4642065792	42.1138776112
12	7.887119542	3.23503308055	0.202938054489	3.14901929601	-2.19362369536	2.85301615746	0.257760696231	2.01301021065	-0.773355122334	-0.915774576522	-0.0940673158226	-0.737484670072	-0.501138642823	1.37255164024	-0.179203871455	2.01833946882	0.0656177837345	0.520585319353	1.93268652078	-0.0385208874148	1.19430561248	28.2534937596	-103.97520946	13.8711440089
13	0.156879476313	-0.14974156355	0.359236972664	0.290695339921	-0.420837486659	0.859777765549	0.288292259266	0.527200219956	-0.152504821706	0.111584393647	-0.35219579288	0.307364487389	0.751195778287	0.638314058488	0.0826958363446	2.7888665709	0.347263471653	0.962251436357	2.0037764217	0.129616293199	1.87679705425	31.6266825705	-104.041849204	12.8150236996
14	2.25757111881	0.309982655273	-1.41749199804	1.93738431546	1.17710057275	3.15642222852	0.242864221833	-0.22410185234	-0.314023444217	0.123536688906	-0.00248970723285	0.245214458444	-0.0470953727176	0.168634063127	-0.062987640836	0.221517209773	0.145531580244	-0.0513732089712	0.118848521557	-0.012249777425	0.440741411453	-2.86100734713	-110.462344454	77.9517442992
15	2.00626383234	-0.0571615923823	-0.690802225427	2.54396086534	0.313553313463	5.25608717343	-0.372933180688	-0.393773925644	-0.389849932254	0.137621150103	0.267301190959	-0.0752170582936	0.738488767254	0.30627718437	-0.201401319787	0.236748003786	0.137084850311	0.0508575032859	0.398792564973	0.181601313621	0.53968245255	2.60688408339	-114.701891754	81.0911571079
16	1.76814154453	-0.631531336481	-1.07878903412	1.66913993281	-0.360778321718	1.04439355584	0.0244869129173	-0.498361447349	0.116604079247	0.251212379233	-0.0295435644309	0.023710816769	-0.0724534149238	0.401249717657	-0.0500415078789	0.297418292379	0.179437288677	0.00114233820843	0.445810091533	-0.0153639204325	0.44891359669	-1.74176409821	-112.155190656	86.9506916739
17	0.779617159546	0.238371000675	-0.471426472049	0.848633698255	-0.0522442608308	1.02357627109	-0.136703927862	-0.264889304217	-0.262006413903	-0.228208786288	0.15494719259	0.258547968425	0.404019251937	0.319591017336	0.0208475436959	0.255359304154	0.321035362498	-0.0666086849114	0.204163217021	-0.0466690367456	0.391666663826	-2.9743514278	-101.278413865	77.4284267018
18	1.85834933713	-2.25410871408	-0.809056477327	4.6589710115	0.407277394521	2.79428738698	0.0551148469834	0.310601036358	0.384452553457	-0.375856004582	0.0918466764492	0.136428629614	-0.57257871002	0.102200779824	-0.121612894542	0.406830239494	-0.113098008217	-0.0583240563577	0.177916923912	0.123039189543	0.527545115484	-2.97913974533	-88.8646869374	68.7707047717
19	2.78527094221	-1.27907203953	0.173490926858	1.85731552581	-0.103672881168	0.703733108582	-0.03808440577	-0.422879796045	0.318624964412	-0.0582698539265	0.26184222599	0.195862061209	0.00108097212533	-0.355100051228	-0.0778900431377	0.0835779991341	0.0312509038528	-0.146930104987	0.221634815069	0.0950028972298	0.69004946962	-3.93847695713	-90.6090864868	74.6945284022
20	1.4344942625	0.395515843625	1.98054325881	2.06054720103	-0.411220241114	3.55487526369	-0.411748439818	0.272039501955	0.0377412709276	-1.52541446643	0.471392012886	0.27654849559	0.667228478819	-0.692274668418	0.0164671964452	1.16731731147	-0.183744229751	-0.20934659529	1.12599868362	0.0691497494325	0.548100852425	12.6616916901	-137.729438148	44.2305710499
21	4.96766553612	-0.823947280184	0.476375942545	0.755924471329	0.247822644541	0.218970771921	0.109404302042	2.50116023097	0.529676589766	-1.72431386495	-0.429317615599	0.145060247062	0.122748580722	-0.678629982825	0.399877739118	3.45375727884	-0.408087948204	-0.488119354865	2.12321773258	0.0840146405696	1.11503428464	8.77783515515	-133.900652276	13.5330876211
22	2.37185588427	-0.174877573838	-1.29340586452	1.33289181427	-0.51155815308	3.45549774416	0.0660801643285	0.610756981829	0.364962708475	-0.311905795825	-0.181128104172	-0.320991912838	-0.212159493965	-0.442202167209	0.0126494718688	0.225172632886	0.27413569489	-0.000325466869855	0.461459864024	-0.0535434465374	0.498086909714	28.2094988183	-123.533158564	81.6604796926
23	2.40944055325	0.27522946289	0.0108559711586	1.02275037336	-0.590183025163	0.877900461595	0.0641494761872	-0.126451129726	0.124228801585	0.00217910036589	0.207373751068	0.414603297299	0.0871562930113	-0.213604297116	-0.102335802479	0.0788111964978	0.332237667036	-0.173416294092	0.645748027463	-0.128861024957	0.317857572434	19.7206044847	-130.471955793	79.7288446047
24	0.884659373122	0.222529307508	-1.11903830406	0.589216767493	-0.549763708314	1.54130334058	0.0815744331387	-0.163992516394	0.305712170122	0.152357036843	0.11966949466	0.204229129081	-0.16200952791	0.0300055053872	-0.29460563247	0.24770207844	0.260621225855	0.0113813992398	1.07010155553	-0.0981222157123	0.482357014923	17.4984695336	-123.595228181	82.8601065505
25	1.3911060921	-1.18199193924	1.17284498078	1.58203007161	-0.353016842885	1.71104356251	0.075241406713	0.31651774308	-0.425030255853	0.162345788782	0.148022493188	0.200612706026	0.155428237994	-0.346693331832	-0.299218635656	0.274205730021	0.184119099371	-0.162530451245	0.492720192676	-0.132717462152	0.630597246873	20.8586160122	-125.986288213	89.3879049455
26	1.15529177745	0.275085238456	-0.731701558418	1.23416546481	0.285486219159	0.654389913402	0.085036157718	0.156299314775	0.255555828605	-0.224770455973	0.466379106353	-0.0916589188308	0.0714661113381	-0.483616701281	-0.0770832077305	-0.0157604505847	0.154915103342	-0.205931812828	0.421069723553	-0.0254424102903	0.392703093585	25.4806615454	-135.096473703	79.6326842714
27	3.11386089982	0.713485543864	-1.93541684852	1.76519977943	-0.303572419008	2.59987305509	-0.331962176948	-0.028804606341	-0.58310318618	-0.161192004416	0.401874071372	-0.128708897921	0.649942181813	0.104948944914	0.0143968857291	0.329435669434	0.0167343705722	0.043154711338	0.383201877866	-0.198902383804	0.476740256331	32.0828014385	-156.036620178	75.1879797702
28	0.682157241762	0.70701637907	-0.754398982715	2.69394355466	-0.115810609165	2.41709016167	-0.199698879815	0.201236981431	-0.114986377857	-0.464926478553	0.451993711835	-0.085460985984	0.0591883110993	0.0497984346885	-0.171704017691	0.247973322829	0.00869068626032	-0.0448275639692	0.426628969486	-0.0899942180056	0.340807441731	29.8802658106	-145.45440969	70.5255075357
29	7.3196612884	-5.3000840842	1.42719564339	6.98553346607	-0.474213414125	2.25398646085	-0.731951993067	-1.24349769699	-0.535657872668	0.194703049217	0.789612504069	-0.0721381951063	-0.0348796476843	-0.165536482456	-0.0816313431099	0.166979103702	0.0469497141818	0.0266702564082	0.601226559379	-0.0310754721711	0.269982144884	23.8205290708	-144.933284517	77.7903942455
30	4.92183736108	-2.14055612826	-1.48266267782	5.2466721984	-0.355156648404	2.1089213393	0.331681191202	0.136696624261	0.15622678682	-0.87074450562	-0.205928491097	-0.390261121137	-0.394047186744	0.454813445028	-0.103543077915	0.516650068578	-0.211377549112	0.0481559301299	0.861121383768	-0.0397855016747	0.500589284513	-0.86236473141	-172.683643754	49.9652924255
31	2.56525417522	0.0622093209857	-1.81590981272	1.84557179194	-2.00060650298	6.2061453393	-0.0807396766733	0.038124856499	0.113172961872	-1.00770798493	-0.219837937682	-0.0617711437919	-0.825123451326	0.509001894761	0.264941079963	1.11502837093	-0.287823395622	0.0975562701447	0.706540108733	-0.0732186275826	0.464536913821	-0.907183966528	-171.809274835	41.2392830377
32	3.42568836397	-0.23873716088	-0.429324255412	1.0092005373	-0.252352165171	5.22368394317	0.380613686295	0.968003225481	1.17103569842	-0.651434279858	0.301545308458	-0.0671901688207	-1.05925411744	0.319602333464	-0.57941030305	2.73113938888	-0.716304174809	0.399061951263	1.29203977635	0.1811526055	1.37599911596	7.29716959764	-159.46791115	12.9461581037
33	8.91518121547	2.24468051594	-0.149017577077	5.59646943992	-1.18660370097	4.40599450954	-0.758262579472	1.22918416293	-1.43108876798	-1.97626925132	-0.0185069729449	-1.53897396052	0.687564481285	0.406605772283	0.818082168176	2.83135468427	-0.316185161924	0.616414912121	1.21672327678	0.153003395223	1.13630558236	12.4630131423	-175.609334202	11.6830882546
34	6.03954930474	0.26565326359	-0.23204340803	2.98825537764	0.6625539818	3.71673516716	-0.394764672831	0.382140965683	-1.274565855	-1.30506636081	0.289640799974	-0.611053419832	0.238171654504	0.73746419457	0.175956527614	2.26986710337	-0.0799895004149	0.419086544633	0.855389643281	-0.0798163505864	0.907154332137	11.3595904981	-177.796221608	20.4618460937
35	7.01883695442	-1.99785111089	-0.395198483471	6.09691284949	0.489136409105	4.93353293181	-0.905992659508	2.11072207806	-0.787081581814	-1.04632636057	-0.465043228757	-0.105394951278	-0.568781906486	-0.28358849952	1.29169292731	2.60461662047	-0.81790938392	0.535187738418	1.62033649624	-0.342492253726	1.05902703841	10.730412534	-171.470991853	8.00084598291
36	0.129095570535	0.120736973242	-0.250810866595	0.261434605119	-0.157117468473	0.522752288306	-0.134922370104	-0.0586435889834	-0.213754334765	-0.0536317178667	-0.027749950421	0.0155882393508	0.160908510585	-0.0808166493176	-0.20924901274	0.393784196379	-0.529177845166	0.036526207974	1.03556627458	0.52053625214	0.365014882973	-28.8521231587	-194.568298718	77.7655023256
37	3.61777806844	0.615170360861	1.26553390662	2.54855227395	-1.00996573164	1.05911744086	0.0665761316179	1.05412599899	-0.00788048247326	-0.52512875334	0.479614282325	0.164713125299	0.00125094461233	0.00820277530633	0.124366970813	0.270907418143	-0.220555035688	0.0329964317046	0.638700407438	0.194615512901	0.218298217848	-23.6332927248	-187.662707196	71.3825878399
38	5.49295867294	-0.915332478264	-0.986526747826	1.69788260869	-1.22161669523	1.43078830996	-0.374991806712	-0.631992384391	-0.454244795178	0.084122318366	0.196096129818	-0.0686642168097	0.597596150228	-0.322692298013	0.0379540257563	0.239790772075	-0.195708433314	-0.0611742459018	0.490055587198	0.0587928821862	0.314440807594	-15.66720195	-191.850680691	75.1705363412
39	7.40437615205	-0.822906808826	0.602874848395	2.14201964563	-1.35224780641	2.12462731589	-0.0892733593917	-0.621655905933	0.237641738618	0.0638665287315	0.312853619122	-0.205808210487	-0.151528027428	-0.409794892401	-0.187271765	0.056797185453	-0.0655256323233	-0.0351452671314	0.505948049595	-0.00343714460443	0.307417843038	-22.360160876	-193.356413252	83.2381027467
40	1.56299117437	-0.0936793395883	0.00493564647937	1.46214209304	0.0123624330956	0.669182190979	-0.175503836805	0.00949617993151	-0.0729683063173	-0.156006665261	0.384692516861	0.496148901387	0.313412858424	-0.301609356003	0.0332915166412	0.207258599593	-0.337641163639	0.0614746064827	0.613763355257	-0.0255420955913	0.29469988897	-24.3960195928	-181.555704722	74.5902234442
41	3.62571012257	0.397780491865	0.183863828405	0.639400902401	-0.925934455652	2.62728228549	-0.020258675302	-0.217265655463	0.392033503638	0.114762947043	0.30072670254	-0.0868602133374	-0.11676561819	-0.837310197891	-0.281873871267	0.277036566757	-0.233916964087	-0.0787622500225	0.58936157454	0.121811773172	0.493911846507	-24.8012609825	-165.997981213	70.79327526
42	1.96598701416	1.42735918046	-0.87544658291	2.19398241932	-0.495173422152	0.406100176848	0.138796120705	0.453063071873	-0.030869661902	-0.173093005065	0.111791564841	0.701988356922	0.171608630643	-0.613271622666	-0.0895626066025	0.220767615918	-0.210442448721	-0.138946031082	0.677703058954	0.0487663848054	0.441019875676	-26.3945401723	-170.22721554	64.2403012353
43	2.06350851717	-2.77782540034	1.09304579596	4.83673703586	-0.831075616433	5.52359419774	-0.107314527042	-0.204997209001	0.0421400989748	-0.278003016413	0.424765976871	0.454356609777	-0.211825085333	-1.33222891844	-0.133718931054	0.295195669782	-0.228918508428	-0.141248996343	0.50738519785	0.0927403498268	0.384284761873	-26.9853663731	-170.909140324	72.7123707911

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 555 through 736 )	A	A	555 - 736	1 - 182
2	2	chain 'A' and (resid 737 through 809 )	A	A	737 - 809	183 - 236
3	3	chain 'A' and (resid 810 through 887 )	A	A	810 - 887	237 - 308
4	4	chain 'H' and (resid 1 through 33 )	H	B	1 - 33	1 - 33
5	5	chain 'H' and (resid 34 through 76 )	H	B	34 - 76	34 - 76
6	6	chain 'H' and (resid 77 through 91 )	H	B	77 - 91	77 - 91
7	7	chain 'H' and (resid 92 through 148 )	H	B	92 - 148	92 - 128
8	8	chain 'H' and (resid 149 through 229 )	H	B	149 - 229	129 - 209
9	9	chain 'H' and (resid 230 through 247 )	H	B	230 - 247	210 - 227
10	10	chain 'B' and (resid 555 through 593 )	B	C	555 - 593	1 - 39
11	11	chain 'B' and (resid 594 through 769 )	B	C	594 - 769	40 - 196
12	12	chain 'B' and (resid 770 through 844 )	B	C	770 - 844	197 - 271
13	13	chain 'B' and (resid 845 through 887 )	B	C	845 - 887	272 - 308
14	14	chain 'I' and (resid 1 through 60 )	I	D	1 - 60	1 - 60
15	15	chain 'I' and (resid 61 through 76 )	I	D	61 - 76	61 - 76
16	16	chain 'I' and (resid 77 through 91 )	I	D	77 - 91	77 - 91
17	17	chain 'I' and (resid 92 through 148 )	I	D	92 - 148	92 - 128
18	18	chain 'I' and (resid 149 through 214 )	I	D	149 - 214	129 - 194
19	19	chain 'I' and (resid 215 through 247 )	I	D	215 - 247	195 - 227
20	20	chain 'C' and (resid 555 through 719 )	C	E	555 - 719	1 - 165
21	21	chain 'C' and (resid 720 through 887 )	C	E	720 - 887	166 - 308
22	22	chain 'J' and (resid 1 through 33 )	J	F	1 - 33	1 - 33
23	23	chain 'J' and (resid 34 through 60 )	J	F	34 - 60	34 - 60
24	24	chain 'J' and (resid 61 through 76 )	J	F	61 - 76	61 - 76
25	25	chain 'J' and (resid 77 through 91 )	J	F	77 - 91	77 - 91
26	26	chain 'J' and (resid 92 through 146 )	J	F	92 - 146	92 - 126
27	27	chain 'J' and (resid 147 through 164 )	J	F	147 - 164	127 - 144
28	28	chain 'J' and (resid 165 through 229 )	J	F	165 - 229	145 - 209
29	29	chain 'J' and (resid 230 through 247 )	J	F	230 - 247	210 - 227
30	30	chain 'D' and (resid 555 through 607 )	D	G	555 - 607	1 - 53
31	31	chain 'D' and (resid 608 through 761 )	D	G	608 - 761	54 - 188
32	32	chain 'D' and (resid 762 through 782 )	D	G	762 - 782	189 - 209
33	33	chain 'D' and (resid 783 through 819 )	D	G	783 - 819	210 - 246
34	34	chain 'D' and (resid 820 through 857 )	D	G	820 - 857	247 - 284
35	35	chain 'D' and (resid 858 through 887 )	D	G	858 - 887	285 - 308
36	36	chain 'K' and (resid 1 through 25 )	K	H	1 - 25	1 - 25
37	37	chain 'K' and (resid 26 through 44 )	K	H	26 - 44	26 - 44
38	38	chain 'K' and (resid 45 through 76 )	K	H	45 - 76	45 - 76
39	39	chain 'K' and (resid 77 through 91 )	K	H	77 - 91	77 - 91
40	40	chain 'K' and (resid 92 through 148 )	K	H	92 - 148	92 - 128
41	41	chain 'K' and (resid 149 through 177 )	K	H	149 - 177	129 - 157
42	42	chain 'K' and (resid 178 through 214 )	K	H	178 - 214	158 - 194
43	43	chain 'K' and (resid 215 through 247 )	K	H	215 - 247	195 - 227

-
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