PDB-2noj: Crystal structure of Ehp / C3d complex

ID or keywords:

Entry

Database: PDB / ID: 2noj

Title

Crystal structure of Ehp / C3d complex

Components

Complement C3
Efb homologous protein

Keywords

IMMUNE SYSTEM / PROTEIN-PROTEIN COMPLEX

Function / homology

Function and homology information

oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function

Extracellular fibrinogen binding protein, C-terminal / Efb, C-terminal domain superfamily / Extracellular fibrinogen binding protein C terminal / Sbi, C3 binding domain IV / Sbi, C3 binding domain IV / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Staphylococcus aureus subsp. aureus Mu50 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Hammel, M. / Geisbrecht, B.V.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus.
Authors: Hammel, M. / Sfyroera, G. / Pyrpassopoulos, S. / Ricklin, D. / Ramyar, K.X. / Pop, M. / Jin, Z. / Lambris, J.D. / Geisbrecht, B.V.

History

Deposition	Oct 25, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 22, 2020	Group: Database references / Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif Item: _struct_ref_seq_dif.details
Revision 1.3	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2noj.cif.gz	259.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2noj.ent.gz	205.5 KB	Display	PDB format
PDBx/mmJSON format	2noj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2noj_validation.pdf.gz	498.5 KB	Display	wwPDB validaton report
Full document	2noj_full_validation.pdf.gz	545.4 KB	Display
Data in XML	2noj_validation.xml.gz	52.7 KB	Display
Data in CIF	2noj_validation.cif.gz	71.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/no/2noj ftp://data.pdbj.org/pub/pdb/validation_reports/no/2noj	HTTPS FTP

-
Related structure data

Related structure data	2goxS S: Starting model for refinement
Similar structure data	3nj3-1 6hm2-2 3niy-2 5ay7-2 5drb-d 1y6j-d 6hly-d 4u0t-2 5ylc-d 3mvh-d 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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2goxS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (1) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1) #189 - Sep 2015 Amyloids similarity (1) #217 - Jan 2018 Opioid Receptors similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #25 - Jan 2002 Thrombin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #224 - Aug 2018 Legumain similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #56 - Aug 2004 Caspases similarity (1) #149 - May 2012 Leptin similarity (1) #83 - Nov 2006 Fibrin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#201 - Sep 2016
Isoprene Synthase
similarity (1)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#96 - Dec 2007
Oxidosqualene Cyclase
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#217 - Jan 2018
Opioid Receptors
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#25 - Jan 2002
Thrombin
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#56 - Aug 2004
Caspases
similarity (1)
#149 - May 2012
Leptin
similarity (1)
#83 - Nov 2006
Fibrin
similarity (1)

Deposited unit

A: Complement C3

B: Efb homologous protein

C: Complement C3

D: Efb homologous protein

E: Complement C3

F: Efb homologous protein

G: Complement C3

H: Efb homologous protein

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

1

A: Complement C3

B: Efb homologous protein

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

2

C: Complement C3

D: Efb homologous protein

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

3

E: Complement C3

F: Efb homologous protein

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

4

G: Complement C3

H: Efb homologous protein

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

Unit cell

Length a, b, c (Å)	67.894, 91.025, 122.595
Angle α, β, γ (deg.)	90.00, 89.93, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological assembly is a tetramer in the asymmetric unit

#1: Protein	Complement C3 Mass: 33143.879 Da / Num. of mol.: 4 / Fragment: Residues 996-1287 / Mutation: C1010A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C3 / Plasmid: pT7- / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01024
#2: Protein	Efb homologous protein Mass: 9596.170 Da / Num. of mol.: 4 / Fragment: Residues 30-109 / Mutation: N63E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Species: Staphylococcus aureus / Strain: Mu50 / ATCC 700699 / Gene: SAV1155 / Plasmid: pT7HMT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q99UV2, UniProt: A0A0H3JUX1*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.51 %
Crystal grow	Temperature: 293 K / pH: 8.2 Details: 0.2M LiSO4, 25% PEG 3350, 0.1M Tris-HCl pH 8.2, additive: CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2006 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.699→50 Å / Num. obs: 33242 / % possible obs: 80.8 % / Redundancy: 2.5 % / R_merge(I) obs: 0.189

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2GOX

2gox

Resolution: 2.7→50 Å / Cor.coef. F_o:F_c: 0.891 / Cor.coef. F_o:F_c free: 0.891 / SU B: 31.446 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.284	1655	5 %	RANDOM
R_work	0.291	-	-	-
obs	0.29	31582	80.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 48.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.04 Å²	0 Å²	-0.33 Å²
2-	-	-2.81 Å²	0 Å²
3-	-	-	1.77 Å²

Refine analyze

Luzzati coordinate error obs: 0.4829 Å

Refinement step

Cycle: LAST / Resolution: 2.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9697	0	0	71	9768

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	9882
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.337	1.932	13494
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.112	5	1322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.747	24.457	368
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.184	15	1363
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.481	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1611
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	7484
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.295	0.2	5707
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.332	0.2	7138
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	439
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.287	0.2	125
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.23	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.88	1.5	6676
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.196	2	10436
X-RAY DIFFRACTION	r_scbond_it	2.293	3	3206
X-RAY DIFFRACTION	r_scangle_it	3.481	4.5	3058
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	123	-
R_work	0.334	2087	-
obs	-	-	73.3 %

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	0.312	0.4257	0.1741	1.2484	0.3226	0.108	-0.0341	-0.0187	0.0789	-0.0359	-0.0237	0.0961	0.1007	0.0354	0.0578	0.0842	-0.018	-0.0087	0.0907	0.0244	0.1144	30.9805	2.491	55.6254
2	0.7117	0.7952	1.0037	1.2479	0.4503	2.6697	0.0152	-0.0551	-0.0551	-0.3957	0.1753	-0.0681	0.0587	0.0296	-0.1904	0.1407	0.006	-0.0168	0.0026	-0.0155	0.0712	33.6484	-11.9051	45.6855
3	0.342	-0.25	0.5245	0.2057	-0.2118	2.0904	-0.4651	-0.2304	-0.2177	-0.853	0.2672	0.0609	-0.4312	-0.0343	0.1979	0.3532	-0.1206	-0.0843	0.0137	-0.0459	-0.0829	27.9195	-7.6826	33.7678
4	1.1486	-0.7156	1.1346	0.4476	-0.7538	2.3655	-0.061	-0.2637	-0.1495	-0.237	-0.267	0.3384	-0.2718	0.3462	0.328	0.2104	-0.0849	-0.2257	0.0197	-0.0293	0.0775	20.6196	3.3559	39.0698
5	1.2935	-1.4467	1.5499	1.618	-1.7334	1.8571	0.3973	0.0237	0.7217	-0.3507	-0.1466	-0.5606	0.0899	-0.0451	-0.2507	0.0702	-0.0412	0.0511	0.0682	-0.0007	0.166	47.741	19.0767	49.3375
6	1.5595	-3.1514	0.286	6.4867	-0.1695	1.4616	0.2105	0.1072	-0.0895	-0.5746	-0.0896	-0.0678	-0.2563	-0.0139	-0.121	0.1133	-0.0069	-0.0263	0.0136	0.0399	0.1459	39.4643	16.4479	49.9148
7	0.5353	-0.7163	-0.7869	1.4692	1.2485	1.2316	-0.2825	-0.2378	-0.1678	-0.0739	0.3329	0.1099	0.1216	0.0011	-0.0504	0.0546	0.0101	0.0085	0.0705	-0.0589	0.1301	44.6191	15.7077	58.0551
8	0.9841	-0.0766	0.6189	0.4696	-0.1939	0.4351	-0.025	-0.1076	0.0276	-0.1007	-0.0927	-0.0596	0.0211	-0.0707	0.1176	0.0719	0.0133	0.0198	0.0702	-0.0229	0.1276	36.7974	39.9709	5.7878
9	0.966	0.3516	0.5005	1.1637	-0.9816	1.5669	0.122	-0.0238	-0.143	0.1383	0.0167	0.0711	-0.0066	0.0128	-0.1387	0.0957	0.0471	-0.0473	0.0519	0.0582	0.1082	34.6183	25.1353	15.7439
10	0.7116	0.7521	0.2447	1.3789	0.9656	0.94	-0.1287	0.0417	-0.3103	0.6073	0.1727	-0.1303	-0.101	-0.0637	-0.044	0.2767	0.0446	-0.1013	0.1373	0.1918	-0.1156	39.8756	29.4395	27.4675
11	0.0266	0.0859	0.2956	2.5712	1.6084	3.4758	-0.2013	0.3693	-0.4361	0.4109	-0.3214	-0.1564	-0.6646	-0.0511	0.5227	0.1358	-0.0457	-0.1294	0.1013	0.1035	0.0533	47.4802	40.8694	21.9919
12	7.788	11.9714	-12.55	31.5046	-16.6571	30.4393	-0.8242	-0.6839	0.5102	-0.1414	0.2769	0.6456	-0.59	-0.5866	0.5473	-0.0318	0.1674	0.1867	0.0246	-0.0417	0.0851	16.1544	52.8346	14.0057
13	1.7463	1.7045	-0.4426	1.8299	0.0535	1.531	-0.0374	-0.0822	0.1124	0.1655	0.0383	0.1131	0.081	0.1198	-0.0009	0.08	0.0093	-0.0319	0.0315	-0.0351	0.1632	26.0162	54.0861	10.7411
14	0.1825	0.3818	-0.359	0.799	-0.7512	0.7062	-0.6215	-0.0771	0.154	-0.3172	0.3933	0.0535	0.1513	0.0691	0.2282	-0.0021	-0.028	0.007	0.1205	-0.0328	0.1936	24.6524	54.7882	2.2382
15	0.0333	-0.1231	0.0239	1.4203	0.358	0.2237	-0.0326	-0.011	-0.0508	-0.0279	0.0306	0.0888	-0.007	0.0708	0.0021	0.0649	0.0205	-0.0119	0.0785	0.0159	0.1278	-1.941	-1.9657	6.565
16	2.6288	1.1276	0.1183	0.6577	0.5599	1.4946	-0.0802	-0.1868	0.4081	0.1897	-0.0311	0.2957	0.1679	-0.0889	0.1113	0.1206	0.0696	-0.0156	0.0241	-0.0448	0.1262	-3.5732	11.6985	16.0308
17	0.424	0.6295	-0.5183	1.4462	-0.083	1.555	-0.1537	0.1561	0.1988	0.9641	0.025	0.2653	0.2002	0.1517	0.1287	0.3011	0.0907	0.1688	0.0938	-0.0657	-0.0677	-8.7936	3.8086	26.6818
18	1.0043	1.3205	-0.3394	2.4754	-2.6757	6.8387	-0.1739	0.1664	0.2697	0.3782	-0.2508	0.2146	0.2031	-0.1491	0.4247	0.1757	0.1608	0.1065	0.0605	-0.0515	0.0077	-12.2844	-4.422	16.307
19	3.0264	5.1794	-0.3812	44.7744	6.2697	1.3823	-1.3018	-0.8552	-0.2864	1.9552	1.9157	-0.8204	1.4124	0.3448	-0.614	0.0975	0.1169	-0.1467	0.068	0.0385	0.1072	18.2319	-15.7867	13.6471
20	1.2411	1.0368	0.9312	1.5679	-0.7004	3.8129	-0.1101	-0.2863	0.053	0.0052	0.0735	0.0176	0.1218	0.0629	0.0366	0.1059	0.0493	0.041	-0.0241	0.0213	0.1443	7.7785	-17.4083	10.8681
21	0.9809	2.1168	0.8262	4.5684	1.7831	0.6959	-0.2151	0.4029	0.1131	0.0382	0.415	0.1935	0.0958	0.1394	-0.1999	0.0547	0.0188	-0.013	0.0627	-0.0099	0.1585	9.8841	-17.3206	2.4964
22	4.3309	-3.8976	0.6579	4.2746	-1.1116	0.4518	0.0241	0.1494	-0.214	-0.1548	-0.0973	0.2262	-0.3881	0.4024	0.0732	-0.014	0.0027	-0.0661	0.1072	-0.0127	0.1744	10.4111	-40.2713	58.1189
23	1.056	-0.3013	-0.2412	0.5923	-0.0438	0.0802	-0.0849	-0.0093	-0.0536	-0.064	0.1024	0.1007	0.0208	-0.0233	-0.0175	0.0984	-0.0015	-0.0071	0.0404	-0.025	0.1396	1.9856	-41.1452	54.679
24	0.8673	-0.5099	-0.7144	0.4211	0.4382	0.5912	0.0694	0.1339	0.2335	-0.166	-0.08	-0.0075	0.0161	-0.1306	0.0106	0.0588	0.0063	-0.0269	0.1267	0.1139	0.11	0.2211	-26.9391	41.5433
25	0.0966	0.3566	-0.0104	1.6706	-0.8165	1.7096	-0.2167	-0.4916	0.2571	-0.6549	0.0395	-0.0826	0.4919	0.172	0.1772	0.2277	-0.0618	0.1524	0.0357	0.0815	0.0346	13.8282	-37.8563	37.5048
26	9.2563	-16.9537	14.2113	31.052	-26.0292	21.8188	-0.5112	-0.5744	0.0948	-2.6696	2.7131	-0.125	1.9019	-1.5448	-2.2019	-0.0237	-0.1383	-0.0708	-0.0264	-0.0139	0.2972	-17.6989	-53.5752	47.7128
27	2.4068	-1.4369	1.2072	0.8837	-0.9762	3.1293	0.0049	-0.0856	0.3731	-0.3311	0.4345	-0.3753	0.5723	-0.2349	-0.4394	0.0928	-0.0215	0.0535	0.0108	-0.0578	0.1155	-5.231	-57.4302	50.1626
28	1.2712	-2.2018	0.5598	3.8278	-0.8407	1.4063	-0.2884	-0.0474	0.0766	0.0646	0.2124	-0.2399	-0.1396	-0.1376	0.076	-0.0052	-0.0293	0.0093	0.0969	0.016	0.1834	-10.7463	-53.1324	57.3727

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1001 - 1097	11 - 107
2	X-RAY DIFFRACTION	2	A	A	1098 - 1156	108 - 166
3	X-RAY DIFFRACTION	3	A	A	1157 - 1228	167 - 238
4	X-RAY DIFFRACTION	4	A	A	1229 - 1286	239 - 296
5	X-RAY DIFFRACTION	5	B	B	52 - 67	23 - 38
6	X-RAY DIFFRACTION	6	B	B	68 - 84	39 - 55
7	X-RAY DIFFRACTION	7	B	B	85 - 109	56 - 80
8	X-RAY DIFFRACTION	8	C	C	1001 - 1098	11 - 108
9	X-RAY DIFFRACTION	9	C	C	1099 - 1154	109 - 164
10	X-RAY DIFFRACTION	10	C	C	1155 - 1228	165 - 238
11	X-RAY DIFFRACTION	11	C	C	1229 - 1287	239 - 297
12	X-RAY DIFFRACTION	12	D	D	52 - 59	23 - 30
13	X-RAY DIFFRACTION	13	D	D	60 - 87	31 - 58
14	X-RAY DIFFRACTION	14	D	D	88 - 109	59 - 80
15	X-RAY DIFFRACTION	15	E	E	997 - 1111	7 - 121
16	X-RAY DIFFRACTION	16	E	E	1112 - 1155	122 - 165
17	X-RAY DIFFRACTION	17	E	E	1156 - 1260	166 - 270
18	X-RAY DIFFRACTION	18	E	E	1261 - 1287	271 - 297
19	X-RAY DIFFRACTION	19	F	F	52 - 59	23 - 30
20	X-RAY DIFFRACTION	20	F	F	60 - 86	31 - 57
21	X-RAY DIFFRACTION	21	F	F	87 - 109	58 - 80
22	X-RAY DIFFRACTION	22	G	G	997 - 1019	7 - 29
23	X-RAY DIFFRACTION	23	G	G	1020 - 1097	30 - 107
24	X-RAY DIFFRACTION	24	G	G	1098 - 1193	108 - 203
25	X-RAY DIFFRACTION	25	G	G	1194 - 1286	204 - 296
26	X-RAY DIFFRACTION	26	H	H	52 - 60	23 - 31
27	X-RAY DIFFRACTION	27	H	H	61 - 81	32 - 52
28	X-RAY DIFFRACTION	28	H	H	82 - 109	53 - 80

-
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