PDB-3hhz: Complex of the vesicular stomatitis virus nucleocapsid and the nu...

ID or keywords:

Entry

Database: PDB / ID: 3hhz

Title

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein

Components

Nucleoprotein
Phosphoprotein
RNA (45-MER)

Keywords

VIRAL PROTEIN/RNA / Protein / RNA / template / replication / negative strand RNA virus / Chaperone / Phosphoprotein / RNA replication / Virion / Ribonucleoprotein / RNA-binding / Viral nucleoprotein / VIRAL PROTEIN / VIRAL PROTEIN-RNA COMPLEX

Function / homology

Function and homology information

helical viral capsid / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function

Biological species

Vesicular stomatitis Indiana virus

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Green, T.J. / Luo, M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P.
Authors: Green, T.J. / Luo, M.

History

Deposition	May 18, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 28, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 6, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3hhz.cif.gz	489.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hhz.ent.gz	404.5 KB	Display	PDB format
PDBx/mmJSON format	3hhz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/3hhz ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hhz	HTTPS FTP

-
Related structure data

Related structure data	3hhwC 2gicS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3hhw-1 5530 2i2x-d 5w68-d 3j4a-d 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	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #32 - Aug 2002 Chaperones similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (5)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#32 - Aug 2002
Chaperones
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Phosphoprotein

B: Phosphoprotein

C: Phosphoprotein

D: Phosphoprotein

E: Phosphoprotein

K: Nucleoprotein

L: Nucleoprotein

M: Nucleoprotein

N: Nucleoprotein

O: Nucleoprotein

R: RNA (45-MER)

299 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoprotein

B: Phosphoprotein

C: Phosphoprotein

D: Phosphoprotein

E: Phosphoprotein

K: Nucleoprotein

L: Nucleoprotein

M: Nucleoprotein

N: Nucleoprotein

O: Nucleoprotein

R: RNA (45-MER)

A: Phosphoprotein

B: Phosphoprotein

C: Phosphoprotein

D: Phosphoprotein

E: Phosphoprotein

K: Nucleoprotein

L: Nucleoprotein

M: Nucleoprotein

N: Nucleoprotein

O: Nucleoprotein

R: RNA (45-MER)

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

Unit cell

Length a, b, c (Å)	166.568, 235.248, 96.138
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Phosphoprotein / Protein P / Protein M1 Mass: 9793.250 Da / Num. of mol.: 5 / Fragment: UNP residues 183-265,nucleocapsid-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: nucleocapsid protein, P / Production host: Escherichia coli (E. coli) / References: UniProt: P04880
#2: Protein	Nucleoprotein / NP / Nucleocapsid protein / Protein N Mass: 47332.750 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: N, phosphoprotein / Production host: Escherichia coli (E. coli) / References: UniProt: Q77E03
#3: RNA chain	RNA (45-MER) Mass: 13732.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: RNA is non-specific encapsidated during E. coli expression. Source: (natural) Escherichia coli (E. coli)

-
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: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 7% PEG 4000, 0.25 M NaCl, and 0.1M citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 25, 2008
Radiation	Monochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.5→30 Å / Num. all: 48185 / Num. obs: 48185 / % possible obs: 98.3 % / R_merge(I) obs: 0.116 / Net I/σ(I): 21.48
Reflection shell	Resolution: 3.5→3.63 Å / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 4.31 / % possible all: 88.4

-
Processing

Software

Name	Version	Classification
Blu-Ice	Ice	data collection
COMO		phasing
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GIC

2gic

Resolution: 3.5→30 Å / Cor.coef. F_o:F_c: 0.869 / Cor.coef. F_o:F_c free: 0.82 / SU B: 85.634 / SU ML: 0.642 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.778 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32333	2443	5.1 %	RANDOM
R_work	0.25425	-	-	-
all	0.25788	45229	-	-
obs	0.25788	45229	98.54 %	-

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: 65.323 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5 Å²	0 Å²	0 Å²
2-	-	0.07 Å²	0 Å²
3-	-	-	-7.57 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19515	900	0	0	20415

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	20934
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.194	2.023	28501
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.328	5	2460
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.325	23.908	870
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.401	15	3515
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.227	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	3175
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	15405
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	9975
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	14239
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	613
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	0.197	0.2	166
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.225	0.2	2
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	0.183	1.5	12553
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.327	2	19800
X-RAY DIFFRACTION	r_scbond_it	0.442	3	9646
X-RAY DIFFRACTION	r_scangle_it	0.741	4.5	8701
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.5→3.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.348	143	-
R_work	0.278	2928	-
obs	-	-	88.3 %

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	4.6073	-0.8324	-3.1623	1.3	1.2379	2.557	0.2118	-1.145	-1.1997	-0.034	0.5769	0.747	2.0934	-0.735	-0.7888	1.1963	0.1482	-0.1148	0.6767	0.0538	0.4029	-14.5747	38.4988	76.5267
2	5.6903	-0.1027	-2.5077	3.1632	6.7773	15.4408	-0.6228	2.3457	2.3879	3.5492	2.9717	0.765	1.6287	1.2399	-2.3489	1.4153	0.4853	0.0319	1.47	0.4466	1.0356	-1.4864	34.2213	78.6327
3	41.4447	-8.8597	11.1478	79.2898	20.0788	9.5175	0.6622	3.464	-2.2829	-2.435	-0.8455	1.5194	0.4241	2.9714	0.1833	1.1225	0.4674	0.0417	0.7794	-0.3376	0.3459	-7.0886	38.3541	72.5085
4	17.8149	-8.008	-23.894	13.8114	19.9072	47.7312	-2.9993	-0.8596	0.1226	0.2084	2.5424	-0.0663	-1.1229	1.606	0.4569	0.5662	0.3025	-0.0093	0.2605	0.1163	0.1602	-13.0111	43.4307	65.6268
5	1.2382	-1.5927	-2.6769	2.0486	3.4432	5.7871	-1.5604	-0.7954	-1.2795	1.0903	2.127	1.1958	-0.7958	-0.191	-0.5666	1.3931	-0.2831	-0.2353	1.3291	0.4299	1.3524	9.7918	39.4071	76.3869
6	8.8671	20.5441	-6.3031	47.5981	-14.6036	4.4805	-2.3294	-0.8998	0.1555	0.9141	2.8672	0.6015	0.5141	-0.084	-0.5378	1.2996	0.2545	0.1542	1.6545	0.3121	1.0558	18.7365	27.9957	77.7525
7	17.3776	16.4746	-21.1961	49.1848	10.4927	53.7262	-4.5954	3.5571	1.2124	1.4326	5.4853	-0.3571	1.589	-1.1632	-0.8899	1.0969	-0.0512	0.1376	1.1989	0.0057	1.1027	15.8948	34.7671	71.118
8	42.9612	-19.0476	9.6807	31.4239	-1.7231	2.4686	-0.7844	-2.8795	3.2709	-2.7423	0.8598	-3.6412	2.4246	-1.7519	-0.0754	1.1107	-0.2097	0.295	1.3389	-0.1575	0.7429	14.5686	43.5439	65.6696
9	9.9921	3.0609	-4.3226	8.414	-5.9788	9.2473	-0.6633	-0.0364	0.2841	0.6329	0.9659	0.9385	-0.2351	-2.5472	-0.3026	0.5868	-0.2726	0.0363	0.752	-0.1914	0.1561	32.4498	26.3804	77.1643
10	28.9134	-27.0663	27.0579	64.4204	-34.2439	27.3549	-0.1986	-2.387	-0.3207	-1.3977	-1.7299	1.2432	2.5413	-1.4015	1.9285	0.8725	0.0249	0.023	0.8218	-0.074	0.7302	29.5205	12.2275	76.1811
11	7.1661	4.078	-6.017	21.2826	-3.8799	17.0919	1.3224	-1.627	-1.5469	-1.3383	0.0629	-0.9779	1.8865	-2.4003	-1.3852	0.705	-0.0224	-0.0891	0.3634	0.0551	0.4618	36.3116	17.4953	75.2617
12	6.2535	5.6634	12.0223	15.3927	6.5879	25.2772	-0.9216	1.2753	0.89	-1.5655	-0.1775	-2.0545	-1.4391	0.6147	1.0991	0.2226	0.0329	-0.0541	0.192	0.1875	0.2853	37.6061	25.7578	65.5271
13	3.6816	-5.3907	1.6384	7.9117	-2.423	0.7602	2.0743	-0.9042	-0.782	2.4924	-0.211	1.4766	3.1673	1.1742	-1.8632	1.4109	0.1911	0.1574	1.4378	-0.2401	1.1734	-42.0382	-3.5159	77.3521
14	12.0654	5.3155	7.0968	11.6734	5.8211	4.9524	1.9839	-0.3394	0.6359	2.2519	0.017	0.5986	2.0146	0.7872	-2.0009	1.476	-0.3286	-0.0539	1.8286	0.0647	1.088	-31.9739	4.4191	76.0727
15	17.1615	-6.8334	-17.9722	7.3345	11.6373	23.1736	2.5447	-1.1677	2.9706	-2.0352	0.0928	-2.4365	1.0195	1.9645	-2.6375	1.1573	0.3709	0.1978	1.4178	-0.0737	1.0717	-39.0499	5.9101	74.5363
16	3.1744	7.0872	-15.6474	70.5789	-11.1249	87.4835	2.5185	-1.7446	0.0405	-3.5983	1.2591	2.8065	-0.0122	-0.3666	-3.7776	0.9389	0.1644	-0.1619	1.0622	0.3065	0.8453	-46.7611	0.4496	66.0487
17	37.9194	34.5113	39.7097	58.686	39.7892	42.0725	2.9095	-2.4707	-0.6141	-2.4037	-5.8413	0.0674	1.5559	0.8678	2.9318	1.0015	0.3835	-0.2457	1.2099	0.0782	0.7347	-25.696	22.4574	84.9722
18	24.7324	-8.512	1.486	5.4511	-1.2864	10.9144	-0.2894	-1.1221	-1.0909	0.6435	0.8453	-0.022	-0.639	0.4202	-0.5559	0.6449	-0.0452	0.0269	0.3501	-0.0864	0.2659	-32.4361	22.5858	73.9041
19	19.8321	4.3674	4.6342	15.08	-8.3115	7.2513	0.3074	-0.6805	0.6041	0.7277	-0.3405	-1.268	0.335	-1.103	0.0331	0.8086	0.1031	-0.1346	0.7854	-0.1333	0.1766	-28.9043	27.6975	74.87
20	3.9654	13.5446	-9.8429	53.1375	-36.6331	25.7526	0.567	-1.8108	0.9749	-1.3745	0.0114	2.7291	-1.9419	2.4072	-0.5784	0.3891	0.0759	0.0723	0.667	-0.2497	0.2412	-36.4477	27.6461	65.2771
21	16.8772	-2.1453	9.1344	0.4207	-0.7362	6.1633	-0.4773	0.0281	1.2549	0.1459	-0.0071	-0.0123	-0.9951	0.3258	0.4845	-0.0038	-0.1573	0.014	-0.4348	-0.0229	0.0134	7.3014	61.1298	35.1513
22	0.0886	-0.7408	-1.0326	6.8308	7.3773	14.5137	-0.2616	0.9365	0.2205	-0.5914	0.6758	0.1076	-0.2135	0.5045	-0.4143	0.4105	0.0213	0.0067	0.4932	0.1245	0.25	-17.5679	57.9633	-2.8996
23	2.8961	2.332	-1.6301	3.5415	1.3794	7.7301	0.057	0.5309	0.6593	-0.2374	-0.0871	0.3	-0.7845	-0.7287	0.0301	0.1541	0.1551	-0.0468	-0.0113	0.2309	-0.0159	-28.6699	62.982	9.2355
24	0.5063	1.7645	0.2383	6.2719	-0.4295	13.059	-0.3974	1.5113	0.7422	-1.3375	-0.4867	-0.654	1.0463	1.0314	0.8841	0.3404	0.0585	-0.0778	0.5004	0.3242	0.4172	-19.6222	51.8411	-1.1255
25	10.4686	9.3097	5.0739	14.2032	0.4409	5.2573	0.3339	0.8708	-1.3927	-0.653	-0.0245	-0.4961	1.4269	0.4367	-0.3095	0.8876	-0.0522	0.2382	0.6067	-0.1405	0.1627	-17.6738	41.202	2.8149
26	1.6415	-1.151	1.2055	1.5839	-2.8373	7.7266	-0.1184	0.3551	0.2208	-0.1687	0.2243	0.0824	0.1365	-0.6921	-0.106	-0.1765	0.0378	0.0759	-0.543	0.062	-0.3562	-20.4488	52.1773	26.0295
27	0.9786	0.2562	-0.3301	1.5054	-0.4485	1.5858	-0.0418	0.1088	0.1784	-0.1931	0.1391	0.0583	-0.2312	-0.3346	-0.0973	-0.2876	0.0995	0.048	-0.5709	0.0259	-0.4375	-14.8938	45.0276	33.6661
28	53.7614	7.9068	-2.6927	1.3343	0.8081	8.5917	1.1939	-7.6558	1.9416	1.0151	-0.5959	0.5129	-0.4537	-0.1328	-0.598	0.7429	0.0142	0.1171	-0.0376	-0.1143	0.1678	-28.5489	35.5967	61.7924
29	4.2627	-0.2589	0.405	4.775	3.4527	11.935	-0.0381	-0.3546	-0.0684	0.4014	0.2473	0.0424	0.2935	-0.0833	-0.2092	-0.3974	0.083	0.0552	-0.5245	0.1331	-0.4175	-11.0394	34.1019	47.5915
30	14.0526	-0.6901	-1.5795	18.4044	5.9447	2.0514	-0.0799	1.291	-0.4502	0.1927	0.532	0.4155	-0.1575	1.6012	-0.4521	-0.482	0.0245	0.0484	-0.6332	0.0201	-0.4253	-4.2701	31.14	33.5314
31	4.6644	-6.5195	5.1016	10.3732	-8.1752	7.2332	0.1518	0.9687	0.6651	0.6103	-0.5615	-0.3271	-1.1534	1.2203	0.4097	-0.042	-0.1903	0.1333	-0.1188	0.0853	0.0217	37.9038	50.7731	28.3102
32	0.3813	1.9345	0.8678	9.8827	5.0807	8.738	-0.995	0.071	0.1315	-0.6024	0.9686	0.6443	0.7623	0.4057	0.0264	0.7151	-0.1194	0.2099	0.942	0.2703	0.3323	15.1102	59.6733	-3.3958
33	3.7237	1.4771	0.5218	3.8676	0.2458	3.6648	0.2454	1.0899	0.6345	-0.0941	0.316	0.5269	-0.014	-0.6262	-0.5614	0.3553	0.1034	0.1402	0.4325	0.4136	0.426	14.4273	63.0714	4.5381
34	21.2191	-10.4752	15.521	15.3668	-8.3686	11.402	0.7655	3.0268	-0.7863	0.9727	-0.6909	0.1447	0.4938	0.8972	-0.0746	1.0265	-0.0135	0.0514	1.0586	-0.0483	0.4701	7.0445	43.6645	3.9449
35	5.4351	-1.5732	1.6768	0.4579	-0.427	1.8713	1.876	2.4706	-0.9728	2.7435	-1.3962	-2.4867	1.2247	0.5453	-0.4799	0.7981	0.0861	-0.3258	0.5469	0.0142	0.5151	21.0323	48.2024	3.9333
36	0.6583	-0.4946	-1.3281	2.8831	0.0162	3.063	0.4257	1.0899	0.5516	-0.3228	-0.1985	0.2403	-0.8549	-1.0663	-0.2271	0.2227	0.2201	0.2198	0.1658	0.231	-0.0026	11.0182	57.8461	15.5792
37	1.7193	0.0895	-0.5218	3.3182	-0.5902	3.7163	0.2668	0.1125	0.6242	-0.3725	-0.1378	-0.2388	-0.4406	-0.0867	-0.129	-0.2408	-0.028	0.1168	-0.5229	-0.0179	-0.2566	18.4712	53.8934	32.6587
38	2.815	-0.9523	-0.4086	2.0731	1.2082	2.0738	0.2461	0.2545	0.1325	-0.1924	-0.0861	-0.0864	-0.3409	-0.102	-0.16	-0.3967	-0.0327	0.0844	-0.6395	-0.0068	-0.5027	13.2128	40.4766	37.6409
39	2.3295	0.6532	-0.6807	3.0398	-3.5142	4.065	-1.199	-2.438	0.6147	1.4387	0.874	-1.4199	-1.7752	0.3949	0.325	0.519	0.0046	0.1123	0.2543	-0.1837	0.1539	-4.1201	46.4216	60.6918
40	5.0624	-0.4858	-1.3494	5.9909	3.1612	7.1033	0.1513	-0.2929	-0.0831	0.4608	0.0505	0.0636	0.4093	-0.1577	-0.2018	-0.5586	-0.0153	0.0048	-0.5497	0.0664	-0.5013	12.0226	32.36	43.8143
41	0.0448	0.0726	0.129	6.1636	-3.7965	3.3567	0.1993	0.1592	0.1512	-0.5488	-1.1035	-1.4183	0.2532	1.3813	0.9041	-0.2917	-0.0703	0.087	0.2331	0.0444	0.3019	60.4648	16.6529	31.4222
42	2.8642	0.5055	1.6424	3.3519	2.6911	6.2084	0.1445	0.3279	-0.1219	-1.3907	0.0299	-0.4742	-0.4465	-0.0811	-0.1743	0.4024	-0.1119	0.1388	0.3137	0.1258	0.1708	47.8885	40.1891	1.1467
43	7.0414	-3.1075	-1.8684	6.2786	3.2124	6.2297	0.8582	1.2735	0.0092	-2.4775	-0.7605	-0.3919	-0.4993	-0.2345	-0.0978	1.0175	0.0522	0.2554	0.5392	0.2912	0.3263	49.3825	42.0069	-2.3939
44	14.5192	4.5634	3.2959	5.2088	5.0339	4.9829	0.1039	0.6734	-1.0987	-1.031	-0.5517	-0.6922	1.0453	-2.6579	0.4478	0.1587	-0.0377	0.0064	0.3871	-0.0303	0.185	37.2067	31.7656	5.6608
45	14.9113	-0.2744	-0.8554	0.005	0.0159	3.4601	0.4763	0.7932	-0.8849	-1.5011	-0.5468	0.2525	0.9378	-1.6187	0.0705	0.7141	0.0325	-0.2073	0.8173	-0.1651	0.2744	33.7356	28.5914	3.2909
46	1.3465	0.6259	-2.3978	2.5803	-3.2816	6.3213	-0.0209	0.392	0.0935	-0.3214	-0.244	-0.4205	-0.1754	0.1617	0.2649	-0.3886	-0.1305	0.0004	-0.2534	-0.0054	-0.3125	44.6142	34.8042	25.3798
47	3.587	0.5471	-0.5099	4.9489	3.1827	5.3545	-0.1228	0.5737	-0.0116	-0.264	0.0431	-0.0618	-0.1643	0.393	0.0797	-0.5578	-0.0793	0.0021	-0.634	-0.0147	-0.5352	35.0785	21.1782	35.8859
48	6.1783	-4.9962	-0.5452	4.9421	1.4557	1.1901	1.2828	-0.5353	0.6895	-1.3871	-0.1691	-0.8622	-0.363	-0.3583	-1.1137	0.3513	-0.0184	0.3418	-0.533	0.0026	-0.2148	25.3971	37.192	48.146
49	8.5855	-20.6689	4.108	49.8373	-10.7869	12.2266	-0.9442	-1.8294	0.2602	4.4098	1.1782	-1.1897	-0.6841	0.6539	-0.234	0.0906	-0.0037	0.1086	0.3602	-0.2308	0.5563	24.1472	39.3377	61.1967
50	4.777	1.236	1.6591	5.3087	3.9544	9.853	0.0943	-0.3456	-0.0945	0.4191	-0.177	0.0109	0.1738	-0.0451	0.0827	-0.4121	0.031	0.0473	-0.5816	0.0762	-0.4156	28.9268	19.0911	43.9315
51	4.0449	2.2494	2.0798	3.2088	0.6192	1.2169	0.3018	-0.0084	-0.4172	-0.5502	-0.0127	0.8454	-0.1613	-0.7012	-0.2891	0.0962	0.2154	-0.063	0.1697	0.09	0.2846	-59.6935	21.6906	30.8699
52	2.8441	-0.6566	0.0239	0.173	-0.1123	0.5327	0.0207	0.8453	-0.0772	-0.7995	-0.3108	0.3385	0.7857	-0.7819	0.2901	1.0682	-0.0283	-0.2247	0.8344	-0.1489	0.7046	-64.6649	-5.5173	2.075
53	6.212	-5.7615	2.5639	5.3437	-2.3779	1.0582	0.384	-1.0071	-0.3022	-2.3413	0.1175	-1.4839	0.4136	1.5021	-0.5015	1.9118	-0.1932	0.4035	1.1647	0.0061	0.4996	-43.5035	-6.5534	3.7317
54	7.5636	-1.3104	3.6452	3.4947	5.228	12.2642	0.2958	0.4861	-0.0295	-0.9323	-0.1917	0.3568	0.3402	-0.3196	-0.1041	0.3167	0.1626	-0.3436	0.3389	0.054	0.303	-59.591	-6.3811	10.1311
55	4.2083	0.2945	0.7338	6.4534	2.6011	10.7868	0.0169	0.618	-0.0127	-0.8947	0.1788	0.626	0.1417	-0.0652	-0.1957	-0.6267	-0.0154	-0.0527	-0.2849	0.0603	-0.2155	-51.8371	-1.2231	33.7507
56	5.5346	0.3958	4.2693	5.2982	2.8161	5.3448	0.4347	0.377	-0.3552	-1.741	-0.6379	1.2546	0.1099	-0.4383	0.2032	-0.1293	0.159	-0.3792	-0.0166	0.0848	0.2508	-60.7206	3.1224	26.6651
57	5.5599	1.6494	-2.3354	4.7039	-1.463	4.7779	0.0231	0.6465	-0.1512	-0.5495	-0.1958	0.153	-0.145	-0.2653	0.1726	-0.67	0.0574	-0.0419	-0.4739	0.0482	-0.4703	-40.8431	3.1535	36.5305
58	5.885	23.5632	-3.045	94.3451	-12.1919	1.5755	1.3515	-1.2792	-0.0089	0.7283	-2.5305	1.5288	0.3457	0.568	1.179	-0.2258	0.0002	0.0285	-0.1571	0.0791	-0.5266	-43.4034	-17.6191	48.317
59	0.1777	3.1906	-0.0108	58.2826	2.7484	8.683	-0.4187	-0.3315	1.2186	4.5668	1.0942	3.7697	0.0871	-0.8075	-0.6755	-0.1996	0.3343	0.0883	0.4775	-0.0958	0.5222	-42.8409	-17.9561	60.5545
60	7.8745	-0.4005	-4.591	4.2477	-0.012	13.2225	0.0334	-0.2888	0.0434	0.224	0.1051	-0.1412	0.0177	0.2151	-0.1385	-0.4513	-0.0031	-0.0491	-0.7092	0.0453	-0.4374	-34.6379	1.5488	43.8214
61	21.5463	7.0292	10.8423	2.3966	4.0006	7.5327	-0.3823	-0.055	0.6899	0.2364	0.2821	0.6087	-0.9284	-0.3884	0.1003	0.106	0.2238	0.0547	-0.4622	0.1829	-0.1028	-29.9001	53.7781	34.9499
62	0.8602	0.5618	-0.2423	1.8413	0.7024	3.803	-0.2059	1.3605	0.2034	-0.6339	0.5151	0.4832	0.2931	-0.9801	-0.3092	0.3572	0.1539	-0.0766	0.8573	0.2456	0.3121	-55.2074	34.443	3.475
63	5.6978	-2.3616	-2.3099	8.4132	3.563	7.8154	-0.3461	1.4034	0.5032	-2.0434	-0.2828	0.529	-0.6503	-0.361	0.6289	0.4979	-0.1091	-0.1086	0.4702	0.2216	0.184	-46.7921	29.8113	-1.2791
64	9.7108	-1.693	2.1744	12.1049	-2.4763	5.4417	-0.0927	1.3925	-1.126	-0.6897	0.3997	-1.3646	1.7049	0.3131	-0.307	0.5537	-0.1023	0.1451	0.7521	0.0081	0.13	-39.544	21.915	2.8181
65	3.3666	-0.2909	1.4993	1.0236	-3.0071	8.9607	-0.4149	0.6248	-0.5376	-0.4604	0.741	0.2951	0.7534	-0.5167	-0.3261	-0.2531	0.0319	-0.0393	0.1293	0.1657	-0.0226	-51.6294	27.4826	13.4742
66	1.3201	0.2565	2.8669	3.4144	-2.5789	9.1493	0.0905	0.3284	0.3999	-0.0415	0.1109	0.4616	-0.3401	-0.5159	-0.2014	-0.5397	0.2282	0.1369	-0.2632	0.1242	-0.2727	-44.9759	34.0686	31.9499
67	4.4692	-0.4253	-1.9363	5.9155	-1.5462	4.3541	-0.0602	0.3897	0.1658	-0.2507	0.2416	0.2644	0.041	-0.1668	-0.1814	-0.5978	0.1058	0.0657	-0.5191	0.0703	-0.5349	-31.3709	27.9416	35.1932
68	0.106	-0.1147	-0.2812	0.1241	0.3043	0.7465	-0.4629	-0.991	1.1028	0.394	0.2054	1.3147	0.012	-0.6936	0.2575	-0.2187	0.0735	0.1111	-0.0071	0.1756	-0.233	-43.2416	12.7309	48.2259
69	9.621	8.9264	-10.4316	8.2819	-9.6785	11.3106	3.8334	-3.6363	-0.6664	4.3021	-3.1487	0.2355	-0.9104	1.076	-0.6847	0.3203	0.0296	0.1154	0.4857	0.0631	0.1482	-44.7678	10.3025	60.9631
70	6.0018	-0.7008	-2.5151	3.4359	-0.1023	10.5278	-0.0561	-0.2558	-0.3798	0.2291	0.0594	0.0188	-0.0638	0.4387	-0.0033	-0.4468	-0.0157	-0.0123	-0.6772	0.0619	-0.4377	-27.1235	21.5631	43.8122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	193 - 225
2	X-RAY DIFFRACTION	2	A	226 - 242
3	X-RAY DIFFRACTION	3	A	243 - 253
4	X-RAY DIFFRACTION	4	A	254 - 265
5	X-RAY DIFFRACTION	5	B	193 - 225
6	X-RAY DIFFRACTION	6	B	226 - 242
7	X-RAY DIFFRACTION	7	B	243 - 254
8	X-RAY DIFFRACTION	8	B	255 - 265
9	X-RAY DIFFRACTION	9	C	193 - 222
10	X-RAY DIFFRACTION	10	C	223 - 237
11	X-RAY DIFFRACTION	11	C	238 - 253
12	X-RAY DIFFRACTION	12	C	254 - 265
13	X-RAY DIFFRACTION	13	D	193 - 217
14	X-RAY DIFFRACTION	14	D	218 - 237
15	X-RAY DIFFRACTION	15	D	238 - 254
16	X-RAY DIFFRACTION	16	D	255 - 265
17	X-RAY DIFFRACTION	17	E	193 - 203
18	X-RAY DIFFRACTION	18	E	204 - 238
19	X-RAY DIFFRACTION	19	E	239 - 253
20	X-RAY DIFFRACTION	20	E	254 - 265
21	X-RAY DIFFRACTION	21	K	2 - 33
22	X-RAY DIFFRACTION	22	K	34 - 65
23	X-RAY DIFFRACTION	23	K	66 - 106
24	X-RAY DIFFRACTION	24	K	107 - 150
25	X-RAY DIFFRACTION	25	K	151 - 190
26	X-RAY DIFFRACTION	26	K	191 - 268
27	X-RAY DIFFRACTION	27	K	269 - 350
28	X-RAY DIFFRACTION	28	K	351 - 370
29	X-RAY DIFFRACTION	29	K	371 - 408
30	X-RAY DIFFRACTION	30	K	409 - 422
31	X-RAY DIFFRACTION	31	L	2 - 44
32	X-RAY DIFFRACTION	32	L	45 - 84
33	X-RAY DIFFRACTION	33	L	85 - 145
34	X-RAY DIFFRACTION	34	L	146 - 179
35	X-RAY DIFFRACTION	35	L	180 - 190
36	X-RAY DIFFRACTION	36	L	191 - 231
37	X-RAY DIFFRACTION	37	L	232 - 288
38	X-RAY DIFFRACTION	38	L	289 - 348
39	X-RAY DIFFRACTION	39	L	349 - 370
40	X-RAY DIFFRACTION	40	L	371 - 422
41	X-RAY DIFFRACTION	41	M	2 - 40
42	X-RAY DIFFRACTION	42	M	41 - 95
43	X-RAY DIFFRACTION	43	M	96 - 132
44	X-RAY DIFFRACTION	44	M	133 - 148
45	X-RAY DIFFRACTION	45	M	149 - 190
46	X-RAY DIFFRACTION	46	M	191 - 296
47	X-RAY DIFFRACTION	47	M	297 - 334
48	X-RAY DIFFRACTION	48	M	335 - 348
49	X-RAY DIFFRACTION	49	M	349 - 370
50	X-RAY DIFFRACTION	50	M	371 - 422
51	X-RAY DIFFRACTION	51	N	2 - 41
52	X-RAY DIFFRACTION	52	N	42 - 144
53	X-RAY DIFFRACTION	53	N	145 - 180
54	X-RAY DIFFRACTION	54	N	181 - 214
55	X-RAY DIFFRACTION	55	N	215 - 257
56	X-RAY DIFFRACTION	56	N	258 - 296
57	X-RAY DIFFRACTION	57	N	297 - 336
58	X-RAY DIFFRACTION	58	N	337 - 348
59	X-RAY DIFFRACTION	59	N	349 - 370
60	X-RAY DIFFRACTION	60	N	371 - 422
61	X-RAY DIFFRACTION	61	O	2 - 33
62	X-RAY DIFFRACTION	62	O	34 - 106
63	X-RAY DIFFRACTION	63	O	107 - 150
64	X-RAY DIFFRACTION	64	O	151 - 190
65	X-RAY DIFFRACTION	65	O	191 - 227
66	X-RAY DIFFRACTION	66	O	228 - 291
67	X-RAY DIFFRACTION	67	O	292 - 334
68	X-RAY DIFFRACTION	68	O	335 - 348
69	X-RAY DIFFRACTION	69	O	349 - 370
70	X-RAY DIFFRACTION	70	O	371 - 422

-
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