PDB-8ezk: Pfs25 in complex with transmission-reducing antibody AS01-04

ID or keywords:

Entry

Database: PDB / ID: 8ezk

Title

Pfs25 in complex with transmission-reducing antibody AS01-04

Components

25 kDa ookinete surface antigen
Transmission-reducing antibody AS01-4, single-chain Fv

Keywords

IMMUNE SYSTEM / Pfs25 / transmission-blocking vaccine

Function / homology

Function and homology information

side of membrane / 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: 2.3 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Npj Vaccines / Year: 2023
Title: A human antibody epitope map of the malaria vaccine antigen Pfs25.
Authors: Shukla, N. / Tang, W.K. / Coelho, C.H. / Long, C.A. / Healy, S.A. / Sagara, I. / Miura, K. / Duffy, P.E. / Tolia, N.H.

History

Deposition	Nov 1, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ezk.cif.gz	545.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ezk.ent.gz	377.8 KB	Display	PDB format
PDBx/mmJSON format	8ezk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ezk_validation.pdf.gz	451.4 KB	Display	wwPDB validaton report
Full document	8ezk_full_validation.pdf.gz	457.7 KB	Display
Data in XML	8ezk_validation.xml.gz	28 KB	Display
Data in CIF	8ezk_validation.cif.gz	38.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/8ezk ftp://data.pdbj.org/pub/pdb/validation_reports/ez/8ezk	HTTPS FTP

-
Related structure data

Related structure data	8ezlC 8ezmC 6phbS 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) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

Deposited unit

A: 25 kDa ookinete surface antigen

B: 25 kDa ookinete surface antigen

H: Transmission-reducing antibody AS01-4, single-chain Fv

I: Transmission-reducing antibody AS01-4, single-chain Fv

95.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 25 kDa ookinete surface antigen

H: Transmission-reducing antibody AS01-4, single-chain Fv

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

2

B: 25 kDa ookinete surface antigen

I: Transmission-reducing antibody AS01-4, single-chain Fv

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

Unit cell

Length a, b, c (Å)	68.250, 91.720, 122.100
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	(chain "B" and resid 0 through 171)
d_1	ens_2	(chain "H" and resid 0 through 254)
d_2	ens_2	(chain "I" and (resid 0 through 123 or resid 144 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	GLY	THR	A	1 - 172
d_2	1	ens_1	GLY	THR	B	1 - 172
d_1	1	ens_2	GLY	THR	C	1 - 235
d_2	1	ens_2	GLY	GLY	D	2 - 125
d_2	2	ens_2	SER	THR	D	127 - 237

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.884638489217, -0.441966824218, -0.148593639453), (-0.456131234231, 0.754149950979, 0.472442746371), (-0.0967421343293, 0.485719237553, -0.868744946297)	-32.163275608, -10.3187947746, -56.7319570988
2	given	(-0.87560398511, -0.468600487287, -0.117180393303), (-0.464883264267, 0.751665890423, 0.467848201642), (-0.131153390593, 0.464124953531, -0.876006173292)	-30.5206628385, -10.7395313158, -57.324792199

#1: Protein	25 kDa ookinete surface antigen / Pfs25 Mass: 20033.076 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote) Strain: isolate NF54 / Plasmid: pHL-Sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P13829
#2: Antibody	Transmission-reducing antibody AS01-4, single-chain Fv Mass: 27552.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-Sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.74 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium thiocyanate, 23% PEG 3350. Cryoprotected in 30% MPD

-
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 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→38.06 Å / Num. obs: 34702 / % possible obs: 99.75 % / Redundancy: 7.9 % / B_iso Wilson estimate: 50.85 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_pim(I) all: 0.04285 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.3→2.382 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 3380 / CC_1/2: 0.694 / CC star: 0.905 / R_pim(I) all: 0.5615 / % possible all: 98.66

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6PHB

6phb

Resolution: 2.3→38.06 Å / SU ML: 0.3172 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2602	1998	5.76 %
R_work	0.2291	32689	-
obs	0.2308	34687	99.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 68.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→38.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6157	0	0	19	6176

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	6269
X-RAY DIFFRACTION	f_angle_d	0.8044	8492
X-RAY DIFFRACTION	f_chiral_restr	0.0503	956
X-RAY DIFFRACTION	f_plane_restr	0.0051	1097
X-RAY DIFFRACTION	f_dihedral_angle_d	10.8257	2298

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	1.46190296923
ens_2	d_2	H	X-RAY DIFFRACTION	Torsion NCS	0.809807968422

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 (%)
2.3-2.36	0.3962	139	0.4103	2272	X-RAY DIFFRACTION	98.29
2.36-2.42	0.3898	140	0.3538	2285	X-RAY DIFFRACTION	99.51
2.42-2.49	0.3482	141	0.315	2295	X-RAY DIFFRACTION	99.84
2.49-2.57	0.2899	140	0.2971	2304	X-RAY DIFFRACTION	99.92
2.57-2.66	0.3353	141	0.2878	2303	X-RAY DIFFRACTION	99.92
2.66-2.77	0.3012	141	0.288	2316	X-RAY DIFFRACTION	99.88
2.77-2.9	0.2737	142	0.2869	2316	X-RAY DIFFRACTION	99.88
2.9-3.05	0.3317	142	0.2669	2326	X-RAY DIFFRACTION	99.96
3.05-3.24	0.2674	142	0.2681	2317	X-RAY DIFFRACTION	99.84
3.24-3.49	0.3092	143	0.2539	2345	X-RAY DIFFRACTION	100
3.49-3.84	0.2659	144	0.224	2347	X-RAY DIFFRACTION	100
3.84-4.4	0.242	145	0.1873	2372	X-RAY DIFFRACTION	99.88
4.4-5.54	0.1943	145	0.1757	2380	X-RAY DIFFRACTION	99.92
5.54-38.06	0.2196	153	0.1934	2511	X-RAY DIFFRACTION	99.89

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	1.24960285547	-0.327403023558	-0.908144867099	1.77040416936	-0.909972133432	2.47914377133	0.00238478774728	-0.0429975565626	0.174250651245	0.11636450712	-0.0199053833287	-0.102317154447	-0.250565241485	0.186160653624	-0.16519098432	0.408830180149	-0.0255957186185	-0.00758120769318	0.522073452566	0.0640113972592	0.603150858299	-35.4354510573	28.6509555642	-27.3764827582
2	2.49027954812	0.988013498203	-0.211206060998	2.52726237261	-0.356098712807	2.13510022331	-0.00800076108792	0.347060849319	-0.207662836229	-0.457083893423	-0.0274534123988	0.0309701703869	0.182955620655	0.260375180356	-0.0593826130546	0.553088590788	0.0797921691161	0.13072313309	0.72325716262	0.104460295672	0.660863753566	-28.6285188695	22.1352646172	-45.5636022496
3	1.07435730842	1.01767847764	-1.35885697144	0.881415395578	-1.1683029297	1.49398700858	-0.957625244404	-0.296355649973	-0.99692059523	0.0250907285412	0.125359444436	-0.365710386186	0.921885699285	-0.315084342133	0.0437220186439	0.827997522188	0.098178119904	0.256789931932	0.757435393189	-0.0312198336224	1.07737763428	-39.6508113803	5.98824809378	-35.9373770128
4	1.07434764492	1.16685787497	-1.45339219251	1.14309842481	-1.16199427327	2.88117342097	-0.182983549328	-0.0959821752465	0.260433196748	0.366330048168	0.151257215294	-0.0712846367046	-0.271820182646	-0.50641088592	0.0830320433865	0.497820690183	0.0211722947172	0.0441486695774	0.486509414343	0.0129326515446	0.511525478694	-10.3653990497	0.292455862544	-15.6630866877
5	2.54841631406	0.048968845392	0.0606346670103	2.70831989089	-0.272646325349	2.79111829451	0.0764478243184	0.0139897489886	0.0792136297852	-0.30190392038	-0.0721842073185	-0.0658877749011	-0.493827452193	-0.325376953869	-0.0354191852842	0.600604766118	0.0474267538176	0.00982117797467	0.498650949361	0.0141440565905	0.567710628721	-7.50464522046	18.6569163224	-19.8639824323
6	0.246754155425	0.689898814174	0.00891604907149	3.04790309259	0.358695382728	0.0118405287141	0.235563404699	0.259062589557	0.382178067451	-0.424219358455	-0.109006855787	0.493087097274	-0.72085680074	-0.376560943059	-0.174213676166	1.11352069947	0.297889702228	0.0461093953014	0.699553550069	-0.0237396595806	0.852652158844	-9.42978399208	32.8684597764	-14.6686552244
7	0.14187605643	0.35423337707	-0.0922026591016	2.92988371027	-0.844227454235	0.134887470078	0.360545011428	-0.12542474133	0.581613923462	1.5034548364	0.0356839797709	0.539747778671	-0.63973189143	-0.510916182051	0.0719108846705	0.649685936017	0.120670638854	0.23940046774	0.696136738576	0.0375117686982	0.802053035001	-11.7167352393	12.8104974058	-3.48368961685
8	1.82585182637	1.42200232796	0.146762253512	1.08846059628	0.114061905057	0.00499559103031	0.536548167803	0.696812257192	-0.61474178709	-0.182336539417	0.366966600046	0.0954461946279	0.72754243678	-0.743050430461	0.0807469865959	0.606281793191	0.0805836497327	-0.127128009288	1.02877972339	0.0091931812935	1.08794462731	-21.6080180831	1.35383186461	-4.7486074195
9	2.37216859138	0.751538336566	-0.822144707679	2.55250387793	1.10368917668	2.20788368305	0.127450421709	-0.449014549874	-0.0762409539599	0.251508826237	0.125878640514	-0.0461436387603	0.504517323973	0.536008819364	0.170606951639	0.655342726861	0.00909483606721	-0.0774750705604	0.56042718938	0.0893401620097	0.658077453339	-5.63048981414	-5.70375663007	-5.96653890399
10	2.21399066863	0.329754412921	-0.116206410505	3.0117653505	-0.726048282436	1.76572887914	-0.319504876512	-0.0544293881577	0.894950793887	-0.538668993019	0.226621574185	-0.30104335509	-0.230810960071	1.19112816763	0.181189276178	0.954964216182	0.0658693908282	0.0220320424137	0.738545116284	0.0307795407558	0.844252334267	8.78582400876	-4.97513103988	-22.2754334551
11	2.69589659065	-0.0324263906892	0.951939578142	1.68352983917	-0.328823024847	2.62050012605	0.121829053622	-0.167199534152	0.058302157218	0.100885566166	-0.16912831725	0.0468666750459	0.246336640751	-0.313972058675	0.0462530994367	0.491214041073	-0.0221702426095	0.0300373358115	0.435046983017	-0.0176050692868	0.548882464829	-35.9198062097	6.18935886256	-7.28249164838
12	2.75230452925	0.0463743258119	0.215471773252	0.852599012369	0.134823994147	0.587942322586	0.110673645636	-0.234254915164	0.164905535887	0.0257433553193	-0.139481240911	0.0551864659784	0.0371253524579	-0.111854661072	-0.0105075289225	0.400269671587	-0.0263598727174	0.0346084670925	0.461482886918	-0.0404951750434	0.452761874853	-47.7666582234	12.5191331415	-6.07006574259
13	3.07096695898	-0.423415554544	0.15900568428	2.02232404331	-0.201504829428	1.93442773306	-0.426297663653	0.730183783035	0.39413153467	-0.635291269904	-0.35172885566	-0.244029196734	0.861744621551	0.0919961147508	0.0694745752348	0.86212655687	-0.103706549981	0.0671080692107	0.529710196541	-0.0845649180048	0.68940716725	-2.04084025345	3.45416003915	-47.4433123631
14	2.08611577976	0.7214221836	0.323149252597	0.902960238681	-0.185369373833	2.04456549866	-0.0276802825101	-0.0235520939712	-0.0956449579458	0.0709139116207	0.0539728253132	0.0814562607121	0.144263299765	-0.0977772917337	0.0329237865673	0.594281989904	-0.0100892787196	-0.0065539318667	0.410519536587	-0.0249968049616	0.499068526477	-4.02207210799	9.80459738575	-37.9845914603
15	0.531611857951	0.583044464703	0.432328186631	0.584797377474	0.056061782272	2.18152050804	-0.0519493322661	0.0992376926235	-0.0971675311114	-0.177604150991	0.0387367841589	-0.0214241565715	0.381879221452	0.050834777255	0.040168566235	0.674142766578	-0.0371873418385	0.0470174067633	0.488768766192	-0.0496461955727	0.498667082206	-0.700113726534	8.87782467235	-41.3465558014
16	0.454852131973	0.00434767091935	-0.24554141089	0.258742163704	-0.0836134572657	0.0883923536247	0.284540716306	0.344685787968	-0.255278079686	0.0976867259319	0.27168369743	-0.64830204072	0.256333966255	-0.250648622241	-0.0114267129293	0.61243090776	-0.0442568410615	0.0215825010199	0.628187345053	-0.00826997153625	0.576865071702	-1.2155383999	23.8669002972	-48.5484365895
17	3.84957316956	-0.00956139474084	-1.1191351256	0.438512131721	-0.0321192063081	1.10120034979	0.402766182859	-0.263430588897	0.641674441326	0.235309412453	-0.240556434811	-0.290806337215	-0.633054101618	0.35384727919	-0.120066877036	0.727274471579	-0.0847278504678	-0.0252253244047	0.637359003859	0.0848192483607	0.502536511999	18.3247923683	30.8589466342	-44.163476632
18	2.65945258357	0.697026371718	-0.434384677767	2.13975660671	-0.96255655364	2.12775332692	0.131656551233	-0.0355443095341	-0.136463487592	-0.237909186354	0.0557482766184	-0.0489851143542	-0.297049020212	0.0394560983832	-0.0448912533586	0.545188503609	0.0301129096296	0.0144226852095	0.435049805296	-0.0186199542639	0.429355464443	9.00675647565	20.4896356471	-36.5403064973
19	1.99968737854	0.656167327375	-0.249192126959	0.945293591981	-1.09810980768	1.90552229741	-0.143641418404	0.130801225364	-0.0133189913035	-0.151608477427	-0.108708811828	0.0765908585528	0.158469075117	0.365868492851	-0.0299839319286	0.567331162887	0.00534616188751	0.00827099030145	0.537428237842	-0.00457091187461	0.54454013944	13.8063339254	23.0276486032	-38.9171403704

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 0 through 88 )	A	A	0 - 88	1 - 89
2	2	chain 'A' and (resid 89 through 149 )	A	A	89 - 149	90 - 150
3	3	chain 'A' and (resid 150 through 171 )	A	A	150 - 171	151 - 172
4	4	chain 'B' and (resid 0 through 24 )	B	B	0 - 24	1 - 25
5	5	chain 'B' and (resid 25 through 61 )	B	B	25 - 61	26 - 62
6	6	chain 'B' and (resid 62 through 72 )	B	B	62 - 72	63 - 73
7	7	chain 'B' and (resid 73 through 99 )	B	B	73 - 99	74 - 100
8	8	chain 'B' and (resid 100 through 109 )	B	B	100 - 109	101 - 110
9	9	chain 'B' and (resid 110 through 157 )	B	B	110 - 157	111 - 158
10	10	chain 'B' and (resid 158 through 172 )	B	B	158 - 172	159 - 173
11	11	chain 'H' and (resid 0 through 52 )	H	C	0 - 52	1 - 53
12	12	chain 'H' and (resid 53 through 255 )	H	C	53 - 255	54 - 236
13	13	chain 'I' and (resid -1 through 25 )	I	D	-1 - 25	1 - 27
14	14	chain 'I' and (resid 26 through 73 )	I	D	26 - 73	28 - 75
15	15	chain 'I' and (resid 74 through 118 )	I	D	74 - 118	76 - 120
16	16	chain 'I' and (resid 119 through 150 )	I	D	119 - 150	121 - 133
17	17	chain 'I' and (resid 151 through 165 )	I	D	151 - 165	134 - 148
18	18	chain 'I' and (resid 166 through 191 )	I	D	166 - 191	149 - 174
19	19	chain 'I' and (resid 192 through 254 )	I	D	192 - 254	175 - 237

-
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