PDB-5l6i: Uba1 in complex with Ub-MLN4924 covalent adduct

ID or keywords:

Entry

Database: PDB / ID: 5l6i

Title

Uba1 in complex with Ub-MLN4924 covalent adduct

Components

Ubiquitin-40S ribosomal protein S31
Ubiquitin-activating enzyme E1 1

Keywords

LIGASE / E1 enzyme / ubiquitin activation / Uba1 inhibitor / adenosyl sulfamate

Function / homology

Function and homology information

Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...
Similarity search - Function

Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain ...Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Zinc-binding ribosomal protein / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.76 Å

Authors

Misra, M. / Schindelin, H.

Funding support

Germany, 1items

Citation

Journal: Structure / Year: 2017
Title: Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme.
Authors: Misra, M. / Kuhn, M. / Lobel, M. / An, H. / Statsyuk, A.V. / Sotriffer, C. / Schindelin, H.

History

Deposition	May 30, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	May 8, 2019	Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4	Jan 10, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5l6i.cif.gz	900.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5l6i.ent.gz	745.1 KB	Display	PDB format
PDBx/mmJSON format	5l6i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5l6i_validation.pdf.gz	1011.3 KB	Display	wwPDB validaton report
Full document	5l6i_full_validation.pdf.gz	1 MB	Display
Data in XML	5l6i_validation.xml.gz	79.9 KB	Display
Data in CIF	5l6i_validation.cif.gz	112.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/5l6i ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l6i	HTTPS FTP

-
Related structure data

Related structure data	5l6hC 5l6jC 4nnjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6dc6-1 6o82-1 3cmm-1 5l6j-2 4ii3-1 6zqh-1 3cmm-2 6zqh-2 4ii3-2 6o82-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (16) #60 - Dec 2004 Ubiquitin similarity (7) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (4) #230 - Feb 2019 Initiation Factor eIF4E similarity (5) #245 - May 2020 Spliceosomes similarity (2) #166 - Oct 2013 Proteasome similarity (1)

Deposited unit

A: Ubiquitin-activating enzyme E1 1

B: Ubiquitin-40S ribosomal protein S31

C: Ubiquitin-activating enzyme E1 1

D: Ubiquitin-40S ribosomal protein S31

E: Ubiquitin-40S ribosomal protein S31

hetero molecules

258 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin-activating enzyme E1 1

B: Ubiquitin-40S ribosomal protein S31

hetero molecules

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

2

C: Ubiquitin-activating enzyme E1 1

D: Ubiquitin-40S ribosomal protein S31

E: Ubiquitin-40S ribosomal protein S31

hetero molecules

defined by author&software
133 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.500, 191.890, 230.197
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D
1	3	B
2	3	E
1	4	D
2	4	E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	LEU	LEU	A	A	11 - 1024	11 - 1024
2	1	ALA	ALA	LEU	LEU	C	C	11 - 1024	11 - 1024
1	2	MET	MET	GLY	GLY	B	B	1 - 76	1 - 76
2	2	MET	MET	GLY	GLY	D	D	1 - 76	1 - 76
1	3	MET	MET	ARG	ARG	B	B	1 - 72	1 - 72
2	3	MET	MET	ARG	ARG	E	E	1 - 72	1 - 72
1	4	MET	MET	ARG	ARG	D	D	1 - 72	1 - 72
2	4	MET	MET	ARG	ARG	E	E	1 - 72	1 - 72

NCS ensembles :

ID
1
2
3
4

-
Protein , 2 types, 5 molecules ACBDE

#1: Protein	Ubiquitin-activating enzyme E1 1 Mass: 114409.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme
#2: Protein	Ubiquitin-40S ribosomal protein S31 Mass: 8568.769 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759

#1: Protein

Ubiquitin-activating enzyme E1 1

Mass: 114409.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBA1, YKL210W / Production host:

Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme

#2: Protein

Ubiquitin-40S ribosomal protein S31

Mass: 8568.769 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host:

Escherichia coli (E. coli) / References: UniProt: P05759

-
Non-polymers , 5 types, 489 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-B39 / [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate Mass: 443.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₅N₅O₄S
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 60.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.76→20 Å / Num. obs: 82916 / % possible obs: 99 % / Redundancy: 5.6 % / R_sym value: 0.133 / Net I/σ(I): 11.2
Reflection shell	Highest resolution: 2.76 Å / R_sym value: 0.828

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NNJ

4nnj

Resolution: 2.76→20 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.923 / SU B: 25.207 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.918 / ESU R Free: 0.299 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21966	4093	5 %	RANDOM
R_work	0.17421	-	-	-
obs	0.17643	78520	99.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 51.743 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	2.1 Å²	-0 Å²
3-	-	-	-2.16 Å²

Refinement step

Cycle: 1 / Resolution: 2.76→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17657	0	184	453	18294

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	18193
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	17400
X-RAY DIFFRACTION	r_angle_refined_deg	1.664	1.978	24584
X-RAY DIFFRACTION	r_angle_other_deg	1.203	3	40236
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.421	5	2236
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.424	25.409	856
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.232	15	3227
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.373	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2767
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	20459
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	3983
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.147	2.82	8947
X-RAY DIFFRACTION	r_mcbond_other	1.147	2.82	8946
X-RAY DIFFRACTION	r_mcangle_it	2	4.226	11173
X-RAY DIFFRACTION	r_mcangle_other	2	4.226	11174
X-RAY DIFFRACTION	r_scbond_it	1.371	2.975	9246
X-RAY DIFFRACTION	r_scbond_other	1.37	2.975	9246
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.289	4.391	13409
X-RAY DIFFRACTION	r_long_range_B_refined	3.915	21.66	19475
X-RAY DIFFRACTION	r_long_range_B_other	3.893	21.619	19408
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	126108	0.07
1	2	C	126108	0.07
2	1	B	9352	0.07
2	2	D	9352	0.07
3	1	B	8754	0.11
3	2	E	8754	0.11
4	1	D	8672	0.12
4	2	E	8672	0.12

LS refinement shell

Resolution: 2.763→2.833 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	284	-
R_work	0.299	5315	-
obs	-	-	94.01 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.079	0.2846	0.0395	1.5682	-0.0422	0.9655	-0.0164	0.0206	0.0258	-0.1209	-0.0438	0.438	0.0887	-0.2674	0.0602	0.0989	0.0059	-0.0376	0.1788	-0.0267	0.1333	-20.777	27.9977	-41.8283
2	4.6877	2.7677	1.2166	6.9409	1.3332	2.8568	-0.0534	0.1039	-0.0035	-0.0748	0.0843	-0.3564	-0.2372	0.1817	-0.0309	0.0458	0.0283	0.0218	0.1134	0.0456	0.045	3.1653	57.0565	-41.8225
3	0.7458	-0.1134	0.1246	1.5776	0.3337	1.0048	-0.0041	0.0141	-0.2091	0.0206	0.0038	0.0487	0.1908	0.0434	0.0002	0.0523	-0.0039	0.0095	0.1115	0.0132	0.0759	-8.1584	18.4237	-31.0587
4	1.0747	0.446	-1.5125	3.0513	-1.2024	4.8345	-0.0122	-0.5231	0.0374	0.369	-0.1009	-0.2767	-0.3548	0.3835	0.1132	0.2693	0.0501	-0.0093	0.3019	-0.0421	0.0961	-10.4177	62.3362	-4.5813
5	0.2	-0.1056	0.2792	0.9146	0.3739	0.7755	-0.019	-0.0303	-0.0789	0.1214	0.0045	0.1839	0.036	-0.0401	0.0145	0.0916	0.0056	0.0431	0.1057	0.0238	0.0701	-5.3194	33.1862	-21.93
6	2.5573	0.3022	1.4172	1.4718	-0.1059	4.5711	-0.0468	-0.4123	0.2346	0.4245	0.1888	0.127	-0.4159	-0.4094	-0.142	0.3956	0.1304	-0.0031	0.1793	0.0217	0.1907	18.0114	15.2066	3.4424
7	3.8145	0.8495	0.123	7.5112	-0.5363	2.4607	-0.0295	0.2785	0.0184	-0.4506	0.0708	-0.8249	0.0653	0.3974	-0.0412	0.1245	0.0007	0.0161	0.2099	0.03	0.1787	15.2529	31.7746	-37.166
8	7.1054	2.9391	-5.4489	1.5929	-3.2107	10.957	0.0824	0.0077	0.2933	-0.0071	0.013	-0.0405	-0.2273	0.1971	-0.0955	0.1608	0.0223	-0.0279	0.0481	-0.0054	0.1618	3.3029	30.9354	-30.5605
9	1.8075	0.0615	0.3327	1.0645	-0.134	1.7133	-0.096	-0.251	-0.0485	0.2081	0.1477	0.209	0.1641	-0.1746	-0.0517	0.0873	0.043	0.0429	0.1476	0.0549	0.0469	-36.1473	64.5556	-39.4898
10	4.2614	-1.5887	-3.4795	4.3167	1.6463	4.1413	-0.0018	0.1383	-0.2145	-0.3454	-0.0161	-0.3805	0.1906	0.3799	0.0179	0.1087	0.0414	-0.0243	0.2408	-0.0011	0.1398	-3.1895	51.8299	-59.9526
11	1.1845	-0.5057	0.3888	1.6809	-0.2694	1.7921	-0.0966	-0.0186	0.1589	0.0856	0.118	0.0694	-0.3298	-0.0542	-0.0215	0.0777	0.0469	0.0213	0.1434	0.0641	0.0618	-36.1427	79.1335	-50.9371
12	0.1492	-0.2855	0.0317	3.0639	0.7759	0.2936	0.2132	0.1864	0.0501	-0.8476	-0.0983	-0.4609	-0.0852	0.0892	-0.1149	0.4212	0.126	0.1037	0.3856	0.0732	0.0869	-28.4248	63.9473	-74.8438
13	3.6555	-1.1401	1.5334	2.1758	0.3293	1.8387	0.1445	0.6294	-0.1535	-0.4526	-0.0099	-0.046	0.2562	0.0457	-0.1345	0.4317	-0.0191	-0.0898	0.351	-0.0726	0.1472	-29.6471	33.4605	-82.5734
14	0.3329	-0.0794	0.0528	0.5055	0.2531	1.7316	-0.0229	0.1202	0.0023	0.0648	0.0703	-0.0312	-0.192	0.0397	-0.0473	0.0397	0.0094	0.0011	0.1811	0.0355	0.0164	-27.7198	72.6098	-65.0866
15	3.7852	0.3438	-0.9589	2.0592	-0.719	5.5453	0.0891	0.1547	-0.1445	-0.1055	-0.0202	0.2435	0.383	-0.5441	-0.0688	0.1643	-0.0024	-0.032	0.2199	0.0938	0.1098	-38.4116	87.2579	-98.1705
16	5.3405	-2.3031	-0.4331	5.8358	-0.4483	3.971	0.1003	0.1018	0.5801	-0.2557	-0.0283	-0.8913	-0.3496	0.4662	-0.072	0.1582	-0.0268	0.0692	0.2925	0.0602	0.1896	-8.7853	77.4342	-66.614
17	8.7876	-0.8371	1.0388	0.4393	-0.8382	1.739	0.027	0.0177	-0.255	-0.0558	-0.0582	-0.0557	0.0453	0.0998	0.0312	0.1286	0.0125	0.0562	0.1367	0.0428	0.1454	-20.7594	70.9645	-65.2324
18	2.0695	3.1074	-0.5337	11.6235	0.7524	5.3254	-0.2553	0.3399	-0.2831	-0.5572	0.3606	0.3631	-0.0224	-0.1851	-0.1054	0.4715	-0.0235	0.0082	0.6152	-0.0279	0.5157	9.9063	58.8716	-81.6376
19	5.6582	-1.5438	-1.4596	6.3871	-0.1396	0.4416	0.0072	0.5439	-0.1938	-0.0274	-0.0141	0.649	-0.0821	-0.1412	0.0069	0.4434	0.026	-0.0033	0.3998	-0.0231	0.3542	2.6918	55.6887	-79.743

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 197
2	X-RAY DIFFRACTION	2	A	198 - 264
3	X-RAY DIFFRACTION	3	A	265 - 624
4	X-RAY DIFFRACTION	4	A	625 - 810
5	X-RAY DIFFRACTION	5	A	811 - 925
6	X-RAY DIFFRACTION	6	A	926 - 1024
7	X-RAY DIFFRACTION	7	B	1 - 65
8	X-RAY DIFFRACTION	8	B	66 - 76
9	X-RAY DIFFRACTION	9	C	11 - 166
10	X-RAY DIFFRACTION	10	C	167 - 264
11	X-RAY DIFFRACTION	11	C	265 - 545
12	X-RAY DIFFRACTION	12	C	546 - 624
13	X-RAY DIFFRACTION	13	C	625 - 844
14	X-RAY DIFFRACTION	14	C	845 - 925
15	X-RAY DIFFRACTION	15	C	926 - 1024
16	X-RAY DIFFRACTION	16	D	1 - 65
17	X-RAY DIFFRACTION	17	D	66 - 76
18	X-RAY DIFFRACTION	18	E	1 - 65
19	X-RAY DIFFRACTION	19	E	66 - 72

-
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

-
Protein , 2 types, 5 molecules ACBDE

-
Non-polymers , 5 types, 489 molecules

-
Details

-
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

-Protein , 2 types, 5 molecules ACBDE

-Non-polymers , 5 types, 489 molecules

-Details

-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

-
Protein , 2 types, 5 molecules ACBDE

-
Non-polymers , 5 types, 489 molecules

-
Details

-
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