PDB-7uc8: Pfs230 D1 domain in complex with 230AS-73

ID or keywords:

Entry

Database: PDB / ID: 7uc8

Title

Pfs230 D1 domain in complex with 230AS-73

Components

230AS-73
Gametocyte surface protein P230

Keywords

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

Function / homology

6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230

Function and homology information

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 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 16, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7uc8.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7uc8.ent.gz	773.4 KB	Display	PDB format
PDBx/mmJSON format	7uc8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7uc8_validation.pdf.gz	473.1 KB	Display	wwPDB validaton report
Full document	7uc8_full_validation.pdf.gz	489.1 KB	Display
Data in XML	7uc8_validation.xml.gz	52.8 KB	Display
Data in CIF	7uc8_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uc/7uc8 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/7uc8	HTTPS FTP

-
Related structure data

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

Deposited unit

A: Gametocyte surface protein P230

B: Gametocyte surface protein P230

C: Gametocyte surface protein P230

H: 230AS-73

I: 230AS-73

J: 230AS-73

hetero molecules

202 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gametocyte surface protein P230

H: 230AS-73

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

2

B: Gametocyte surface protein P230

I: 230AS-73

hetero molecules

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

3

C: Gametocyte surface protein P230

J: 230AS-73

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.460, 89.460, 225.920
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁
Space group name Hall	P3₁
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 557 through 740 or resid 761 through 886))
d_2	ens_1	(chain "B" and (resid 557 through 740 or resid 761 through 886))
d_3	ens_1	(chain "C" and (resid 557 through 740 or resid 761 through 886))
d_1	ens_2	(chain "H" and (resid 1 through 32 or resid 34 through 254))
d_2	ens_2	(chain "I" and (resid 1 through 32 or resid 34 through 254))
d_3	ens_2	(chain "J" and (resid 1 through 32 or resid 34 through 254))

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	LEU	A	2 - 185
d_1	2	ens_1	LYS	GLU	A	187 - 297
d_2	1	ens_1	LEU	LEU	B	1 - 184
d_2	2	ens_1	LYS	GLU	B	186 - 296
d_3	1	ens_1	LEU	LEU	C	1 - 184
d_3	2	ens_1	LYS	GLU	C	186 - 296
d_1	1	ens_2	GLN	TYR	D	1 - 32
d_1	2	ens_2	TRP	LYS	D	34 - 234
d_2	1	ens_2	GLN	TYR	E	1 - 32
d_2	2	ens_2	TRP	LYS	E	34 - 234
d_3	1	ens_2	GLN	TYR	F	1 - 32
d_3	2	ens_2	TRP	LYS	F	34 - 234

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.998273859937, 0.0461370671208, -0.0363410457101), (-0.0478216472135, 0.997752495404, -0.0469366378595), (0.0340938502314, 0.0485935073158, 0.998236585396)	42.0641630296, -27.4459177644, -13.0429933894
2	given	(0.823679602029, 0.566869084128, -0.0145380418481), (0.567050196303, -0.823290553589, 0.0254310684531), (0.00244705396115, -0.0291908518265, -0.999570860968)	-1.62502756567, -50.482864131, -81.7024467941
3	given	(0.999473983681, 0.000580267053696, -0.0324255953688), (-0.00203497214515, 0.998991754296, -0.0448478955626), (0.0323668786454, 0.0448902900211, 0.998467449158)	42.0518389286, -26.8866123297, -13.1931913167
4	given	(0.833099088917, 0.552995609664, -0.0119064578282), (0.553000536062, -0.832266110278, 0.0390324070259), (0.0116754083761, -0.0391021402931, -0.999167006793)	-1.38126406683, -50.1801510075, -81.7176056053

#1: Protein	Gametocyte surface protein P230 Mass: 39593.773 Da / Num. of mol.: 3 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-73 Mass: 27884.902 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.29 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium dihydrogen phosphate, 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 EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→19.85 Å / Num. obs: 44584 / % possible obs: 99.5 % / Redundancy: 6.5 % / B_iso Wilson estimate: 53.21 Å² / CC_1/2: 0.99 / Net I/σ(I): 9.98
Reflection shell	Resolution: 2.9→2.98 Å / Num. unique obs: 3320 / CC_1/2: 0.89

-
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: 2.9→19.85 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.1503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2517	2024	4.54 %
R_work	0.2154	42559	-
obs	0.217	44583	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 54.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→19.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12560	0	2	23	12585

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0032	12833
X-RAY DIFFRACTION	f_angle_d	0.7187	17378
X-RAY DIFFRACTION	f_chiral_restr	0.0506	1942
X-RAY DIFFRACTION	f_plane_restr	0.0047	2186
X-RAY DIFFRACTION	f_dihedral_angle_d	11.2478	4737

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	0.887350355039
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.883482884539
ens_2	d_2	H	X-RAY DIFFRACTION	Torsion NCS	0.578893612372
ens_2	d_3	H	X-RAY DIFFRACTION	Torsion NCS	0.607869085166

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 (%)
2.9-2.97	0.326	148	0.3089	3068	X-RAY DIFFRACTION	99.94
2.97-3.05	0.3098	142	0.293	3016	X-RAY DIFFRACTION	99.91
3.05-3.14	0.34	141	0.27	3019	X-RAY DIFFRACTION	99.56
3.14-3.24	0.2993	146	0.2608	3040	X-RAY DIFFRACTION	99.69
3.24-3.36	0.2644	148	0.2594	3045	X-RAY DIFFRACTION	99.94
3.36-3.49	0.2912	149	0.2438	3014	X-RAY DIFFRACTION	99.68
3.49-3.65	0.2643	147	0.2292	3044	X-RAY DIFFRACTION	99.47
3.65-3.84	0.2541	148	0.2278	3040	X-RAY DIFFRACTION	99.91
3.84-4.08	0.2595	154	0.2074	3089	X-RAY DIFFRACTION	99.97
4.08-4.39	0.2328	140	0.185	2979	X-RAY DIFFRACTION	99.97
4.39-4.83	0.1926	139	0.1678	3071	X-RAY DIFFRACTION	99.81
4.83-5.51	0.198	139	0.1748	3042	X-RAY DIFFRACTION	99.56
5.51-6.9	0.2592	145	0.2094	3055	X-RAY DIFFRACTION	100
6.9-19.85	0.2352	138	0.196	3037	X-RAY DIFFRACTION	99.75

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	2.5227401606	0.134851867688	-1.0941035424	2.22572641106	0.802790754443	4.37340556392	-0.16497827973	0.378004324252	-0.488701409601	0.28012255881	0.241147605662	0.189339839705	0.877028851836	-0.666390112821	-0.0761887129536	0.438996646126	-0.168420760915	0.0241157638511	0.424135921842	-0.0494867922137	0.566215142333	-13.8775515871	-18.4906801844	-45.3865162961
2	4.38739264622	0.218561699684	0.658537018574	2.41330551028	0.952053215913	6.02726176876	-0.00596933922212	0.177184857379	-0.204414429514	0.0246879006414	0.0137526963113	0.343173441566	0.199031765923	-0.827444583637	-0.0308987100539	0.26727498783	-0.0486625411173	0.0859058136654	0.260158438782	0.0395792080639	0.271000215625	-17.4366816775	-10.1841368295	-39.9636108543
3	1.81619026354	0.106308529769	1.16318454989	1.62299092454	2.2225215477	5.49778510589	-0.189298261802	-0.394131185892	-0.112998002994	0.360712713459	0.426721925089	-0.227689314487	0.304806859778	0.263886743711	-0.139715691159	0.426735296585	0.0691021122804	-0.0605659992814	0.422252259249	0.0435677721107	0.456736974904	-4.01165028167	-1.8519250958	-16.2965043427
4	4.72735464228	0.537193796402	0.456118462031	3.32745822322	2.87194880038	4.86644722931	-0.398472660154	-0.514736069433	0.345503376453	0.403354216437	0.474520065183	-0.0770310592327	-0.161968706621	-0.134396723409	0.0629108464773	0.311892073506	0.17277545259	-0.136244489514	0.353046658621	-0.0178349751087	0.256193009812	-7.02100978158	1.80576186617	-12.9756605247
5	3.67544940562	0.522905955955	1.87083833145	3.24601921621	0.944969202707	3.79628790663	-0.00513055645312	0.0390547988386	-0.368080483897	0.183290745523	0.016474216465	0.0533003166207	0.563881729035	0.0475035431608	0.0378264407826	0.380322477769	0.00339610466601	0.0718225045573	0.305352944297	-0.0278926823707	0.401957611062	27.1878612318	-35.7396857692	-60.4998715744
6	4.17801859056	0.378702661952	2.79326969851	1.93540398978	1.20148710503	6.16146716493	0.206451018629	-0.154707374455	-0.282990814714	0.00139062207562	-0.206089311708	0.148090404918	0.41213590195	-0.225822370322	0.0534770908961	0.288702058245	-0.0124579814681	0.0749491134509	0.191313190243	-0.0108870083402	0.339663834278	25.8418413161	-36.4369632921	-52.71433008
7	0.309505531389	-0.125028270514	0.588138502918	0.591815512996	1.86625732869	6.45773872809	-0.0104042507571	-0.257076459484	0.00347815132083	0.163705777471	0.0115427471995	-0.055261764056	0.0773975527556	0.130847348097	0.0633652214625	0.413210972025	0.0104606728346	-0.0614236435956	0.628151389584	0.0291043843336	0.443148720947	37.5418425969	-27.0975070383	-28.422214748
8	3.08587401957	-0.51622191584	-1.04597176831	2.89598179506	1.44905516932	1.94918778019	0.152076140293	-0.349290322723	-0.0370074347657	-0.152035991888	-0.144823539324	0.250080180364	0.547392989863	-0.592444992215	-0.0326809147197	0.648533286554	-0.301368743264	-0.0316514749574	0.773982941244	0.0641133385967	0.388515581485	-20.5868923289	-51.7185951016	-35.0021223388
9	3.28119383486	-0.276237849232	-1.69392511766	2.0164656008	-0.732587920393	4.73035467644	0.0499332972789	0.256274324408	-0.158967492116	0.048966309864	0.0604748403798	0.202777674946	0.501242539443	-0.987691237233	-0.0725000308759	0.511645349857	-0.24738105106	-0.0533787548788	0.577153001278	0.0597710298325	0.32944244521	-20.5973952504	-51.2823717287	-45.3139641594
10	2.83906103854	-0.120399128268	-1.61753206265	2.07476483418	0.941263653059	7.19363796572	-0.214067066518	-0.348886319139	-0.0356764722019	-0.0105243928722	0.110254377697	0.0324877987723	0.35097757816	-0.548859187758	-0.182942695328	0.309871387088	-0.194709169449	-0.100226860363	0.508158734717	0.0805064968092	0.394995651266	-17.2786143105	-49.4574339371	-42.067887707
11	2.61997111491	-0.159405974309	-1.09184537534	1.22452148405	0.812482512733	4.9433237807	0.080407121739	-0.0122172676982	0.327597721344	-0.171890167413	0.0692539599784	-0.127398423083	-0.82451449683	0.00438621252334	-0.343599123447	0.715686653088	-0.190899139054	0.0350555835294	0.503825743457	0.0410945607994	0.527989283583	-5.05302664934	-47.1956661527	-69.8073267439
12	2.10836423591	-1.47259972754	-2.17982783826	0.943023516622	1.28904226853	4.32271031478	-0.295082119304	0.189695240894	-0.441293070981	0.099799906523	0.081682933407	0.284477353632	0.838128016578	-0.318321531324	0.170061842738	0.708627300904	-0.250657462261	0.0276245571478	0.404016272011	0.0375485772892	0.522197979012	-5.76700763402	-59.2417422187	-68.8979574598
13	2.62172653951	-0.276639117433	-2.52006693871	2.45458361133	-0.652437831029	5.12771734872	-0.0928242297665	0.846103564872	1.17450201017	-0.200290687302	0.400796951679	0.521934212545	-1.54299416982	-0.480020623658	-0.308418325215	0.791782371224	-0.255742273819	-0.0872514006271	0.58735841075	0.172781438887	0.376579035409	2.3949483457	9.44201607527	-68.3997253678
14	6.25286982698	0.80961432495	-2.98953313353	2.36887026811	-0.0889126131834	5.5448885458	-0.306234013462	0.80997342907	0.468992726038	0.162279592728	0.286546601859	0.154387356226	-0.154906010834	-0.417866328125	0.158535015863	0.326977489798	-0.0478910717461	-0.101897748739	0.187993029515	-0.00685170226357	0.213380094481	-0.808830962198	2.48673078703	-60.8669930791
15	3.92946839112	0.970552238046	-0.704957669709	2.97432431074	1.3417706868	2.34740352097	-0.516017972491	-0.670720285367	-0.136190374165	0.596369366067	0.0317517793637	-0.397470863422	0.00721050551036	1.36435179438	-0.323321445242	0.208207620251	-0.25246124083	-0.191588955687	0.493019553932	0.148269835161	0.311901426127	8.91822612061	1.97725208311	-56.3755353726
16	7.088350723	1.06947881485	-3.24342096926	3.04226760147	-0.211209663835	5.89257292637	0.366403652508	0.698115448061	1.02695307197	0.162252016571	-0.0407942765384	-0.198539074838	-1.00364786423	0.299101382851	-0.0681895149027	0.554744358058	-0.081736358593	-0.102385836196	0.331787528303	0.09822455881	0.255558231897	4.49554877586	9.47023808821	-60.4559314348
17	2.13025835858	1.23733255666	-3.47922019918	4.62597382916	-2.79225419737	6.283386885	-0.0331636007081	0.195625396298	-0.0333861904562	0.0528103632554	-0.0219440750897	0.192390417003	-0.0171256205643	0.158629872389	0.0391119352489	0.138556520438	-0.0468940307661	-0.067195766066	0.306021822138	-0.00419427881458	0.254311727788	1.76432628832	-4.82056263508	-59.3223665339
18	3.28943421294	0.563753828381	0.0958960462678	6.68447691247	0.655726575905	1.82360316893	0.186608816487	0.608978552247	-0.254093398193	-1.4171691635	-0.257183805124	-0.611621445863	-0.0904997829649	0.0943665427301	-0.277438869083	0.200871547445	-0.102697349783	0.0957397300633	0.632830822464	-0.219432927938	0.475254133778	11.780225712	-16.8337919774	-70.5823904315
19	3.71507591181	-1.03642371831	-1.23297468557	4.91269586091	-0.515453454283	3.55820213149	-0.12560401081	0.200438858988	-0.0630914138776	-0.364576332034	0.0681656408846	0.0406386738671	0.526902022011	-0.597424203449	-0.0902789445519	0.191073627593	-0.101742949215	0.00714007008714	0.332616199208	-0.105149548078	0.308381577551	1.24380249198	-16.3759116561	-63.9602906344
20	4.03251459733	0.275603884138	-0.601911839939	4.72757047183	0.0408460001102	5.64133424858	-0.0489394842274	0.851201062857	-0.433518317606	-0.463182696982	0.00459319025744	-0.0974003287866	0.479229140205	-0.0114099972311	0.167738069819	0.164958807782	-0.0471307077172	0.0225941942195	0.430614977384	-0.0898096782805	0.432388022367	6.34292711651	-17.9549199427	-67.7650511469
21	3.28542535433	0.623728012543	-1.35410929751	4.13532033367	-0.532225751684	6.34253430084	0.167789142933	0.102876384753	1.24924330308	0.0340325729375	0.219463386428	0.131001042474	-1.61986892064	0.0435031754228	-0.211299311891	0.807212974368	0.0322342886998	0.146387856359	0.290579493548	-0.02478576803	0.544832419292	46.6432837964	-14.5490803799	-81.0741772243
22	3.73447565757	1.05015210542	-1.4404767517	3.22951942032	-0.227843268125	5.87691267716	0.339192612399	-0.340709006908	0.319570019346	0.213579812372	-0.170007622757	-0.228433434933	-0.805961603558	0.490659098602	-0.128348837743	0.414945767879	-0.0823261181917	-0.00531957024983	0.251692967185	-0.0856456254913	0.389579320297	48.0951446891	-21.7269985783	-71.267465009
23	2.6726532154	-0.0678502171848	0.428209613573	4.26232147934	1.52674298736	2.22724081338	-0.0423036577218	0.123598762803	-0.158419422496	-0.507023728811	0.167196012384	-0.497868520151	0.161772174278	0.697163547813	-0.146284011884	0.366300787121	0.0406882661435	0.102545055548	0.399609015224	-0.0692515282505	0.519710739554	52.1350118482	-36.0593980754	-81.3463295107
24	3.01251514931	-0.0107295825222	-2.04027079797	4.30634508558	1.89158134656	6.13543744599	-0.0783945842392	0.0557367382485	-0.501389638955	-0.0198917152415	-0.00309523407185	-0.0880077452465	0.62919217723	-0.00115257967963	0.173021689053	0.354839148349	0.0682514867546	0.0308732856128	0.24069759495	-0.0773265980425	0.43861989257	46.5733083895	-42.3492355286	-77.6388405458
25	4.37354466809	0.617492364005	0.764022181978	6.9222679688	2.08711782141	8.04423973839	-0.350418642592	0.501031817225	-0.198713934796	-0.528926626345	0.167384690682	0.0636166816265	0.507229557847	0.848079971061	0.210057771705	0.232647167095	0.113269677278	0.0603296372862	0.310459762654	-0.0593806280712	0.389293354427	50.6265738696	-39.4068662936	-82.936156958
26	4.71019050194	0.270214927573	3.25154101084	5.88641123679	0.351140911171	7.30010215848	0.604534955369	-0.867982244941	-1.16649750394	0.407175338749	-0.0433652187417	-0.375841073608	1.21471944232	1.13598595649	-0.390787434778	0.772596378871	0.084112536269	0.0463094255335	0.826144351827	0.14957186477	0.458426644498	7.15710921659	-59.4218793047	-13.9865854178
27	4.08503016542	-0.166837677242	0.702632178569	3.66776070063	-0.795946876101	4.90585677421	0.0609904519166	0.258090364708	0.185621375174	-0.431787473651	-0.105009027275	-0.364418412151	0.545908162224	1.0135324502	-0.0360824971975	0.341307330796	0.0227448199778	0.0713045728432	0.62445953041	0.111543744167	0.367518224395	4.00219863152	-52.1323126748	-23.5302682445
28	8.49338208414	-0.619132935237	4.98209259011	2.82253663007	-1.38600231154	6.25670731541	0.189691029663	-0.229272663671	-0.550477347158	-0.290236601159	-0.402986604278	-0.0207703849247	0.702577333321	0.898354473222	0.357407606949	0.253393132155	-0.0955784312199	-0.0435921211911	0.601657137837	-0.0456343742955	0.315214238173	-2.02135823806	-48.8187233233	-18.1880347092
29	1.80752934542	-1.5816216678	-1.08072067164	3.13477915428	-0.341707491251	1.99742958458	-0.138799265282	-0.453704875366	0.435848076632	0.745087845717	0.155550532633	-1.19068548104	-0.454206185348	0.756887080968	-0.1790526384	0.544215248979	-0.554513290491	-0.252414270331	0.906265949051	0.153406910699	0.781429082412	6.27733805752	-36.3052387592	-12.2453759334
30	5.62659802939	-3.28461345177	-2.92280492203	2.94362376644	-0.753416482062	7.40849916757	-0.0275032555033	0.198780329481	1.24222671086	0.153164994773	1.07834863468	1.00608184491	-1.53243025323	0.120978162997	-1.26768827403	0.834257335009	-0.243529531413	0.0636034960199	0.454741183601	0.0699567365843	0.696966816607	-7.58469740647	-27.7045779454	-8.30847211684
31	4.45177570198	-0.56001679684	2.13320982753	5.08058058965	1.90948916899	4.65873282166	-0.0575472337761	-0.170585912524	0.191634376723	0.246992515361	-0.0182733862894	0.195268219023	-0.24842242289	-0.746986700991	0.113903571415	0.269328999621	-0.0500450031851	0.0345171559454	0.426963973393	0.0737901550999	0.32211611861	-8.55926436312	-38.3471749187	-17.1690814257
32	7.68943720159	-0.447367719675	-0.0664551803295	6.68731303814	-0.563157254677	3.794682477	0.194752031778	-0.531686637305	0.480566031825	0.800036154773	-0.397899552459	0.882030669929	-1.6883269934	-9.6474962453E-5	0.299993356604	0.404224626855	-0.184756858636	-0.0166274005735	0.519766768666	-0.0713120738569	0.592931343242	-8.59970058164	-33.3028725261	-12.1450424267
33	2.61189589668	-1.545063564	0.29284472864	1.95714221081	1.89179274829	5.24612292534	0.0160903730579	-0.220927002534	0.631184728126	0.454446838721	-0.0557597089112	0.00853215809631	-0.232084850463	1.27282428183	-0.0676330463674	0.381093603178	-0.235159189892	-0.0459713243507	0.494295577871	0.0303313562556	0.456862912464	0.242754524865	-36.1330217922	-15.0685774206

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 556 through 583 )	A	A	556 - 583	1 - 28
2	2	chain 'A' and (resid 584 through 719 )	A	A	584 - 719	29 - 164
3	3	chain 'A' and (resid 720 through 834 )	A	A	720 - 834	165 - 252
4	4	chain 'A' and (resid 835 through 886 )	A	A	835 - 886	253 - 297
5	5	chain 'B' and (resid 557 through 607 )	B	B	557 - 607	1 - 51
6	6	chain 'B' and (resid 608 through 719 )	B	B	608 - 719	52 - 163
7	7	chain 'B' and (resid 720 through 886 )	B	B	720 - 886	164 - 296
8	8	chain 'C' and (resid 557 through 607 )	C	C	557 - 607	1 - 51
9	9	chain 'C' and (resid 608 through 699 )	C	C	608 - 699	52 - 143
10	10	chain 'C' and (resid 700 through 760 )	C	C	700 - 760	144 - 185
11	11	chain 'C' and (resid 761 through 804 )	C	C	761 - 804	186 - 229
12	12	chain 'C' and (resid 805 through 886 )	C	C	805 - 886	230 - 296
13	13	chain 'H' and (resid 1 through 17 )	H	D	1 - 17	1 - 17
14	14	chain 'H' and (resid 18 through 40 )	H	D	18 - 40	18 - 40
15	15	chain 'H' and (resid 41 through 67 )	H	D	41 - 67	41 - 67
16	16	chain 'H' and (resid 68 through 90 )	H	D	68 - 90	68 - 90
17	17	chain 'H' and (resid 91 through 122 )	H	D	91 - 122	91 - 122
18	18	chain 'H' and (resid 123 through 171 )	H	D	123 - 171	123 - 151
19	19	chain 'H' and (resid 172 through 208 )	H	D	172 - 208	152 - 188
20	20	chain 'H' and (resid 209 through 254 )	H	D	209 - 254	189 - 234
21	21	chain 'I' and (resid 1 through 17 )	I	E	1 - 17	1 - 17
22	22	chain 'I' and (resid 18 through 108 )	I	E	18 - 108	18 - 108
23	23	chain 'I' and (resid 109 through 171 )	I	E	109 - 171	109 - 151
24	24	chain 'I' and (resid 172 through 222 )	I	E	172 - 222	152 - 202
25	25	chain 'I' and (resid 223 through 254 )	I	E	223 - 254	203 - 234
26	26	chain 'J' and (resid 1 through 19 )	J	F	1 - 19	1 - 19
27	27	chain 'J' and (resid 20 through 108 )	J	F	20 - 108	20 - 108
28	28	chain 'J' and (resid 109 through 122 )	J	F	109 - 122	109 - 122
29	29	chain 'J' and (resid 123 through 158 )	J	F	123 - 158	123 - 138
30	30	chain 'J' and (resid 159 through 171 )	J	F	159 - 171	139 - 151
31	31	chain 'J' and (resid 172 through 208 )	J	F	172 - 208	152 - 188
32	32	chain 'J' and (resid 209 through 237 )	J	F	209 - 237	189 - 217
33	33	chain 'J' and (resid 238 through 254 )	J	F	238 - 254	218 - 234

-
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