PDB-6vzd: N-terminal domain of mouse surfactant protein B (K46E/R51E mutant...

ID or keywords:

Entry

Database: PDB / ID: 6vzd

Title

N-terminal domain of mouse surfactant protein B (K46E/R51E mutant) with bound lipid

Components

Pulmonary surfactant-associated protein B

Keywords

SURFACTANT PROTEIN / Lipid-binding / Lipid transfer / Saposin-like

Function / homology

Function and homology information

Surfactant metabolism / alveolar lamellar body / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / multivesicular body / collagen-containing extracellular matrix / lysosome / extracellular space / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Rapoport, T.A. / Bodnar, N.O.

Funding support

United States, 1items

Citation

Journal: Mol.Cell / Year: 2021
Title: Mechanism of Lamellar Body Formation by Lung Surfactant Protein B.
Authors: Sever, N. / Milicic, G. / Bodnar, N.O. / Wu, X. / Rapoport, T.A.

History

Deposition	Feb 28, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2020	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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Dec 9, 2020	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 20, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6vzd.cif.gz	277.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6vzd.ent.gz	194.3 KB	Display	PDB format
PDBx/mmJSON format	6vzd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6vzd_validation.pdf.gz	354.5 KB	Display	wwPDB validaton report
Full document	6vzd_full_validation.pdf.gz	372.6 KB	Display
Data in XML	6vzd_validation.xml.gz	5.9 KB	Display
Data in CIF	6vzd_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzd ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzd	HTTPS FTP

-
Related structure data

Related structure data	6vynSC 6vz0C 6vzeC 6w1bC 7mbkC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mnx-4 2czu-1 3gqe-1 1zw6-d 4oy7-3 6ypv-d 1p2v-d 3k8y-d 3pir-d 2wmc-7 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/768 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/768
Experimental dataset #2	Data reference: 10.15785/SBGRID/769 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/769
Experimental dataset #3	Data reference: 10.15785/SBGRID/770 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/770
Experimental dataset #4	Data reference: 10.15785/SBGRID/771 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/771

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pulmonary surfactant-associated protein B

E: Pulmonary surfactant-associated protein B

B: Pulmonary surfactant-associated protein B

C: Pulmonary surfactant-associated protein B

hetero molecules

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

1

A: Pulmonary surfactant-associated protein B

E: Pulmonary surfactant-associated protein B

hetero molecules

defined by author&software
Evidence: gel filtration, The dimer is active in lipid binding and transport.
22 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pulmonary surfactant-associated protein B

C: Pulmonary surfactant-associated protein B

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.793, 66.124, 59.620
Angle α, β, γ (deg.)	90.000, 97.370, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Pulmonary surfactant-associated protein B / SP-B / Pulmonary surfactant-associated proteolipid SPL(Phe) Mass: 9921.431 Da / Num. of mol.: 4 / Mutation: K46E, R51E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sftpb, Sftp3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2 / References: UniProt: P50405
#2: Chemical	ChemComp-RXY / (7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphapentacos-7-en-19-yl (9Z)-octadec-9-enoate Mass: 715.981 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₉H₇₄NO₈P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.45 Å³/Da / Density % sol: 49.85 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 100 mM citrate buffer pH 5.4, 23-25% PEG 4000, 14-15% 2-propanol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.88→59.13 Å / Num. obs: 31237 / % possible obs: 92.19 % / Redundancy: 53.8 % / B_iso Wilson estimate: 18.78 Å² / CC_1/2: 1 / R_merge(I) obs: 0.1001 / Net I/σ(I): 40.86
Reflection shell	Resolution: 1.88→1.947 Å / R_merge(I) obs: 1.511 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 2186 / CC_1/2: 0.897

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
Coot		model building
XDS		data scaling
PHENIX		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6VYN (lipid removed)

6vyn

Resolution: 1.88→59.13 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.6668

	R_factor	Num. reflection	% reflection
R_free	0.2175	1841	6.37 %
R_work	0.1697	-	-
obs	0.1727	28915	91.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 35.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→59.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2571	0	294	318	3183

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	3042
X-RAY DIFFRACTION	f_angle_d	0.7357	4043
X-RAY DIFFRACTION	f_chiral_restr	0.0437	434
X-RAY DIFFRACTION	f_plane_restr	0.0054	509
X-RAY DIFFRACTION	f_dihedral_angle_d	30.7408	1294

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 (%)
1.88-1.93	0.3909	103	0.3233	1514	X-RAY DIFFRACTION	66.68
1.93-1.98	0.2488	111	0.2526	1694	X-RAY DIFFRACTION	75.65
1.98-2.05	0.2738	132	0.2203	1864	X-RAY DIFFRACTION	83.06
2.05-2.12	0.2194	142	0.1854	1997	X-RAY DIFFRACTION	88.06
2.12-2.21	0.222	138	0.1652	2064	X-RAY DIFFRACTION	91.83
2.21-2.31	0.2358	142	0.1584	2150	X-RAY DIFFRACTION	95.74
2.31-2.43	0.2327	145	0.16	2201	X-RAY DIFFRACTION	97.06
2.43-2.58	0.1829	153	0.1608	2226	X-RAY DIFFRACTION	98.18
2.58-2.78	0.2059	152	0.1606	2259	X-RAY DIFFRACTION	98.85
2.78-3.06	0.2469	153	0.1621	2237	X-RAY DIFFRACTION	99.05
3.06-3.5	0.1844	155	0.15	2264	X-RAY DIFFRACTION	99.75
3.5-4.41	0.1798	157	0.1385	2284	X-RAY DIFFRACTION	100
4.41-59.13	0.2307	158	0.1869	2320	X-RAY DIFFRACTION	99.64

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	2.63775591188	-0.159069466943	-1.26467935517	5.19007850595	-0.456769376546	6.9887142201	-0.225332893662	0.487810988127	0.134762819825	-0.364138932422	0.12950098888	-0.0899327276327	0.0272557064272	-0.0366305193634	-0.0143849519414	0.122051320794	-0.027094699281	-0.0142901798525	0.119020002534	0.0263670842356	0.0800507537352	-22.69976057	9.50393040363	-18.4373114391
2	5.90599487405	3.37134091835	4.76940742661	2.43147277134	2.96149295852	4.58237443911	0.220842456429	-0.353516654333	-0.146399006857	0.249481783569	-0.0942958832213	0.0705514097252	0.227420513433	-0.450348471203	-0.186955105237	0.118301405112	-0.0600048897205	0.0470029165926	0.159390035164	0.00240492229197	0.158482768591	-25.7236512227	4.12005513163	1.56124011326
3	5.00422738951	-2.12717284902	3.67682985434	1.3420244167	-1.84712097032	5.03019670037	-0.134179348737	-0.42631618599	0.0816574769584	0.115169026126	0.153818457743	-0.0763504705597	-0.146886931464	-0.408907076441	-0.0190307222116	0.128153945319	-0.0270765546582	0.00921256880273	0.101018156956	-0.0245484230786	0.13714429047	-23.1110826825	13.4037620834	2.5900631861
4	7.90479608119	-2.00793041318	0.664173213393	4.60064113657	1.25804022164	2.36321711313	-0.0736226081447	0.269997891	0.634552929594	-0.306966244491	-0.0201646548583	-0.297651404433	-0.604006607109	0.134765545932	0.0217151387169	0.293971433601	-0.0541411892541	-0.0858215244093	0.15350039179	0.0642512233281	0.228521259942	-22.2446498792	19.7148068241	-18.641892743
5	4.69594877179	0.270233400193	-0.327263698048	4.33862147588	-0.506268329301	4.36543443895	-0.177716658978	0.362631800812	-0.324121504154	-0.311297196121	0.123335551046	-0.155358101302	0.360985954072	0.0976118773463	0.00360178104302	0.180410735491	-0.00388065407969	0.0458827744426	0.104865124665	-0.0261883894209	0.0968922368441	-19.3757301832	1.30058662161	-14.9274238248
6	3.66190478358	-1.44546873574	-1.51704811601	4.58442421533	3.40367258003	5.88519503269	-0.000940780755435	0.373095658543	0.388439949239	-0.323890010397	0.194311544756	-0.645554275807	-0.660722152459	0.459132271323	-0.285908973074	0.165605509195	-0.06112160686	0.0141824528005	0.209572195713	0.0616915227197	0.291069958218	-9.1886450525	19.596789652	-11.5030107989
7	3.85557941571	-0.947347088124	-0.225740057007	5.88120136373	0.120596769368	3.44772647223	-0.0157571766019	0.013202778602	0.232583226574	-0.17215496382	0.0232074606805	-0.323007195626	-0.165263865106	0.114682375602	-0.0485352857405	0.139528759593	-0.00128396126035	1.28449610091E-5	0.0780260773963	0.0133894289244	0.16743687884	-9.40604956533	15.9424395872	-2.59085449088
8	8.12578685564	-1.71712910169	-6.75219990941	3.42323270572	1.137853042	6.07270214234	0.428100989083	-0.585546563271	0.426420905143	0.0597367125667	0.18377177839	-0.500264731409	-0.0529962202018	0.532193534882	-0.604053158972	0.204151324004	0.00220230847871	0.00659293570204	0.150235105536	-0.0501146372523	0.186320212363	-13.7152068785	-3.08054576556	-7.66149198993
9	4.72182669473	1.16470050496	2.31470048238	2.14776405634	4.07434234752	7.73564486499	0.0286533784812	0.233256196584	-0.551270743862	-0.209464345909	0.158660212427	-0.188138176044	0.720606658701	-0.159428251942	-0.168953253373	0.236338844865	-0.0540356610218	0.0156762752031	0.157444085694	0.0113404160805	0.250403154329	-23.2808601013	-6.58587750472	-6.71067671767
10	5.20319649669	-2.71808740155	-2.63741824875	5.04452929605	0.772218555021	8.38430102454	-0.0192043070552	-0.318392135679	-0.206590977202	0.170295992271	-0.0911974738989	0.0753438608092	0.136629194178	0.0521776783304	0.149831135702	0.207792546808	-0.0800480815608	-0.0547455324988	0.20014960695	0.0907656745215	0.157649920822	-31.4786582389	8.94963337874	-26.2776464207
11	5.30075046149	-1.27227161571	3.57296176008	4.55972429429	-2.00172845044	5.63949422864	-0.2376524335	0.884496797539	0.209240816689	-0.222701394514	-0.0483800174545	-0.437763365786	-0.193319519854	1.20628222026	0.223649490289	0.194632814957	-0.016727085687	0.0428607158048	0.35361801799	0.0625590221335	0.253348196757	-28.0509779107	11.3403112071	-46.2249935891
12	4.32052195436	0.122229517427	0.116988312573	7.58188793894	5.24602514444	3.76924050636	-0.268013641946	0.38290323021	0.621351466166	-0.499012008514	-0.220006439542	-0.21770333649	-0.406352797231	0.47636529592	0.367444268107	0.226707722995	0.0058924745117	-0.0285505167228	0.176856713516	0.0445223752632	0.249022718564	-42.1630992128	15.2988397415	-51.918275982
13	0.16920590385	0.093987878141	-0.157988465038	0.487128366165	-0.480990113673	0.795128270239	-0.0403622586396	0.07086471005	0.0340511631456	-0.134517751799	-0.0193240611084	-0.0546228936757	0.00731656874497	0.0329645274086	0.00568842961431	0.340007493576	-0.206347257447	-0.0493708536841	0.17457979133	0.301491123123	0.198654013858	-31.0651217257	20.3631368676	-42.2184396145
14	6.38058148289	2.96899492766	-0.158395945678	6.92039396844	0.821016427702	5.87647569956	-0.0907117510351	-0.0805546960786	0.0268241472075	0.233723937403	-0.24056873078	0.100094432651	-0.273224383888	-0.451895294977	0.259858581618	0.187741825166	-0.03149758573	-0.0693492665393	0.193471743719	0.0476675867109	0.144526709823	-35.6206841789	17.2785414802	-23.5814141468
15	4.70174768116	-1.78572649441	-2.69053659873	6.9151603212	-0.446241753175	5.35668388314	-0.202957971311	-0.57018525993	-1.03199425467	0.0363958316023	-0.198428423418	-0.219268660366	1.00007678236	0.218163302624	0.374773918015	0.458633698975	-0.0466355933387	-0.0804351517182	0.244360431392	0.127308580708	0.31586969338	-33.4660598584	1.10789443983	-31.5750486227
16	5.66977294579	-2.14112109216	0.144397663058	9.1287762099	-5.82868369382	7.92839395353	0.12293143897	-0.519520914729	-0.289314895844	0.441927188912	0.0233726664269	0.905561429795	-0.12381039489	-0.938184679399	-0.205736549273	0.207557890029	-0.0835202148831	0.00553750810883	0.520203816276	-0.0702927783718	0.244884511562	-48.7577530946	14.2203281266	-30.7058738333
17	7.9673625774	1.71773622351	0.90247762788	2.89500333617	-1.11477088849	7.33634951043	0.0927873894448	-0.151777328367	0.227489383399	0.0113538057026	-0.154001697823	0.46261481332	-0.20961144811	-0.439006873303	0.056323664385	0.182272551981	-0.00477349518114	-0.046258471118	0.249323550141	-0.0596940712866	0.147922205514	-47.6378026771	14.1545716742	-40.5521485965
18	2.4981743898	1.75643779	-2.90655025535	5.68885781476	-6.6228039491	8.25084160149	-0.683380599536	0.675407021864	-3.01769535793	0.510329481811	0.441558345708	0.495102017001	2.43379764163	-0.254687702859	0.212572418083	0.887078443711	-0.0491181176624	-0.104194384265	0.511498599642	-0.0977701750712	1.25735217029	-41.9528563714	-5.00296873857	-37.266355111
19	6.01717172737	3.78650074325	-2.29427988583	3.74289820685	-3.69519733048	4.6042318956	0.0468147584907	-0.478706993873	-1.69591387214	-0.181251099864	-0.219146413708	-0.869763623922	1.64435196242	0.845846658818	0.210999825387	0.524330127144	0.0679461320972	-0.0827097096735	0.318673970811	0.0575041903944	0.509438733101	-29.9833560069	-0.153545644095	-42.1111962549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 84 )
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 3 through 24 )
6	X-RAY DIFFRACTION	6	chain 'E' and (resid 25 through 41 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 42 through 69 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 70 through 79 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 80 through 87 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 7 through 24 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 41 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 42 through 51 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 52 through 67 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 68 through 84 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 7 through 24 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 25 through 41 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 42 through 67 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 68 through 72 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 73 through 84 )

-
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