[English] 日本語

Yorodumi

- PDB-7b28: Complement inhibitor CirpA3 from Rhipicephalus pulchellus -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7b28

Title

Complement inhibitor CirpA3 from Rhipicephalus pulchellus

Components

CirpA3

Keywords

IMMUNOSUPPRESSANT / Inhibitor / Complement / tick

Biological species

Rhipicephalus pulchellus (arthropod)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Lea, S.M. / Johnson, S. / Braunger, K.

Funding support

United Kingdom, 5items

Organization	Grant number	Country
Wellcome Trust	100298	United Kingdom
Wellcome Trust	209194	United Kingdom
Wellcome Trust	219477	United Kingdom
Medical Research Council (MRC, United Kingdom)	S021264	United Kingdom
European Molecular Biology Organization (EMBO)	ALTF 554-2019	United Kingdom

Citation

Journal: Nat Commun / Year: 2022
Title: Structure and function of a family of tick-derived complement inhibitors targeting properdin.
Authors: Braunger, K. / Ahn, J. / Jore, M.M. / Johnson, S. / Tang, T.T.L. / Pedersen, D.V. / Andersen, G.R. / Lea, S.M.

History

Deposition	Nov 26, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 2, 2022	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.journal_volume / _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 1.2	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7b28.cif.gz	628.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7b28.ent.gz	430.8 KB	Display	PDB format
PDBx/mmJSON format	7b28.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7b28_validation.pdf.gz	487.3 KB	Display	wwPDB validaton report
Full document	7b28_full_validation.pdf.gz	500.3 KB	Display
Data in XML	7b28_validation.xml.gz	51 KB	Display
Data in CIF	7b28_validation.cif.gz	71.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/7b28 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b28	HTTPS FTP

-
Related structure data

Related structure data	7b26C 7b29C 7b2aC 7b2dC C: citing same article (ref.)
Similar structure data	7b2d-d 1fho-d 7b28-8 2c8s-d 7b2a-d 1xm5-1 1ib5-d 5a88-1 2hzq-d 7b28-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

-
Assembly

Deposited unit

F: CirpA3

A: CirpA3

B: CirpA3

C: CirpA3

D: CirpA3

E: CirpA3

G: CirpA3

H: CirpA3

hetero molecules

153 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

F: CirpA3

defined by author
Evidence: light scattering
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

B: CirpA3

hetero molecules

defined by author
19.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

C: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

D: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

E: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

G: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

H: CirpA3

defined by author
19.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.366, 150.298, 68.430
Angle α, β, γ (deg.)	90.000, 91.833, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 49 through 94 or resid 96...
d_2	ens_1	(chain "B" and (resid 49 through 94 or resid 96...
d_3	ens_1	(chain "C" and (resid 49 through 94 or resid 96...
d_4	ens_1	(chain "D" and (resid 49 through 94 or resid 96...
d_5	ens_1	(chain "E" and (resid 49 through 94 or resid 96...
d_6	ens_1	(chain "F" and (resid 49 through 94 or resid 96...
d_7	ens_1	(chain "G" and (resid 49 through 94 or resid 96...
d_8	ens_1	(chain "H" and (resid 49 through 94 or resid 96...

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	SER	LYS	B	2 - 48
d_1	2	ens_1	ASN	GLY	B	50 - 51
d_1	3	ens_1	ILE	GLU	B	53 - 69
d_1	4	ens_1	VAL	LEU	B	71 - 89
d_1	5	ens_1	TYR	ALA	B	91 - 105
d_1	6	ens_1	ASN	GLY	B	109 - 118
d_1	7	ens_1	PRO	GLY	B	120 - 123
d_1	8	ens_1	LEU	CYS	B	125 - 129
d_1	9	ens_1	GLU	ALA	B	132 - 135
d_1	10	ens_1	VAL	GLU	B	137 - 139
d_1	11	ens_1	ASN	GLN	B	141 - 151
d_2	1	ens_1	SER	LYS	C	2 - 48
d_2	2	ens_1	ASN	GLY	C	50 - 51
d_2	3	ens_1	ILE	GLU	C	53 - 69
d_2	4	ens_1	VAL	LEU	C	71 - 89
d_2	5	ens_1	TYR	ALA	C	91 - 105
d_2	6	ens_1	ASN	GLY	C	109 - 118
d_2	7	ens_1	PRO	GLY	C	120 - 123
d_2	8	ens_1	LEU	CYS	C	125 - 129
d_2	9	ens_1	GLU	ALA	C	132 - 135
d_2	10	ens_1	VAL	GLU	C	137 - 139
d_2	11	ens_1	ASN	GLN	C	141 - 151
d_3	1	ens_1	SER	LYS	D	2 - 48
d_3	2	ens_1	ASN	GLY	D	50 - 51
d_3	3	ens_1	ILE	GLU	D	53 - 69
d_3	4	ens_1	VAL	LEU	D	71 - 89
d_3	5	ens_1	TYR	ALA	D	91 - 105
d_3	6	ens_1	ASN	GLY	D	109 - 118
d_3	7	ens_1	PRO	GLY	D	120 - 123
d_3	8	ens_1	LEU	CYS	D	125 - 129
d_3	9	ens_1	GLU	ALA	D	132 - 135
d_3	10	ens_1	VAL	GLU	D	137 - 139
d_3	11	ens_1	ASN	GLN	D	143 - 153
d_4	1	ens_1	SER	LYS	E	2 - 48
d_4	2	ens_1	ASN	GLY	E	50 - 51
d_4	3	ens_1	ILE	GLU	E	53 - 69
d_4	4	ens_1	VAL	LEU	E	71 - 89
d_4	5	ens_1	TYR	ALA	E	91 - 105
d_4	6	ens_1	ASN	GLY	E	109 - 118
d_4	7	ens_1	PRO	GLY	E	120 - 123
d_4	8	ens_1	LEU	CYS	E	125 - 129
d_4	9	ens_1	GLU	ALA	E	132 - 135
d_4	10	ens_1	VAL	GLU	E	137 - 139
d_4	11	ens_1	ASN	GLN	E	141 - 151
d_5	1	ens_1	SER	LYS	F	2 - 48
d_5	2	ens_1	ASN	GLY	F	50 - 51
d_5	3	ens_1	ILE	GLU	F	53 - 69
d_5	4	ens_1	VAL	LEU	F	71 - 89
d_5	5	ens_1	TYR	ALA	F	91 - 105
d_5	6	ens_1	ASN	GLY	F	109 - 118
d_5	7	ens_1	PRO	GLY	F	120 - 123
d_5	8	ens_1	LEU	CYS	F	125 - 129
d_5	9	ens_1	GLU	ALA	F	132 - 135
d_5	10	ens_1	VAL	GLU	F	137 - 139
d_5	11	ens_1	ASN	GLN	F	141 - 151
d_6	1	ens_1	SER	LYS	A	2 - 48
d_6	2	ens_1	ASN	GLY	A	50 - 51
d_6	3	ens_1	ILE	GLU	A	53 - 69
d_6	4	ens_1	VAL	LEU	A	71 - 89
d_6	5	ens_1	TYR	ALA	A	91 - 105
d_6	6	ens_1	ASN	GLY	A	109 - 118
d_6	7	ens_1	PRO	GLY	A	120 - 123
d_6	8	ens_1	LEU	CYS	A	125 - 129
d_6	9	ens_1	GLU	ALA	A	132 - 135
d_6	10	ens_1	VAL	GLU	A	137 - 139
d_6	11	ens_1	ASN	GLN	A	145 - 155
d_7	1	ens_1	SER	LYS	G	2 - 48
d_7	2	ens_1	ASN	GLY	G	50 - 51
d_7	3	ens_1	ILE	GLU	G	53 - 69
d_7	4	ens_1	VAL	LEU	G	71 - 89
d_7	5	ens_1	TYR	ALA	G	91 - 105
d_7	6	ens_1	ASN	GLY	G	109 - 118
d_7	7	ens_1	PRO	GLY	G	120 - 123
d_7	8	ens_1	LEU	CYS	G	125 - 129
d_7	9	ens_1	GLU	ALA	G	132 - 135
d_7	10	ens_1	VAL	GLU	G	137 - 139
d_7	11	ens_1	ASN	GLN	G	144 - 154
d_8	1	ens_1	SER	LYS	H	2 - 48
d_8	2	ens_1	ASN	GLY	H	50 - 51
d_8	3	ens_1	ILE	GLU	H	53 - 69
d_8	4	ens_1	VAL	LEU	H	71 - 89
d_8	5	ens_1	TYR	ALA	H	91 - 105
d_8	6	ens_1	ASN	GLY	H	109 - 118
d_8	7	ens_1	PRO	GLY	H	120 - 123
d_8	8	ens_1	LEU	CYS	H	125 - 129
d_8	9	ens_1	GLU	ALA	H	132 - 135
d_8	10	ens_1	VAL	GLU	H	137 - 139
d_8	11	ens_1	ASN	GLN	H	141 - 151

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.998782668342, -0.0488332071929, -0.006964143521), (-0.0488270316925, 0.998806692892, -0.00105413947877), (0.00700731017062, -0.000712817785001, -0.99997519444)	43.1923728806, 1.24732958191, 31.8833466596
2	given	(0.110328985629, -0.98487623634, 0.133590097023), (0.989308461301, 0.0959252172104, -0.109850448802), (0.095374437502, 0.144281501919, 0.984929725856)	-14.4960222595, -38.1849328979, -13.6770975506
3	given	(-0.157912892627, 0.978547505722, -0.132318923013), (0.982975102535, 0.143032052526, -0.115333341872), (-0.0939333068689, -0.148278828547, -0.984474439925)	59.5440143921, -36.2644185612, 45.8509719637
4	given	(0.0228387154739, -0.0140930965429, -0.999639823989), (-0.222571932433, 0.974734464619, -0.018827065008), (0.974648720293, 0.222921753343, 0.0191249553685)	61.8815204133, -32.2743245543, -6.91557488695
5	given	(-0.0323065097333, 0.0101104416702, 0.99942686996), (0.14352091018, 0.989632704338, -0.00537204292965), (-0.989119829834, 0.143265102078, -0.0334226383859)	-37.3589222613, -40.3736622886, 35.5629158841
6	given	(0.0839664403234, 0.182356718262, 0.979640579092), (0.994960433325, -0.0694113348167, -0.0723588468409), (0.0548030383883, 0.980779329872, -0.187265942124)	-50.2752688528, -82.0884510093, 44.0701463321
7	given	(-0.0874723482952, -0.174570289708, -0.980751651661), (0.946530098725, 0.29233677287, -0.13645506013), (0.310530772212, -0.940247002218, 0.139664649536)	74.8282870617, -67.9509807976, -30.0533951171

-
Components

#1: Protein	CirpA3 Mass: 19122.100 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhipicephalus pulchellus (arthropod) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, 30% (w/v) PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.1→68.33 Å / Num. obs: 78899 / % possible obs: 99 % / Redundancy: 3.4 % / CC_1/2: 0.991 / Net I/σ(I): 5.1
Reflection shell	Resolution: 2.11→2.14 Å / Num. unique obs: 11656 / CC_1/2: 0.471

-
Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
Coot		model building
PHENIX	1.18rc4_3812	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: CirpA1

Resolution: 2.1→62.25 Å / Cross valid method: FREE R-VALUE / Phase error: 31.4472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2504	3223	5.32 %
R_work	0.217	57306	-
obs	0.2218	60529	75.38 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→62.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9935	0	5	711	10651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	10148
X-RAY DIFFRACTION	f_angle_d	0.5313	13672
X-RAY DIFFRACTION	f_chiral_restr	0.0456	1407
X-RAY DIFFRACTION	f_plane_restr	0.003	1818
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8165	3750

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	B	X-RAY DIFFRACTION	Torsion NCS	0.551172516361
ens_1	d_3	B	X-RAY DIFFRACTION	Torsion NCS	0.679551702071
ens_1	d_4	B	X-RAY DIFFRACTION	Torsion NCS	0.770527807564
ens_1	d_5	B	X-RAY DIFFRACTION	Torsion NCS	0.553848935171
ens_1	d_6	B	X-RAY DIFFRACTION	Torsion NCS	0.430795804876
ens_1	d_7	B	X-RAY DIFFRACTION	Torsion NCS	0.681371969605
ens_1	d_8	B	X-RAY DIFFRACTION	Torsion NCS	0.723289356428

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 (%)
2.1-2.14	0.386	57	0.2832	1221	X-RAY DIFFRACTION	30.14
2.14-2.18	0.2752	47	0.2767	1336	X-RAY DIFFRACTION	33.99
2.18-2.22	0.3211	88	0.2721	1576	X-RAY DIFFRACTION	39.16
2.22-2.26	0.3303	93	0.2643	1741	X-RAY DIFFRACTION	43.57
2.26-2.31	0.2949	100	0.2619	1953	X-RAY DIFFRACTION	48.67
2.31-2.37	0.2802	128	0.2656	2214	X-RAY DIFFRACTION	54.83
2.37-2.42	0.3357	143	0.2675	2407	X-RAY DIFFRACTION	60.17
2.42-2.49	0.277	142	0.2699	2631	X-RAY DIFFRACTION	66.61
2.49-2.56	0.292	165	0.2602	2853	X-RAY DIFFRACTION	70.85
2.56-2.65	0.2802	149	0.2592	3091	X-RAY DIFFRACTION	76.53
2.65-2.74	0.2818	166	0.2565	3220	X-RAY DIFFRACTION	80.54
2.74-2.85	0.2933	190	0.2546	3435	X-RAY DIFFRACTION	85.28
2.85-2.98	0.3222	209	0.2459	3606	X-RAY DIFFRACTION	89.9
2.98-3.14	0.2581	194	0.2331	3719	X-RAY DIFFRACTION	93.63
3.14-3.33	0.2987	188	0.2254	3747	X-RAY DIFFRACTION	93.96
3.33-3.59	0.2426	217	0.2123	3766	X-RAY DIFFRACTION	92.55
3.59-3.95	0.2086	199	0.2004	3672	X-RAY DIFFRACTION	91.78
3.95-4.52	0.2288	213	0.1755	3686	X-RAY DIFFRACTION	91.49
4.52-5.7	0.1932	208	0.177	3756	X-RAY DIFFRACTION	92.63
5.7-62.25	0.2288	183	0.2034	3820	X-RAY DIFFRACTION	93.74

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	2.35212000149	-1.41630997109	1.80068195722	1.7311428131	-0.106218908162	2.1353217142	0.127015121484	0.579322544085	0.0118312288493	-0.165593718712	-0.352441622702	-0.0623790862164	0.0105307748251	0.154011740797	0.260560475145	0.118527832226	0.0111504291328	0.0408675492416	0.341941714598	0.0603367779995	0.256475597607	1.94563824096	-47.7972453183	-9.77681759176
2	2.25002943072	1.07031370712	0.352113911568	2.2694685703	3.3029470209	7.92504698936	-0.0300848336305	0.182519104437	-0.242081258616	0.193304746909	-0.236898727935	0.0254398285992	0.460264237561	-0.247226558673	0.218485056059	0.153466517816	0.0414183383113	0.0251401808995	0.196685062947	0.0445471202507	0.190826977627	-0.894137980871	-53.4584915631	-3.50266180816
3	8.84868546529	-0.913634529845	3.31042602917	4.75123597775	-0.209837201889	7.32992456275	0.110653087599	-0.254696341707	-0.608134657447	0.504639691237	0.013054859977	0.0652204761089	0.138678246712	-0.0974554416965	-0.130853330702	0.192137186718	0.0318896939973	0.0283539582686	0.217710492843	-0.05268082374	0.184502974079	-2.29080575726	-58.7418732577	-2.17660634049
4	5.91524234394	-1.29809696657	-1.10834537072	9.11152103147	5.33447967624	3.12356028277	0.544059988678	0.204822161181	0.737346424917	-1.00244528888	-0.119448523272	0.687338843352	-1.57727916582	0.602453281711	-0.354745850544	0.298081484084	0.0170069797938	0.0239977132657	0.737240439223	0.145191804029	0.260233323823	-15.5473881467	-41.3451569632	-12.7167716392
5	2.47352546113	0.963467657586	-1.63351258472	1.58101419779	-0.197353114198	1.53558267189	-0.130100498937	-0.403985686325	-0.041677360083	-0.0884094954022	0.0327437870758	-0.0667617733537	0.0858005988921	-0.0740404896335	0.0975571358027	0.111756987856	0.0510822921124	-0.0203229233946	0.354063968717	0.0408652578333	0.195021407701	-0.511631139504	-45.7650766918	-3.30749515288
6	3.18105386494	-0.844789364939	-4.52875567598	8.04125034679	-1.68046348587	7.8830122087	-0.170071232852	0.544176450862	-0.0984911450287	0.377566890964	-0.30412991578	-0.147830551233	-0.0351474585355	0.942135377739	0.415104779935	0.134508724308	-0.0200844461065	-0.0171152288271	0.531656279827	0.0698691580255	0.261048762227	6.30912761994	-34.5885117938	-1.87090497371
7	6.85252476376	-3.91711018067	-0.247939512511	7.75166030222	-0.559056905513	5.15035295733	-0.652533253281	-0.496056779654	0.274471063855	1.33655644242	0.664221923505	0.298745095146	-0.167295289991	0.549513824852	0.125557121547	0.393142104234	-0.0654814801357	0.024971494143	0.216734269007	0.0633631942279	0.251848091089	7.66536678253	-45.0435314936	5.61380048324
8	4.47857031426	-0.129392590392	0.276197322541	1.20591158547	0.474954207287	3.02591889485	0.174348974836	-0.307536411241	0.221956559446	0.00582035653205	-0.0389740472818	0.000186745371712	0.124559420554	0.344105599062	-0.110929659852	0.334961284978	-0.0488357628285	0.070423185247	0.149141624069	-0.0544168812151	0.152815751281	37.3467013972	-13.2354753058	40.9810257165
9	7.09970736324	2.34381377038	-6.39860128337	6.96823637198	-3.31587269642	7.73644404615	-0.277535086739	-0.140910105226	-0.910808513407	-0.197399261713	-0.409121318876	-0.796774061052	0.465374326979	0.492489492184	0.709100452781	0.201894670962	0.00570414704133	0.028545647863	0.277162167581	-0.0369369785135	0.334389399388	44.0693257112	-22.3597927727	34.6835166846
10	4.71063939247	0.431503793243	-2.29399347423	3.16953698285	-0.845597583417	7.20605498819	-0.603101723351	-0.354436169448	-0.202593546981	-0.278423408001	0.474966670644	0.481444113096	1.23779737442	0.17499987347	0.111679258123	0.389772691853	0.0254912366084	0.0845124287457	0.149488624418	-0.0499156613079	0.370612436757	33.4959019477	-23.2883663354	36.3273765588
11	2.82186462721	-0.570132861305	-1.37529223386	2.74893999534	-1.42405479423	3.20790372742	0.328866007935	0.909134563081	0.00338044761896	-0.403111496947	0.128113655255	-0.0297924129654	0.33025149548	0.942635653983	-0.313559877594	0.128478057502	0.0217439469556	0.178834356712	0.936062824374	-0.0887712209374	0.161737742251	40.8620780303	-11.6693797414	25.7558822456
12	2.22904723839	2.70260414971	-0.0991234485058	6.38109365143	1.4099913934	4.41418317481	-0.117832956274	-0.464265227174	-0.0968079929145	-0.319544953689	0.0986878038354	-0.468732387152	-0.230262067457	0.397078495182	0.0205696645829	0.145475065666	0.0544873636862	0.055463119894	0.214003453501	-0.0295008738476	0.341956594025	41.9704459367	-8.35729622966	37.7725669706
13	4.07702494569	-0.684320055704	0.28207202293	1.63185984356	0.386714576861	0.536620960488	-0.0753089028198	-0.200899693235	0.121975585474	0.207229852458	0.00465604242948	-0.0582588304374	0.123615106938	0.0859871000335	0.0663755271006	0.227884875568	0.000330120928653	0.0485451966631	0.1136985035	0.0181567206842	0.129566718987	34.78844045	-9.60130424475	41.3351424324
14	9.7758372083	-4.69658680884	3.99875604185	6.74910272604	-5.66820597162	4.73590072439	-0.132468053412	-0.988678878385	1.25932917191	-0.134899717014	-0.385942288975	-0.506243445285	0.121971193005	-0.598358353992	0.470034165867	0.327990242033	-0.117655056506	0.00543517172552	0.340942096008	-0.149957204151	0.357567573533	36.2302713476	1.21115736052	44.2598408069
15	5.36655743716	-2.95316423058	1.49646429642	5.81140533541	-4.80952082755	8.20737046599	0.0313725810677	0.339661082588	-0.678641377759	0.397084425819	-0.474413513845	0.765244003262	0.134310007121	0.170276050658	0.42860297106	0.273233564852	-0.036351994308	0.112083642261	0.314718130786	-0.102462792499	0.303232787436	28.5384782083	-13.3965921897	49.1858615409
16	4.76806615389	1.17234325545	-1.84059447635	2.80179328395	0.12636933317	3.5937726094	-0.150636731799	0.175352296397	0.0721890883741	-0.0664289602654	0.110936536772	0.227977693094	0.115280387843	-0.177678563729	0.0484490302481	0.1439091976	0.0271863659782	-0.0243023031536	0.12939327203	0.0249812602184	0.124166613391	6.24831244797	-13.8283271623	-8.8157286207
17	4.22535492004	-0.091213184112	3.64838609899	3.72988420084	-0.192532790245	6.34272916567	0.000932012669096	-0.78919613068	-0.219294476071	-0.684098350442	0.334203272013	0.102148400059	-0.596685986548	-1.75851751937	-0.0410111568045	0.221270475842	-0.250334630411	-0.0911812910203	0.0196345019544	-0.10361601817	0.259453698207	-0.101054470964	-23.3218786619	-2.579958361
18	5.04153020412	-1.09567528989	-4.1186639257	5.18945649684	2.59315418052	8.98713346819	-0.347403403013	-0.294222379609	-0.385015675901	-0.345267211944	0.110181383864	-0.335640196578	0.236770727567	0.828162040777	0.228793546793	0.253947451417	-0.00802692872333	0.00680173916356	0.163260419334	0.0399167707403	0.216537405105	10.5562527784	-23.7075713176	-4.3277075705
19	0.897908281236	-0.040789594969	0.877384985117	3.64500147338	-2.30992153059	2.21220292776	-0.922785685108	-0.56562923307	0.839561715292	1.35832714712	-0.0366437836261	0.782539107312	-1.19862840023	-1.95313621318	0.599599221541	0.221109640777	0.217555242922	0.154005685296	1.11351424927	-0.15225522255	0.384521902984	-3.48833434478	-8.76110151107	8.77457945282
20	2.0694587242	-2.92521842618	-3.16433962455	2.03017519131	0.766132513524	4.49198535188	-0.198876970322	-1.23260724075	-0.696310520107	0.466584263056	0.532878446424	-1.25812841822	-0.610017856737	0.33970008527	-0.407871057023	0.445650127962	-0.0172186414148	-0.102338214043	0.527179565628	-0.117909344386	0.438438639547	10.816217358	-17.3550159458	3.41656923289
21	2.9817306853	0.644252866113	3.23356608335	4.05411584081	-0.0113231680757	8.06986520607	-0.147827714186	0.580186922922	-0.0969894638464	-0.0610621020396	0.106292139386	0.399531502196	-0.560223106827	-0.337331032616	0.0312278126977	0.184375150821	0.0902822517669	0.0118400013341	0.272188580379	-0.0181287428515	0.221563947793	1.45288681449	-9.26536207523	-5.70143816772
22	2.19527668084	0.723326069053	2.06338796331	1.8904995303	0.172636701711	2.20445769974	-0.033474655401	-0.202670226034	0.0745023720543	-0.247423820033	0.0621170961033	0.0370256575889	-0.322408121715	-0.213817866061	-0.0119440772898	0.196697051407	0.0266865378053	0.0476668570553	0.155019745634	0.00543197570679	0.14875809191	8.692943835	-10.0759402684	-9.13804490611
23	7.36795885497	6.94093907665	3.49089309791	8.74656872466	1.97694661175	2.41064959036	1.09741800825	-1.26131298357	1.45260515982	0.102586640788	-0.602653399129	0.0813974728074	-0.735868676887	-0.17999191108	-0.259021477615	0.617063308458	0.0467279193545	0.223855327499	0.449649246806	-0.010740554404	0.451841286565	6.16022205168	0.385578267109	-12.4151944182
24	6.67912649858	-1.93037478372	-1.63993595159	8.22630895393	5.15025409942	6.04182665543	0.326643838981	-1.07312443588	0.111970255841	0.750085668032	-0.803107152772	-0.58497679001	0.422634533695	-0.22217573307	0.319513916299	0.22539266311	-0.0785307062965	-0.0143363065414	0.583530052006	0.0617777030337	0.369297314647	14.6527070505	-12.0076446736	-16.1065918705
25	4.49074301198	1.35779734231	-0.940192828893	2.33859546537	-0.249032851599	3.38232206309	0.0867882093579	0.0817050244428	0.0944932879882	-0.0746632820812	0.0639048612349	-0.05151408219	-0.217159941555	-0.203610447427	-0.0931451210823	0.186482466345	0.0396444184148	0.0201062356657	0.168318745767	-0.00237276248358	0.0993754394016	13.0288258751	-7.53124415754	24.8025748529
26	7.2752885839	1.68249672019	-2.82102935399	3.19015804419	4.85513434055	2.01062266512	-0.181703241135	0.804634730065	1.1666433587	-0.69469696064	0.209518706156	0.6146549476	-1.12233628601	-1.75605581251	0.0455359215365	0.703001895244	0.134473905303	0.0761705995602	0.3663559417	0.116882487706	0.664873746574	1.12269559732	4.9176070512	13.2529134911
27	1.96633175363	1.44208973175	1.73412568262	2.4763672101	-0.249540904209	6.13341840959	0.00299046410123	-0.0438536047378	0.113042709778	0.0980638916097	0.035223833572	0.094189040185	-0.241968835502	-0.300458003176	-0.0315949051344	0.150172191799	0.0725439102031	0.0142314050493	0.215085738098	0.00958416847733	0.169853732089	4.95708517897	-7.46788831549	25.9076429464
28	1.54587135766	2.35415604809	0.254631832023	2.08884783817	1.1131681287	0.28103287849	-0.322603472245	-0.53224677677	0.42334655172	-0.110432411402	0.270561631111	2.49417446386	-0.269167132208	-0.637979213605	0.0473813263126	0.279596777487	0.0337830956269	0.0131758467015	0.981033797495	0.141751533393	0.673269900666	-5.51757100891	-6.65880100559	34.1861305304
29	3.39132517681	-0.503850554957	-0.85356573788	5.13044621051	-0.413637952311	4.99238560603	0.375442962138	0.050998434593	-0.211643121497	-0.444456870458	-0.217394600733	0.153990963484	0.0154479852734	-0.960739302086	-0.160798614325	0.367126748623	-0.0285576277892	0.0498068510392	0.374020573061	0.007289740929	0.182354267202	4.75137300967	-16.5522048215	33.3012978228
30	5.31875016596	-0.0946604534722	-0.199536455937	2.14058230207	0.0350636285916	5.05655511402	0.0754046761755	-0.0800896562879	0.128345055466	0.08153801868	-0.052062433796	0.0429081599984	-0.0463878653148	0.271243989625	-0.0144076435653	0.270502392514	-0.0425263810785	0.0547549578697	0.178959073899	-0.013705813611	0.111249529679	30.566837354	-6.88939518708	7.56650855738
31	7.45432941705	-3.02981134054	0.442370996809	4.61043278547	-5.25368440749	7.61584634759	-1.26669609747	-1.2068646493	1.98298501814	1.53635686717	0.445858099345	-0.563941311493	-2.32856359288	1.80266698963	0.716145712199	1.12646054795	-0.165602012967	0.0904735352453	0.602952575609	-0.184275354958	0.816098232835	41.5665707957	6.18168134624	19.35862702
32	3.12436445066	-1.45357688231	0.0220945207567	2.60728250116	-0.165928742131	4.30162732606	-0.0911265404653	0.167128526445	0.0851858227181	-0.14030024305	0.0946488855629	-0.108820314728	-0.0515109892113	0.367570519779	-0.010593404823	0.266591198536	-0.0707947588604	0.0242860463084	0.24751373971	-0.0692474814453	0.159904654001	38.4227345013	-6.54851600389	6.30298678534
33	5.0236125324	-1.67084735714	-1.55952181363	5.54656061956	-2.04923084892	1.89602243501	-0.138596461687	-0.748636577896	0.498724239639	0.0456087445933	0.515547785857	-1.38264634202	-0.446100194052	0.778665571157	-0.334032404435	0.381156112553	-0.108015142562	0.116640138088	1.03321718573	-0.0818259287076	0.40408085821	48.8016078744	-5.35132087539	-2.04672483839
34	8.2128156781	1.07318759284	-0.88806860473	4.75721623896	-0.211996838882	0.777894857391	0.203409125163	0.677364057089	-0.621437457348	-0.832861053214	-0.00854665861159	-0.340104382265	0.0136901735159	1.08535248398	-0.198630589522	0.305222444851	0.0267964858529	0.113725120236	0.5870319405	-0.0411028983771	0.199015329973	36.9263589238	-14.9776166958	-2.36473776199
35	2.21186379935	0.466670206594	-1.0995696247	3.93177918775	-0.815980199299	2.98832009426	0.0344805295453	-0.289575032851	0.0285451622137	0.455056192246	-0.00682655113568	0.0310617697262	-0.111847799436	0.0643012820163	-0.0207450696327	0.169544192059	0.0237322910023	-0.0300783405836	0.19365021474	0.0144960434129	0.196011491158	21.8055521544	-54.3226252709	27.3267563014
36	4.8607777515	0.616646123881	-1.03993279024	5.37291823727	-1.62021729788	1.32166562328	-0.275791875385	-0.700604782944	-0.365930202695	0.255888232785	0.272118477683	-0.188594920824	-0.286083024776	-0.107938409506	-0.0618466370674	0.179875822195	-0.0220132840817	0.0136650516574	0.543466286473	0.167156800083	0.23138926143	28.4834617566	-64.652239692	31.8225756478
37	8.18199884841	0.557027218809	2.36402197176	4.42586169129	-1.30996755553	4.39578495433	-0.17146214162	0.524938341804	-0.871115188961	-0.301954544463	0.244066154037	-0.0227414247634	-0.206232230454	0.0205641566812	-0.0835741432947	0.261585621865	-0.0255468836039	0.0304331104634	0.0868694608681	0.0716106887372	0.276982752409	26.707249367	-63.0231916692	21.2617754805
38	8.76150193522	-3.16537624129	-5.39553965324	4.94494523129	1.15749904902	3.45224122821	0.210780169774	-2.11624565948	1.28341180222	0.46276988192	-0.23362435432	-1.08465409447	-0.866949946082	-0.554227460166	0.126669207926	0.622966039131	-0.0977110469923	-0.204443626235	0.969421704471	0.119208099983	0.254016358603	39.5463928666	-50.5561669508	37.629758127
39	5.21373311621	-1.03210899674	0.788958849915	2.4526126664	-0.153870929011	2.3070185378	0.00567698036417	-0.503854027548	0.0420283125191	-0.0394402602494	-0.102034837726	-0.20453970448	-0.00408367508646	0.260210672456	0.115481333548	0.284082153214	-0.0582401875551	-0.0307113925463	0.150611521742	0.0959938805895	0.237274661086	28.4970522609	-52.8839956005	28.732060974
40	1.72458567881	0.524236472451	-0.57215203812	1.24704301635	-0.163013548683	2.01918489978	-0.242154915225	-0.402284758655	0.372504332292	-0.219843245532	-0.174129866936	-0.0526152618377	-0.274016777385	-0.172323001861	0.332986688354	0.335824264273	0.0469490368361	-0.0634029456998	0.152326471316	0.0469762547611	0.206413130859	26.5660763744	-49.2012902127	23.9826832577
41	2.59027939253	-1.91435744765	2.30134089518	1.4084824345	-1.70935812268	1.99532277867	0.459040550396	0.825802520833	0.0994510656615	0.479443649916	-0.394041814239	0.727772030984	0.252926318484	-0.564793863147	-0.0200381772196	0.160968430272	0.07202586818	0.0686833670265	0.530540187153	-0.00533518218645	0.375699269553	8.95271901833	-52.3265201256	29.5868439649
42	9.10200543365	2.14388602651	2.38332772342	4.17024382454	-4.67708844212	8.16487045142	0.457964369213	-1.23501620686	1.24966784431	-0.333605954221	0.134446527676	-0.630857901579	-2.1800469414	-1.58447836425	-0.102969713177	0.804125938579	0.150169663392	0.174200761212	0.24429233296	-0.311710274354	0.71689210068	18.2722573813	-40.3706191335	29.7664517256
43	3.49589323544	-2.70419654326	-1.77262768264	2.08060148607	1.00534865038	7.32667336227	0.405199528762	-0.259515255709	-0.187553002174	0.000720005973616	-0.249911477324	-0.370800361089	-0.0327311479681	0.96912523379	-0.0886807474216	0.431267184206	0.162724536898	-0.0894694463123	0.376891433816	0.119448117218	0.276566646717	14.6240455925	-51.0801881734	19.3919059034
44	3.17733240736	0.0853893435756	0.133505296303	3.30858197609	-0.45007537614	3.24742097743	-0.177783482206	-0.334065097016	0.0834382295476	0.423236956905	0.11412266387	0.24107730827	-0.109429698051	-0.302698367362	0.0794146662489	0.161014106988	0.051166386067	0.0191344870224	0.26851126692	0.0200777431992	0.163166589856	-14.8947293515	-45.1446529667	22.8470010593
45	6.27554874378	1.35370084204	-0.567288906284	5.29212564322	-1.08297521726	2.3871119851	-0.143655357689	-0.560004937812	0.131371635808	0.308745716186	0.04352801694	0.0315994915969	0.149747742194	0.113845994035	0.085918668001	0.181690991071	0.0658281276806	0.0314591832345	0.435847393467	-0.0120383240586	0.142741868101	-14.671168948	-48.2273245805	29.2646991716
46	2.85987355676	-0.162536751905	0.365195983438	4.55819266977	-0.499543289127	5.6353091702	-0.103266103055	-0.865859732976	-0.181266499248	0.659022331245	-0.0521034609429	-0.097889364993	0.308737370964	0.369996282288	0.133993075889	0.2546809376	0.0899126975317	-0.00507356552124	0.455397556315	0.0727501749859	0.292394407086	-1.83397094574	-52.0257643865	30.8513602315
47	3.82870182013	-0.259164358117	-0.666315045267	2.18833397207	1.21579473632	3.92723575965	0.0777779836945	-0.263864564661	-0.0719417516346	0.00981200261764	-0.0508895580093	-0.00485708781955	-0.0432645862939	0.21234492003	-0.0255294183185	0.109179355692	0.0247107082086	-0.010812120721	0.168228561832	0.0627975546198	0.144901358705	37.1800925467	-43.7309480137	4.32897580227
48	2.31196917136	-1.19815210554	2.46147254634	1.42710930469	0.176831212949	5.13359103507	0.000969672648583	1.14328881478	2.54206232908	-1.06258717749	0.326530271319	-1.01466675695	-2.26008933017	0.947447129992	-0.168765173633	0.756696507764	-0.262285180939	0.227121079765	0.488744631102	0.2245984342	1.10317412937	48.6765133174	-29.2765738902	-4.31722166965
49	4.8376543627	-1.57158105355	-2.20306831582	4.03921637891	1.80606531273	4.22213649256	-0.0967303597876	-0.164572919404	-0.176028164103	0.0866126246021	0.216366662821	0.225561478352	0.0361314891051	0.0475748423048	-0.133169484796	0.128277837131	-0.0175068669328	0.0100585001992	0.163759152881	0.0534962614743	0.209947480669	38.9087375897	-41.937362587	-4.22706497038
50	4.71302422784	-1.16144367787	-0.19127794753	5.49239875619	-0.514462883166	6.15584138698	0.218606184975	0.65586383628	-0.0851853470554	-0.349025528312	-0.372509382836	-0.0779016598825	0.115933352728	-0.0181532763998	0.0981277932962	0.135768795125	0.0163654583707	-0.0154322008281	0.204262111688	0.00914431185277	0.233071471315	25.6038039211	-44.2764013963	-6.25006698775

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 'F' and (resid 48 through 66 )	F	A	48 - 66	1 - 20
2	2	chain 'F' and (resid 67 through 85 )	F	A	67 - 85	21 - 39
3	3	chain 'F' and (resid 86 through 108 )	F	A	86 - 108	40 - 62
4	4	chain 'F' and (resid 109 through 119 )	F	A	109 - 119	63 - 73
5	5	chain 'F' and (resid 120 through 176 )	F	A	120 - 176	74 - 126
6	6	chain 'F' and (resid 177 through 188 )	F	A	177 - 188	127 - 138
7	7	chain 'F' and (resid 189 through 203 )	F	A	189 - 203	139 - 155
8	8	chain 'A' and (resid 48 through 75 )	A	B	48 - 75	1 - 29
9	9	chain 'A' and (resid 76 through 85 )	A	B	76 - 85	30 - 39
10	10	chain 'A' and (resid 86 through 108 )	A	B	86 - 108	40 - 62
11	11	chain 'A' and (resid 109 through 129 )	A	B	109 - 129	63 - 83
12	12	chain 'A' and (resid 130 through 143 )	A	B	130 - 143	84 - 97
13	13	chain 'A' and (resid 144 through 176 )	A	B	144 - 176	98 - 126
14	14	chain 'A' and (resid 177 through 189 )	A	B	177 - 189	127 - 139
15	15	chain 'A' and (resid 190 through 203 )	A	B	190 - 203	140 - 151
16	16	chain 'B' and (resid 48 through 75 )	B	C	48 - 75	1 - 29
17	17	chain 'B' and (resid 76 through 85 )	B	C	76 - 85	30 - 39
18	18	chain 'B' and (resid 86 through 108 )	B	C	86 - 108	40 - 62
19	19	chain 'B' and (resid 109 through 119 )	B	C	109 - 119	63 - 73
20	20	chain 'B' and (resid 120 through 129 )	B	C	120 - 129	74 - 83
21	21	chain 'B' and (resid 130 through 143 )	B	C	130 - 143	84 - 97
22	22	chain 'B' and (resid 144 through 176 )	B	C	144 - 176	98 - 126
23	23	chain 'B' and (resid 177 through 188 )	B	C	177 - 188	127 - 138
24	24	chain 'B' and (resid 189 through 203 )	B	C	189 - 203	139 - 151
25	25	chain 'C' and (resid 48 through 108 )	C	D	48 - 108	1 - 62
26	26	chain 'C' and (resid 109 through 119 )	C	D	109 - 119	63 - 73
27	27	chain 'C' and (resid 120 through 176 )	C	D	120 - 176	74 - 126
28	28	chain 'C' and (resid 177 through 188 )	C	D	177 - 188	127 - 138
29	29	chain 'C' and (resid 189 through 203 )	C	D	189 - 203	139 - 153
30	30	chain 'D' and (resid 48 through 108 )	D	E	48 - 108	1 - 62
31	31	chain 'D' and (resid 109 through 119 )	D	E	109 - 119	63 - 73
32	32	chain 'D' and (resid 120 through 176 )	D	E	120 - 176	74 - 126
33	33	chain 'D' and (resid 177 through 188 )	D	E	177 - 188	127 - 138
34	34	chain 'D' and (resid 189 through 203 )	D	E	189 - 203	139 - 151
35	35	chain 'E' and (resid 48 through 75 )	E	F	48 - 75	1 - 29
36	36	chain 'E' and (resid 76 through 85 )	E	F	76 - 85	30 - 39
37	37	chain 'E' and (resid 86 through 108 )	E	F	86 - 108	40 - 62
38	38	chain 'E' and (resid 109 through 119 )	E	F	109 - 119	63 - 73
39	39	chain 'E' and (resid 120 through 143 )	E	F	120 - 143	74 - 97
40	40	chain 'E' and (resid 144 through 166 )	E	F	144 - 166	98 - 117
41	41	chain 'E' and (resid 167 through 176 )	E	F	167 - 176	118 - 126
42	42	chain 'E' and (resid 177 through 188 )	E	F	177 - 188	127 - 138
43	43	chain 'E' and (resid 189 through 203 )	E	F	189 - 203	139 - 151
44	44	chain 'G' and (resid 48 through 119 )	G	G	48 - 119	1 - 73
45	45	chain 'G' and (resid 120 through 166 )	G	G	120 - 166	74 - 117
46	46	chain 'G' and (resid 167 through 203 )	G	G	167 - 203	118 - 154
47	47	chain 'H' and (resid 48 through 107 )	H	H	48 - 107	1 - 61
48	48	chain 'H' and (resid 108 through 119 )	H	H	108 - 119	62 - 73
49	49	chain 'H' and (resid 120 through 166 )	H	H	120 - 166	74 - 117
50	50	chain 'H' and (resid 167 through 203 )	H	H	167 - 203	118 - 151

+
About Yorodumi

-
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