PDB-7zm5: Structure of Mossman virus receptor binding protein

ID or keywords:

Entry

Database: PDB / ID: 7zm5

Title

Structure of Mossman virus receptor binding protein

Components

Attachment glycoprotein

Keywords

VIRAL PROTEIN / Attachment glycoprotein / glycoprotein / receptor binding protein

Function / homology

Function and homology information

host cell membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function

Biological species

Mossman narmovirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.62 Å

Authors

Stelfox, A.J. / Bowden, T.A. / Rissanen, I. / Harlos, K.

Funding support

United Kingdom,

Finland,

United States, 11items

Organization	Grant number	Country
Medical Research Council (MRC, United Kingdom)	MR/L009528/1	United Kingdom
Medical Research Council (MRC, United Kingdom)	MR/S007555/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/K503113/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/L505031/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/M50659X/1	United Kingdom
Engineering and Physical Sciences Research Council	EP/M508111/1	United Kingdom
Academy of Finland	309605	Finland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI123449	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI069317	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI115226	United States
Wellcome Trust	203141/Z/16Z	United Kingdom

Citation

Journal: Mbio / Year: 2023
Title: Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein.
Authors: Stelfox, A.J. / Oguntuyo, K.Y. / Rissanen, I. / Harlos, K. / Rambo, R. / Lee, B. / Bowden, T.A.

History

Deposition	Apr 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.2	Oct 4, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Nov 29, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7zm5.cif.gz	444.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7zm5.ent.gz	297 KB	Display	PDB format
PDBx/mmJSON format	7zm5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7zm5_validation.pdf.gz	468 KB	Display	wwPDB validaton report
Full document	7zm5_full_validation.pdf.gz	471.8 KB	Display
Data in XML	7zm5_validation.xml.gz	37.5 KB	Display
Data in CIF	7zm5_validation.cif.gz	56.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/7zm5 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zm5	HTTPS FTP

-
Related structure data

Related structure data	7zm6C 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	#231 - Mar 2019 Measles Virus Proteins similarity (3) #113 - May 2009 Influenza Neuraminidase similarity (1)

Deposited unit

A: Attachment glycoprotein

B: Attachment glycoprotein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: SAXS, Size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS) was performed to assess the oligomerisation state of glycosylated (high mannose) Mossman virus receptor ...Evidence: SAXS, Size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS) was performed to assess the oligomerisation state of glycosylated (high mannose) Mossman virus receptor binding protein in solution. Using the dimeric crystal structure data a best fitting model was generated using molecular dynamics, which considered the flexibility of the high mannose N-linked glycans and C- and N-termini. The extensive homodimeric interface observed in the crystal structure was largely retained.

Unit cell

Length a, b, c (Å)	80.200, 83.930, 122.120
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" and resid 204 through 631)
d_2	ens_1	chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 204 - 631 / Label seq-ID: 204 - 631

Dom-ID	Auth asym-ID	Label asym-ID
d_1	A	A
d_2	B	B

NCS oper: (Code: givenMatrix: (-0.999962989198, 0.00606648240466, 0.00610065780899), (0.00815171301114, 0.89482704962, 0.446338549583), (-0.00275132867039, 0.446371761047, -0.894843383576)Vector: -75. ...

#1: Protein

Attachment glycoprotein

Mass: 70311.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mossman narmovirus
Cell line (production host): Human embryonic kidney 293T cells
Production host:

Homo sapiens (human) / References: UniProt: Q6WGM0

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.13 Å³/Da / Density % sol: 42.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M potassium bromide, 0.2 M potassium thiocynate, 0.1 M sodium cacodylate pH 6.5, 3% PGA-LM, 20% w/v polyethylene glycol (PEG) 550 MME

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.62→69.17 Å / Num. obs: 105014 / % possible obs: 99.8 % / Redundancy: 6.5 % / B_iso Wilson estimate: 23.01 Å² / CC_1/2: 1 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.03 / Net I/σ(I): 13
Reflection shell	Resolution: 1.62→1.65 Å / R_merge(I) obs: 1.47 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10324 / CC_1/2: 0.5 / R_pim(I) all: 0.68 / % possible all: 99.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
xia2		data reduction
xia2		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.62→52.38 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2116	5029	4.79 %
R_work	0.1765	99892	-
obs	0.1782	104921	99.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→52.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6766	0	14	692	7472

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6946
X-RAY DIFFRACTION	f_angle_d	0.8863	9464
X-RAY DIFFRACTION	f_chiral_restr	0.0578	1063
X-RAY DIFFRACTION	f_plane_restr	0.0065	1226
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1528	2525

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.663009456905 Å

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 (%)
1.62-1.64	0.3854	165	0.3361	3266	X-RAY DIFFRACTION	99.19
1.64-1.66	0.355	175	0.3204	3267	X-RAY DIFFRACTION	99.28
1.66-1.68	0.3083	156	0.2964	3295	X-RAY DIFFRACTION	99.6
1.68-1.7	0.3035	164	0.2788	3277	X-RAY DIFFRACTION	99.48
1.7-1.72	0.2582	164	0.266	3314	X-RAY DIFFRACTION	99.86
1.72-1.75	0.2997	159	0.2451	3315	X-RAY DIFFRACTION	99.43
1.75-1.77	0.2722	153	0.234	3276	X-RAY DIFFRACTION	99.74
1.77-1.8	0.2685	152	0.2275	3304	X-RAY DIFFRACTION	99.77
1.8-1.82	0.2228	165	0.2255	3326	X-RAY DIFFRACTION	99.77
1.82-1.85	0.2779	144	0.2251	3302	X-RAY DIFFRACTION	99.71
1.85-1.89	0.2398	169	0.2142	3273	X-RAY DIFFRACTION	99.62
1.89-1.92	0.2387	186	0.2124	3303	X-RAY DIFFRACTION	99.71
1.92-1.96	0.262	177	0.2047	3326	X-RAY DIFFRACTION	99.83
1.96-2	0.2368	185	0.1837	3278	X-RAY DIFFRACTION	99.65
2-2.04	0.2151	154	0.1745	3316	X-RAY DIFFRACTION	99.88
2.04-2.09	0.2284	167	0.1689	3293	X-RAY DIFFRACTION	99.88
2.09-2.14	0.1754	152	0.1598	3366	X-RAY DIFFRACTION	99.83
2.14-2.2	0.2034	173	0.1676	3274	X-RAY DIFFRACTION	99.71
2.2-2.26	0.2107	165	0.1819	3339	X-RAY DIFFRACTION	99.94
2.26-2.34	0.2472	154	0.184	3352	X-RAY DIFFRACTION	99.94
2.34-2.42	0.2181	185	0.1801	3317	X-RAY DIFFRACTION	99.97
2.42-2.52	0.2108	183	0.1771	3328	X-RAY DIFFRACTION	99.86
2.52-2.63	0.2137	212	0.1729	3289	X-RAY DIFFRACTION	99.97
2.63-2.77	0.2158	194	0.1729	3333	X-RAY DIFFRACTION	99.8
2.77-2.94	0.2129	146	0.1741	3360	X-RAY DIFFRACTION	99.91
2.94-3.17	0.208	147	0.1743	3384	X-RAY DIFFRACTION	99.8
3.17-3.49	0.1923	142	0.159	3438	X-RAY DIFFRACTION	99.97
3.49-3.99	0.1899	187	0.1559	3382	X-RAY DIFFRACTION	99.89
3.99-5.03	0.1675	185	0.1381	3418	X-RAY DIFFRACTION	99.72
5.03-52.38	0.2014	169	0.1676	3581	X-RAY DIFFRACTION	99.5

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	3.13620581148	1.40580922222	0.44814681128	2.49893468603	0.24973291168	2.35071748557	0.0540832824627	-0.494796412045	-0.384405429225	0.309403484473	-0.135301321249	-0.193113145078	0.0704589361786	0.303008017067	0.0733840628857	0.204668201778	-0.0178399464917	-0.0172047036292	0.411491288429	0.0893435644427	0.207044961651	-16.1487617351	0.194467658777	-1.60380683034
2	3.55446747609	0.628139485533	0.321587075162	1.4423441868	0.524705687213	2.49356756793	-0.0376216114338	0.040398265949	-0.183817316819	-0.0544404519999	-0.0527200407785	0.0339026161401	-0.032565440419	0.0147960350869	0.0876980846381	0.154815273822	0.0228740755143	0.0035709379057	0.101395006371	0.0153036201228	0.193192528388	-31.3498913773	-0.752672894682	-17.05209793
3	3.19284953999	-0.163445205269	0.682153721969	1.62596115366	-1.50399273116	5.31857158177	0.0205130087745	0.114779612123	-0.0616267469537	-0.0343916422659	-0.0611154710667	-0.0307883250218	0.089134733152	-0.000667346394774	0.0721666937337	0.116997683171	0.00124823138763	0.00339446655853	0.0793510921397	-0.00883938399997	0.178552258667	-31.8092495502	4.2532795928	-18.2543207125
4	2.76047540304	0.0493296148961	-1.25667421571	1.47453200367	-0.497033262565	2.65808084616	0.129896677222	0.160873327081	0.279973325594	-0.0420840395432	-0.00489306784091	-0.0411438833377	-0.275170432849	-0.0112028319967	-0.0804229761646	0.206305161294	-0.00580300349785	0.00183615754854	0.132626743222	0.0189028180712	0.208919560595	-29.1161311473	10.9696536538	-18.9392436707
5	2.43936273766	0.176977086191	-0.731719455747	1.46930698382	-0.171698045125	2.92266013005	0.131168036488	0.444647304976	0.240477415301	-0.206894675286	-0.0707187673774	-0.110951481574	-0.380172043536	0.133461460383	-0.101760251206	0.241040433116	0.0156884071112	0.0117481969609	0.274897737572	0.0938033666093	0.270467272516	-22.2954237666	15.6823112362	-30.7240627569
6	2.2750718688	-0.00935237018787	-0.720152046395	2.51174872578	-0.702986687474	2.43909392878	0.0661814410816	0.466167000405	0.146358259087	-0.212569246568	-0.064685617944	-0.261278889333	0.00917231324468	0.476805933323	-0.0658091346025	0.155411337741	-0.00336004160125	0.0114671817722	0.346322048791	0.053846831093	0.19367597432	-10.3883232215	8.86836054225	-30.8453748148
7	2.84799583287	-1.19379388801	-0.48061659374	6.53335534612	1.21515155241	3.14184794514	0.0119757287995	0.768346969822	-0.509615326213	-0.486606469848	-0.102896875552	-0.122138761962	0.297040437622	0.506080462689	0.0842135488772	0.243206139521	0.0732645307507	0.0555927227121	0.590823133102	-0.0496174061076	0.336505830002	-7.40049847939	-2.49702167451	-36.8672730551
8	3.45793650803	-0.281510743988	0.0353990195281	1.24347943265	-0.33769268518	3.49678444485	0.062185622185	0.211818118565	0.347608893241	-0.0597048853786	-0.0825676926213	-0.148445298646	-0.331719205737	0.429801384169	0.000905363231555	0.180787675111	-0.04501343099	0.0200847449421	0.295794584136	0.0615212419864	0.234194055605	-8.07285017232	9.41734883345	-22.8059055593
9	3.75394656511	0.0623335865994	1.24602285308	6.17025870057	1.7649836316	4.8500103353	-0.0461515302824	0.272151057602	-0.310323024683	-0.325703996529	-0.158085596953	-0.357139441575	-0.0196520870399	0.613758815608	0.183886953455	0.179807290162	0.064290102406	0.0407448076522	0.396248882193	0.0564286619056	0.212392352477	-6.70074940996	-1.43318220854	-24.3543061453
10	2.2961638116	-0.313273267705	-0.680579297804	1.38627466543	-0.297193588619	3.02430706139	-0.0647499244083	0.222533891362	-0.777671161918	-0.177366563142	-0.189188369883	0.0333610241217	0.627622607276	0.224469515482	0.213526799568	0.302653334085	0.111008607086	0.0505150631632	0.28787781291	-0.0250506478605	0.428262835117	-11.8201052342	-11.1300895154	-25.3254682901
11	3.66456579217	-0.118725075854	0.160220107628	1.54010080364	-1.07932008876	1.89033454143	-0.0186596126268	-0.184246158481	-0.869328133011	-0.0810933996047	-0.0891271463072	-0.270810563088	0.3823778426	0.255956573964	0.0626074564167	0.239012962267	0.0629197982223	0.0398015757006	0.222465456839	0.0735042964487	0.389332668042	-16.2245568985	-12.1683832212	-12.7054513939
12	2.5558918923	0.590180261979	0.332170935932	2.310653617	1.37815995181	3.73383617257	0.051266505575	-0.291615641631	-0.178039900736	0.20544804986	-0.106719814063	-0.0322864049099	0.171449108108	0.259989939652	0.027447947037	0.162383271991	0.0177069481937	-0.00520702020756	0.194576347361	0.072973331997	0.21374053449	-21.0573040446	-1.71909475298	-8.11069537797
13	3.99999812771	0.426084809064	3.5483584412	2.63973350256	1.04611147436	8.05098613022	-0.0182312063526	0.0178952371276	-0.50993365161	0.0983697883655	-0.107076977522	-0.140098292585	0.269392140868	0.367568124741	0.00480894402847	0.136792145768	0.00469993579924	0.0707176322804	0.124082676332	0.0742457096219	0.265521690991	-25.6167162488	-8.22036894708	-12.3968156131
14	3.34979542958	-0.0175187885531	-0.0292944461109	1.30856992183	-0.541611840471	2.58828108501	0.0281373926359	0.181071412538	-0.0273624777349	-0.00507510225914	0.0335120687177	0.0464021622011	-0.0798173601826	-0.186704755333	-0.0456212604212	0.137345968865	-0.00670180678635	0.0102428427369	0.10835212584	-0.0105796123865	0.154581750772	-48.2261724695	3.9533338461	-15.5602434072
15	3.07164997375	0.717087661215	-0.76313941405	1.77579115792	-0.310878834781	1.35731603654	0.130311670579	-0.620390085083	0.00192276551113	0.261619750856	-0.116893169349	0.0356970681376	-0.0699306016903	0.0621366578273	-0.0304268082182	0.224763529519	0.000661493649988	0.0216785010932	0.253063727803	-0.0223338542957	0.154361349246	-58.2018755474	5.10330701606	3.29287340143
16	2.548890775	1.87944971943	-0.0746932764647	6.18487025422	0.391160276938	1.56652592523	-0.00732141369481	-0.292518013835	-0.261487817713	0.144218158996	0.0190504538351	0.0746594404741	0.0919896988932	-0.0616565745878	-0.0215049671406	0.154852576099	0.0246620063232	0.0577768914729	0.2551476278	0.0394058377845	0.188484100793	-67.8712435737	-5.16536235462	1.34336437485
17	2.46838497191	0.212832938195	-0.676272497272	0.857532089465	-0.193721859213	1.16872828175	-0.0725474985958	0.358288062382	-0.290052498103	-0.0885309497955	0.0211656651694	0.0539154589839	0.161820526176	-0.22212065246	0.0237180405331	0.176128683538	-0.0238610228833	-0.000788460267713	0.191344366591	-0.0403198627068	0.169427012886	-61.0849803018	-5.83969634066	-16.5719195286

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 203 through 229 )	A	A	203 - 229	1 - 27
2	2	chain 'A' and (resid 230 through 258 )	A	A	230 - 258	28 - 56
3	3	chain 'A' and (resid 259 through 293 )	A	A	259 - 293	57 - 91
4	4	chain 'A' and (resid 294 through 320 )	A	A	294 - 320	92 - 118
5	5	chain 'A' and (resid 321 through 371 )	A	A	321 - 371	119 - 169
6	6	chain 'A' and (resid 372 through 407 )	A	A	372 - 407	170 - 205
7	7	chain 'A' and (resid 408 through 442 )	A	A	408 - 442	206 - 240
8	8	chain 'A' and (resid 443 through 482 )	A	A	443 - 482	241 - 280
9	9	chain 'A' and (resid 483 through 502 )	A	A	483 - 502	281 - 300
10	10	chain 'A' and (resid 503 through 540 )	A	A	503 - 540	301 - 338
11	11	chain 'A' and (resid 541 through 582 )	A	A	541 - 582	339 - 380
12	12	chain 'A' and (resid 583 through 609 )	A	A	583 - 609	381 - 407
13	13	chain 'A' and (resid 610 through 631 )	A	A	610 - 631	408 - 429
14	14	chain 'B' and (resid 204 through 320 )	B	C	204 - 320	1 - 117
15	15	chain 'B' and (resid 321 through 407 )	B	C	321 - 407	118 - 204
16	16	chain 'B' and (resid 408 through 451 )	B	C	408 - 451	205 - 248
17	17	chain 'B' and (resid 452 through 631 )	B	C	452 - 631	249 - 428

-
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