PDB-9bjh: Crystal structure of neutralizing human monoclonal antibody 75C8 ...

ID or keywords:

Entry

Database: PDB / ID: 9bjh

Title

Crystal structure of neutralizing human monoclonal antibody 75C8 in complex with AMA1 DI-DII

Components

75C8 Fab Heavy Chain
75C8 Fab Light Chain
Apical membrane antigen 1

Keywords

STRUCTURAL PROTEIN / Apical membrane antigen 1 / AMA1 / Plasmodium / Malaria / Antigen-Antibody complex

Function / homology

Function and homology information

apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Cell Rep Med / Year: 2025
Title: A strain-transcending anti-AMA1 human monoclonal antibody neutralizes malaria parasites independent of direct RON2L receptor blockade.
Authors: Patel, P.N. / Diouf, A. / Dickey, T.H. / Tang, W.K. / Hopp, C.S. / Traore, B. / Long, C.A. / Miura, K. / Crompton, P.D. / Tolia, N.H.

History

Deposition	Apr 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2025	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Apr 2, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9bjh.cif.gz	973.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9bjh.ent.gz	678.8 KB	Display	PDB format
PDBx/mmJSON format	9bjh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/9bjh ftp://data.pdbj.org/pub/pdb/validation_reports/bj/9bjh	HTTPS FTP

-
Related structure data

Related structure data	9bjgC 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: Apical membrane antigen 1

B: Apical membrane antigen 1

H: 75C8 Fab Heavy Chain

I: 75C8 Fab Heavy Chain

L: 75C8 Fab Light Chain

M: 75C8 Fab Light Chain

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

1

A: Apical membrane antigen 1

H: 75C8 Fab Heavy Chain

L: 75C8 Fab Light Chain

defined by author
Evidence: gel filtration
89.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Apical membrane antigen 1

I: 75C8 Fab Heavy Chain

M: 75C8 Fab Light Chain

defined by author
Evidence: gel filtration
89.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.868, 71.620, 132.927
Angle α, β, γ (deg.)	94.105, 99.195, 112.393
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Apical membrane antigen 1 / Merozoite surface antigen Mass: 39655.469 Da / Num. of mol.: 2 / Mutation: T64A, T188A, S273A, S323A, S324A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1133400 / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q7KQK5
#2: Antibody	75C8 Fab Heavy Chain Mass: 25851.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody	75C8 Fab Light Chain Mass: 23993.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	The author states that all N-linked glycosylation sites (NXS/T) were modified by substituting the ...The author states that all N-linked glycosylation sites (NXS/T) were modified by substituting the serine or threonine residue with an alanine residue to prevent N-linked glycosylation.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.4 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 50% (v/v) PEG 400, 0.2M sodium chloride, 0.1M CHES

-
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: Sep 17, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→19.87 Å / Num. obs: 41930 / % possible obs: 86.57 % / Redundancy: 1.9 % / B_iso Wilson estimate: 43.06 Å² / CC_1/2: 0.976 / CC star: 0.994 / R_merge(I) obs: 0.1122 / R_pim(I) all: 0.1122 / R_rim(I) all: 0.1586 / Net I/σ(I): 3.52
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.4818 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 3285 / CC_1/2: 0.591 / CC star: 0.862 / R_pim(I) all: 0.4818 / R_rim(I) all: 0.6814 / % possible all: 74.25

-
Processing

Software

Name	Version	Classification
SERGUI		data collection
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20.1-4487	phasing
Coot		model building
PHENIX	1.19.2_4158	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→19.87 Å / SU ML: 0.3948 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.1523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2529	1860	4.78 %
R_work	0.2107	37075	-
obs	0.2128	38941	86.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11215	0	0	21	11236

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11494
X-RAY DIFFRACTION	f_angle_d	0.4731	15645
X-RAY DIFFRACTION	f_chiral_restr	0.0426	1725
X-RAY DIFFRACTION	f_plane_restr	0.0038	2023
X-RAY DIFFRACTION	f_dihedral_angle_d	10.7723	4175

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 (%)
2.8-2.87	0.3832	120	0.3105	2537	X-RAY DIFFRACTION	74.2
2.87-2.96	0.324	130	0.2915	2453	X-RAY DIFFRACTION	76.69
2.96-3.05	0.3507	127	0.2752	2598	X-RAY DIFFRACTION	78.76
3.05-3.16	0.317	120	0.273	2507	X-RAY DIFFRACTION	75.97
3.16-3.29	0.3342	141	0.2545	2902	X-RAY DIFFRACTION	87.49
3.29-3.44	0.27	152	0.2413	2962	X-RAY DIFFRACTION	89.46
3.44-3.62	0.3035	150	0.2128	2973	X-RAY DIFFRACTION	90.6
3.62-3.84	0.2603	157	0.21	2969	X-RAY DIFFRACTION	91.75
3.84-4.14	0.2226	150	0.1952	2995	X-RAY DIFFRACTION	91.13
4.14-4.55	0.2351	141	0.1746	2969	X-RAY DIFFRACTION	89.19
4.55-5.2	0.2135	156	0.1634	3025	X-RAY DIFFRACTION	92.31
5.2-6.51	0.2167	162	0.1961	3147	X-RAY DIFFRACTION	95.39
6.51-19.87	0.191	154	0.1914	3038	X-RAY DIFFRACTION	92.55

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	2.81050005221	0.222039242418	0.146238843883	4.24648716302	-1.2075917361	3.89253136154	-0.205551262354	-0.355099973889	0.284951262739	1.06908609031	-0.128304733868	-0.260132163195	-1.35443508004	-0.545295992138	-0.268234376462	0.298198875344	0.111286043531	0.0116532953667	0.41719401803	-0.0392252424568	0.346966565302	-30.0715416199	12.3724969103	-2.65007836176
2	3.71132380254	0.833988438949	-0.753083917837	4.049340028	-0.339973656101	3.36572922907	-0.146461321415	-0.278079673449	-0.553939997487	0.324794490844	0.125170334594	0.127633063633	0.284771447149	-0.141739639341	0.00575091035011	0.320879537313	0.0547752662931	0.0100666538122	0.360559772557	0.0677259329947	0.35075046181	-32.7994182484	-8.72383306126	-4.51444945715
3	5.54140947161	0.127810807618	-0.592911497624	3.99737041483	-0.0588949171262	4.58993232281	-0.0342888980018	-0.372262904686	0.0737005305178	0.507425758214	0.0678227491944	0.222936725487	0.148514206767	-0.417337083837	-0.00506935274395	0.384883090431	0.00781381025179	0.039487758017	0.292728808655	0.0649541306715	0.382151895141	-36.220459811	-2.99801890647	-1.71173517664
4	5.76834658791	0.972910025252	0.141336439359	3.94105478995	1.12304113799	5.24248534258	0.144035176716	-0.216459363281	0.203796191062	-0.218771025135	-0.267712926571	-0.26085458063	0.491942161911	0.0936968495504	-0.150144499067	0.369343251899	0.0249458717948	0.00801519167642	0.259011516197	0.112234419568	0.282876063956	-22.3912978722	-4.28045341597	-8.95771567928
5	0.0931107381816	0.162900296367	-0.119229751481	3.51751913227	-2.23333237961	2.03250031939	0.210029781552	0.209845903687	0.208587851355	-0.107065685498	0.00146421676795	0.478564834257	-0.535258704304	-0.902506925928	-0.424233751329	0.463871661094	0.0944162666835	-0.026291486291	0.400306225009	0.0305709634455	0.617831466193	-32.6429430196	14.5535649286	-14.8359489793
6	2.39434107681	0.400727644574	-0.269543452274	0.829301542179	0.321886261003	2.98400197669	-0.00322236158891	-0.0882504838574	0.38075688085	-0.0874542124585	-0.0851073303415	-0.0696514186113	-0.344958455707	0.0189552840359	0.0825591857981	0.376035416823	0.0588244899673	-0.0306907054815	0.248140877987	0.0839513704762	0.478813562865	-20.1039821267	14.3708277256	-15.2348710174
7	3.43970918849	1.23200444881	0.660162737437	1.94399271393	0.539608069104	2.89855148379	0.0311026723725	0.156502075338	0.00240003283317	-0.167776448205	-0.251622799698	0.0290157982168	0.254729120766	-0.109271953109	0.174063200311	0.272561906404	0.0727646358198	0.0154740258867	0.388107616356	0.0132617811373	0.50253669095	-28.7307574227	-63.1244604893	20.9662687669
8	1.74896717742	-0.773475672481	1.86415746587	3.14385486299	0.379539165297	6.19121019801	-0.0349024577338	0.251395923011	0.135269221492	-0.471881824475	-0.123330478523	0.505542467822	-0.204522121987	-0.443226514367	0.142937665193	0.355563620846	0.0765489824544	-0.0530112400964	0.451907348511	0.0524094484798	0.446890894888	-40.6576819872	-49.0248843599	18.6462756536
9	4.01826519954	-0.158492666881	-1.40794806522	4.85067052257	0.01938597759	6.28772356952	0.142690495382	0.162490870181	0.492772977283	-0.262951100682	-0.0415771577757	-0.409950621482	-0.00281405997343	0.13392409319	-0.0762031465551	0.310669808103	0.0778848126836	-0.0257567063199	0.276953858152	0.0791510397831	0.36841338137	-25.2781855471	-50.6838614142	23.4875521799
10	3.06998811305	-0.135128355267	0.724659189533	2.48314008627	-0.196146510385	3.27899377596	0.0245614591269	0.0195762894428	-0.505111595796	0.0928017227171	-0.0895104967002	0.259832182436	0.357345504588	-0.184682863847	0.104536225833	0.326212991103	-0.0275650123446	0.0299731601883	0.287791258076	0.0335796311306	0.512973628425	-23.2049239333	-69.6442417312	32.028110005
11	2.54863925714	0.260083385534	3.94082010786	2.94679720238	3.44297115075	8.43714036296	0.143544182967	0.270244164993	-0.14591185199	0.586880556466	0.0493462903471	0.619122068753	0.943494370658	0.653692642924	-0.380367530747	0.494037884782	0.0267701869732	0.121169451048	0.355696812547	0.178637385406	0.639114153954	-6.7735015268	-24.5654073938	-27.5155888147
12	1.71377664285	0.698288632441	-0.0534965193692	2.1695990249	0.390843121371	2.19056140385	0.0192221038019	0.222574461314	-0.100714970181	-0.192724383139	-0.0308221374404	0.0533124995397	0.0939675564111	0.0713588091218	0.0811257807392	0.368190555928	0.0618145397035	-0.0070068139034	0.319525132476	0.14028731185	0.489336058233	-11.7506838388	-14.1985166408	-24.7687070635
13	1.72112465941	-0.0227140938961	0.263495335053	3.88270148391	2.32094032063	2.95904635357	0.0284158232561	-0.0521412227696	0.0864620471755	0.589981574286	0.217657101413	-0.374308749434	0.248223576359	0.250802278925	-0.150039466781	0.290843243179	0.0314867776454	0.0371913350317	0.244092887555	0.114325886889	0.394030551703	-5.73131267801	-12.3030568593	-26.9958238256
14	3.72817140185	-0.300423034954	-0.578788361011	1.46190314131	0.249937436728	0.944804591243	0.164926624457	-0.32995395917	-0.435587956844	0.0674031858184	-0.133796081125	-0.117493590048	0.128178848693	0.221299789898	-0.0557838441219	0.420072468627	0.0412638914096	0.00363768510467	0.266104703805	0.101389547027	0.469906503226	14.3635155009	-35.307760331	-36.6565825907
15	2.47192720256	-1.71764861016	-0.724761471367	2.76755456403	1.45569970691	0.893957589215	0.0685547968095	0.751223282656	0.637175735613	-0.658632269108	0.213214961761	0.11238951132	-0.334983704283	0.0498264490987	-0.259513493604	0.506706341624	0.193075430884	-0.263178142181	0.162581751406	0.198859339986	0.966775202292	-6.84389826682	-30.6272851618	44.574742748
16	4.49036458565	-0.21739486873	-0.0752912216854	4.23779514318	0.864464589061	3.15924021967	-0.0905651290425	-0.0531772682138	0.263241896786	0.114045159311	-0.0908472434402	0.26493800113	0.0194403590135	-0.10992219193	0.227666781504	0.292249780742	0.00789444789884	-0.0303059402587	0.282696670989	0.0975838952756	0.379692281965	-9.94665078212	-42.5221970797	41.4245569112
17	2.02357221142	-0.967551503614	0.859473107529	2.77889902713	0.114698388557	0.825959198534	-0.150599052173	0.0142244240764	0.138915299307	-0.0248703370018	-0.00559164239954	0.26042145684	0.0746939178146	-0.000661286954718	0.207717786391	0.244152177414	0.0122357734147	0.0332219684213	0.341712790991	0.0645876078429	0.527330445939	-11.5333384007	-41.4697544777	43.4520590573
18	1.28376703013	1.31448182615	0.176359806867	1.75911221572	0.578647059422	1.06088032186	0.0736049737643	-0.0867643392379	0.229550060085	0.134817404036	0.0711235575642	-0.335933156514	-0.127510668342	0.118721989707	-0.0767444499923	0.441899963133	0.123401378619	-0.0892963645929	0.431582244845	-0.0726540711945	0.951566972058	10.9029114014	-24.15944129	53.8017144801
19	5.27482349321	-0.53451961579	-0.470370830468	0.563003792162	1.2428765202	2.0378957014	-0.0699717862127	0.795134577712	1.30592980522	-0.373771185419	0.116461261235	-0.384303439499	-0.389458481625	0.544856088731	-0.0435741263034	0.518089883885	0.000314880624198	0.00172526689612	0.568273292789	0.205064216616	1.12124406712	15.1208363007	-15.9399361735	48.3673425797
20	1.61215922674	-0.869011691911	-0.143903851219	0.545797186657	-0.697809519131	2.54918911111	0.0145135870956	0.107471834745	0.0999692557173	-0.575946514216	-0.014537263995	0.0459425293567	-0.478621789255	0.0848776281377	-0.108915738418	0.706630949607	-0.0340026939911	0.0760049620142	0.365447126957	0.155004513098	0.556309007699	8.28890093886	-1.43934500435	-40.6069921011
21	5.80631689305	-2.23843790499	3.75631169472	3.21323239954	-0.192690901492	3.9267237148	0.0112250251134	0.745195146096	0.346630310922	-0.763781912212	0.0847157611151	0.105272606531	-0.374914384827	-0.0221519846204	-0.111727412976	0.614610729272	0.0100856139393	0.0367422359186	0.327602784148	0.205884843573	0.532750744009	-0.780216556937	5.28134159125	-38.1980634271
22	3.91032238371	-1.93518008461	-0.639551860443	1.55389033509	1.62777772545	3.54858676662	0.0742633026764	-0.0617196641508	0.191521555423	-0.168271522381	0.142522065454	-0.330711235737	-0.22031250353	0.314237278717	-0.195037301114	0.343713532315	-0.00145549310859	0.0413204664556	0.251836832029	0.0727950519395	0.453907861694	6.96903968329	-0.793059586156	-29.9061249721
23	3.27854366255	0.822967488377	-1.02545385834	1.0398972899	-0.423639477434	1.34568466164	-0.0695817201526	0.691762469213	0.347778573871	-0.24819181057	0.0576206147471	-0.151166555709	-0.0372972787732	-0.3003096638	-0.0819027276851	0.406675884467	-0.0205610303745	0.0123226165967	0.323596569064	0.0994471641421	0.431170143909	6.93936153301	-6.50868422006	-38.0243300961
24	3.16948675465	-0.0740731186864	0.933183096839	4.4289085013	3.30327596943	2.90399632687	0.147155193418	0.139988747735	-0.315021798381	-0.140547573129	-0.182219828168	0.0100918276561	-0.0794574355683	0.22787185656	0.0127640163391	0.235085726352	0.0307068646842	-0.00826531850085	0.277134072879	0.0649196495567	0.461498442635	19.4308494684	-32.149536486	-48.4890917144
25	2.69654515637	0.786803408888	-0.0978964103685	1.73507367983	0.742621038734	0.57252707644	0.306086362789	0.0261527263507	-0.107207001394	-0.0292473681263	-0.00185820267537	-0.281369896588	-0.107256839781	0.134311790504	-0.177929706544	0.418249563888	0.0370269068479	0.00476388711586	0.360114016757	0.124071009624	0.402639996464	17.3579001648	-25.0099417664	-48.0650596121
26	4.18770501431	1.92722140791	0.244015823821	3.96184211236	1.58486521883	2.14706034939	-0.274924645791	0.369062329239	-0.659331275253	-0.66348464115	0.252604621889	-0.262905843774	-0.00407239703534	0.0729566229171	-0.00771443254611	0.427981571942	0.0621293607682	0.0526438712201	0.364868931699	0.0655980922982	0.505805584361	21.6860523784	-34.1448396272	-54.0466867838
27	2.44332496577	1.37250422202	-1.16873674648	2.39233102772	-0.966335987773	3.63569453481	-0.0573778811618	0.0960111448885	-0.153886674684	0.684132814091	0.0880317261057	0.00225747419503	0.572166945236	-0.0118130957183	-0.0133061975528	0.604821873335	0.162052770144	-0.093990177402	0.305317209486	0.121733672531	0.413215518697	6.08042439952	-53.9886161158	57.523323173
28	2.48727640497	1.19531124187	1.4007188476	1.27212113531	0.44265514652	3.54164091599	0.043696909352	0.119071847053	-0.0535078761896	0.0586385964749	0.125471185928	-0.192415817189	0.224375246605	0.349167505445	-0.217683432556	0.38423053255	0.118860589911	-0.0264560121581	0.294810856593	0.036445638927	0.480262678923	5.70289794763	-55.3678721961	48.112679891
29	1.91939246164	-0.640266253196	-1.2772104522	2.72841875979	-0.168434094874	1.68139862766	0.143895126389	-0.643238678371	-0.0851938239795	0.594430626217	0.228387204975	-0.460246504377	0.245221710204	-0.0617792374591	-0.111794229766	0.511241729963	0.13503808913	-0.0688429659063	0.353235036419	0.0671985872084	0.408604389731	6.8704694862	-48.8956771587	55.0065550752
30	2.09826962072	2.60384204745	0.0992095696009	4.24603554739	1.0444834033	2.22037219191	0.110178857847	-0.126764000841	0.332504739019	0.605209722917	-0.0534182726875	-0.187988317385	0.00666143524089	0.183321610601	-0.11831987598	0.558205143543	0.139601184944	-0.215556478054	0.652422345997	-0.127601915728	0.822562224338	19.1055693147	-23.3409746364	65.8570699628
31	0.506850687378	-1.22052451994	-0.30706946006	5.3172826506	1.47308628998	2.84282424716	0.132999460581	-0.132656955235	-0.0290551858181	0.336088409261	-0.215899358743	-0.466661484112	0.0673405312733	-0.324293961427	0.0805084336531	0.392031408556	0.079051446489	-0.147614920024	0.606560991909	0.0537634496885	0.634333871295	17.3393103995	-30.9961939724	64.901537148
32	0.123186066581	-0.513474120665	-0.550228104889	5.23896846578	2.58471317148	2.04383684395	-0.183051221239	0.149542645155	-0.0694607214554	1.15062659908	0.0973539838788	-0.182205196335	0.117990273512	0.321120124334	0.0525579402721	0.776236803213	0.0907362540636	-0.337676917807	0.65560244626	-0.16424812191	1.06564149229	21.4029846297	-20.5716425768	72.322947163

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 108 through 144 )	A	A	108 - 144	1 - 37
2	2	chain 'A' and (resid 145 through 201 )	A	A	145 - 201	38 - 91
3	3	chain 'A' and (resid 202 through 264 )	A	A	202 - 264	92 - 154
4	4	chain 'A' and (resid 265 through 290 )	A	A	265 - 290	155 - 173
5	5	chain 'A' and (resid 291 through 316 )	A	A	291 - 316	174 - 199
6	6	chain 'A' and (resid 317 through 438 )	A	A	317 - 438	200 - 285
7	7	chain 'B' and (resid 108 through 163 )	B	B	108 - 163	1 - 56
8	8	chain 'B' and (resid 164 through 237 )	B	B	164 - 237	57 - 126
9	9	chain 'B' and (resid 238 through 290 )	B	B	238 - 290	127 - 170
10	10	chain 'B' and (resid 291 through 438 )	B	B	291 - 438	171 - 283
11	11	chain 'H' and (resid 2 through 18 )	H	C	2 - 18	1 - 17
12	12	chain 'H' and (resid 19 through 83 )	H	C	19 - 83	18 - 82
13	13	chain 'H' and (resid 84 through 118 )	H	C	84 - 118	83 - 117
14	14	chain 'H' and (resid 119 through 223 )	H	C	119 - 223	118 - 222
15	15	chain 'I' and (resid 2 through 18 )	I	D	2 - 18	1 - 17
16	16	chain 'I' and (resid 19 through 60 )	I	D	19 - 60	18 - 59
17	17	chain 'I' and (resid 61 through 108 )	I	D	61 - 108	60 - 107
18	18	chain 'I' and (resid 109 through 197 )	I	D	109 - 197	108 - 192
19	19	chain 'I' and (resid 198 through 222 )	I	D	198 - 222	193 - 217
20	20	chain 'L' and (resid 1 through 18 )	L	E	1 - 18	1 - 18
21	21	chain 'L' and (resid 19 through 30 )	L	E	19 - 30	19 - 30
22	22	chain 'L' and (resid 31 through 91 )	L	E	31 - 91	31 - 91
23	23	chain 'L' and (resid 92 through 114 )	L	E	92 - 114	92 - 114
24	24	chain 'L' and (resid 115 through 151 )	L	E	115 - 151	115 - 151
25	25	chain 'L' and (resid 152 through 173 )	L	E	152 - 173	152 - 173
26	26	chain 'L' and (resid 174 through 214 )	L	E	174 - 214	174 - 214
27	27	chain 'M' and (resid -1 through 18 )	M	F	-1 - 18	1 - 20
28	28	chain 'M' and (resid 19 through 91 )	M	F	19 - 91	21 - 93
29	29	chain 'M' and (resid 92 through 114 )	M	F	92 - 114	94 - 116
30	30	chain 'M' and (resid 115 through 151 )	M	F	115 - 151	117 - 153
31	31	chain 'M' and (resid 152 through 175 )	M	F	152 - 175	154 - 177
32	32	chain 'M' and (resid 176 through 214 )	M	F	176 - 214	178 - 216

-
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