PDB-3tmm: TFAM imposes a U-turn on mitochondrial DNA

ID or keywords:

Entry

Database: PDB / ID: 3tmm

Title

TFAM imposes a U-turn on mitochondrial DNA

Components

(DNA (28-MER)) x 2
Transcription factor A, mitochondrial

Keywords

TRANSCRIPTION/DNA / HMG /

High Mobility Group /

Transcription /

LSP1 /

DNA /

Mitochondria / TRANSCRIPTION-DNA complex

Function / homology

Function and homology information

Mitochondrial transcription initiation / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / mitochondrial transcription factor activity /

transcription initiation at mitochondrial promoter / mitochondrial transcription / mitochondrial nucleoid /

heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5001 Å

Authors

Ngo, H.B. / Kaiser, J.T. / Chan, D.C.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.
Authors: Ngo, H.B. / Kaiser, J.T. / Chan, D.C.

History

Deposition	Aug 31, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2011	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tmm.cif.gz	158.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3tmm.ent.gz	131.4 KB	Display	PDB format
PDBx/mmJSON format	3tmm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	3lm7-d 6hb4-1 5f72-1 4fqc-d 3da8-d 1l1e-d 6ibw-d 6t78-d 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	#255 - Mar 2021 Cisplatin and DNA similarity (8) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (6) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #84 - Dec 2006 Transposase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #23 - Nov 2001 DNA similarity (2) #139 - Jul 2011 DNA Methyltransferase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#255 - Mar 2021
Cisplatin and DNA
similarity (8)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (6)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#23 - Nov 2001
DNA
similarity (2)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Transcription factor A, mitochondrial

B: DNA (28-MER)

C: DNA (28-MER)

45.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.438, 81.911, 161.254
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Details

20_bss: 99

#1: Protein	Transcription factor A, mitochondrial / mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / ...mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / Transcription factor 6-like 2 Mass: 28425.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mitochondrial / Source: (gene. exp.) Homo sapiens (human) / Gene: TCF6, TCF6L2, TFAM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q00059
#2: DNA chain	DNA (28-MER) Mass: 8786.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Oligonucleotide
#3: DNA chain	DNA (28-MER) Mass: 8422.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Oligonucleotide
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 29% PEG 400, 0.15 M calcium acetate, 0.1 M sodium acetate,pH 4.2, 400 mM NDSB211, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL12-2	1	0.97864, 0.91837, 0.97898
SYNCHROTRON	SSRL	BL12-2	2	0.97864, 0.91837, 0.97898

Detector

Type	ID	Detector	Date
MARMOSAIC 325 mm CCD	1	CCD	Dec 18, 2009
MARMOSAIC 325 mm CCD	2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97864	1
2	0.91837	1
3	0.97898	1

Reflection

Resolution: 2.5→24.192 Å / Num. obs: 15812 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Net I/σ(I): 10.6

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
2.5-2.64	1,2	99.5
2.64-2.8	1,2	99.1
2.8-2.99	1,2	99.2
2.99-3.23	1,2	98.8
3.23-3.54	1,2	99.1
3.54-3.95	1,2	98.9
3.95-4.56	1,2	98.6
4.56-5.59	1,2	95.1
5.59-7.91	1,2	97.2
7.91-25	1,2	87.9

-
Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.6_289)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.5001→24.192 Å / SU ML: 0.78 / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2478	756	4.78 %
R_work	0.1948	-	-
obs	0.1973	15812	98.49 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.55 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.2956 Å²	-0 Å²	0 Å²
2-	-	-0.3081 Å²	0 Å²
3-	-	-	-5.9875 Å²

Refinement step

Cycle: LAST / Resolution: 2.5001→24.192 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1641	1148	0	80	2869

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2958
X-RAY DIFFRACTION	f_angle_d	1.225	4215
X-RAY DIFFRACTION	f_dihedral_angle_d	23.272	1239
X-RAY DIFFRACTION	f_chiral_restr	0.064	457
X-RAY DIFFRACTION	f_plane_restr	0.004	339

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 (%)
2.5001-2.6929	0.3703	150	0.3233	3003	X-RAY DIFFRACTION	100
2.6929-2.9635	0.3679	152	0.2825	3016	X-RAY DIFFRACTION	100
2.9635-3.3913	0.2518	131	0.2165	3004	X-RAY DIFFRACTION	99
3.3913-4.2689	0.2426	158	0.1784	3017	X-RAY DIFFRACTION	99
4.2689-24.1926	0.1966	165	0.1501	3016	X-RAY DIFFRACTION	95

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	9.5308	2.4716	-4.5475	5.3277	-7.1303	9.753	0.3833	-0.7975	1.2687	0.7799	0.3117	0.2801	-1.5812	-0.41	0.1953	0.4653	-0.0008	-0.2431	0.3771	0.1572	0.4361	25.2764	2.649	26.2307
2	0.56	-0.0815	0.4287	0.0389	-0.2268	0.6369	-0.0652	-0.0979	-0.2314	-0.3512	0.1176	-0.0445	-0.5148	0.0007	-0.1421	0.5574	0.021	-0.191	0.3976	-0.0531	0.3825	40.6925	-7.3623	35.4732
3	7.7278	1.615	3.3809	4.272	-0.9673	6.7358	0.4961	-0.0194	0.5506	1.9397	-0.2222	-0.1928	-0.0489	0.2561	-0.3193	0.7152	0.0077	-0.1384	0.3782	-0.0629	0.3518	48.9605	0.8486	46.8327
4	1.8679	-0.2612	0.6707	3.968	-1.3347	2.3189	0.882	-0.9561	0.5428	1.5963	-0.1338	-1.2521	-0.6538	1.2067	-0.3899	0.6605	-0.1868	-0.0814	0.7394	-0.1122	0.4714	54.9786	4.8755	40.6697
5	0.6798	-1.8529	1.2407	6.8713	-4.2662	3.4533	-0.8909	-0.0349	-0.017	0.6312	0.6842	-0.9347	-0.403	0.4151	0.3787	0.553	0.1006	-0.1448	0.4414	0.0181	0.5127	55.6096	-7.2334	40.5213
6	6.7476	-1.9547	-1.0409	0.715	0.1626	0.5297	0.3409	0.9939	-1.0018	0.2284	-0.1182	0.1351	0.5153	-0.3074	-1.4275	0.4182	0.0726	-0.1773	-0.1156	0.0626	0.1557	44.0287	-17.4163	39.6262
7	3.6438	-1.2852	1.7681	0.8155	-0.8074	3.7972	0.1363	0.6432	-0.598	0.2646	0.2174	0.357	1.0049	0.3676	-0.2794	0.7411	0.0042	-0.0953	0.2339	-0.0384	0.3616	29.0795	-13.0421	31.138
8	4.5412	5.6711	3.3876	8.4977	3.6967	2.9052	-0.0706	-1.358	0.408	0.033	-0.8537	0.7237	-1.0675	0.7033	0.7043	0.7033	-0.0508	-0.16	0.4696	-0.0511	0.2551	21.2536	-8.9458	25.8908
9	5.9238	-1.0212	1.3425	8.3647	5.2271	3.9143	-0.0238	-0.0955	0.6786	-0.9343	-0.2513	-0.1329	-1.0746	0.0126	0.1366	0.3638	-0.0164	-0.1754	0.2853	0.0449	0.3268	18.6365	-1.1309	18.8605
10	2.988	1.9185	1.8009	7.021	5.076	6.7001	-0.6669	0.6347	-0.151	0.8	0.3883	-0.9456	0.8756	-0.3053	-0.1613	0.2504	-0.095	-0.1638	0.2387	0.0437	0.283	27.3373	2.3016	17.8749
11	8.0433	-1.6926	4.9897	2.0068	-3.0937	6.2232	0.5094	-0.0878	-1.4786	-0.8415	0.1147	0.8754	2.2919	-0.0751	-0.4488	0.6271	-0.0747	0.0005	0.2153	0.0651	0.5715	37.2216	4.905	17.0034
12	5.4194	-1.4174	-3.0679	7.9658	3.936	3.8594	1.2543	0.5241	-0.0042	0.7186	-1.2202	1.0021	-0.3923	-0.1931	0.0115	0.4558	-0.0437	0.0474	0.2427	0.1749	0.6495	47.5815	10.4772	17.6709
13	0.5957	-1.0937	-0.9927	6.5072	0.1841	2.0752	0.4086	-0.0464	-0.2772	0.0402	-1.1388	-1.2725	-0.1334	-0.1874	0.3089	0.206	-0.0503	-0.0201	0.415	0.0624	0.6339	53.4115	18.499	13.4128
14	5.3106	1.0582	-1.5035	7.4864	-3.9629	3.8833	0.2902	-0.1011	0.6022	1.557	-0.1297	0.1646	-1.0157	-0.4866	-1.0341	0.3876	0.1171	0.0537	0.324	-0.0769	0.3323	40.1409	36.6168	17.3224
15	0.2799	0.9069	-0.0959	4.1338	0.3345	6.3226	0.3154	0.6474	0.518	-0.4124	-0.7643	1.2785	-0.6707	-0.5864	0.3608	0.2661	0.12	0.0649	0.4377	-0.062	0.5857	33.5221	38.2531	13.3336
16	5.3496	-0.3852	3.8269	8.7474	-5.9836	6.7222	-0.3093	0.4306	0.4333	0.7653	-0.006	-0.4652	-1.0921	0.4468	0.5072	0.3372	-0.0539	0.0254	0.3774	0.1107	0.3472	46.1554	42.4611	5.9302
17	1.7989	0.9362	2.5102	4.8651	1.0675	9.2387	-0.89	-0.8992	-0.1138	-1.4512	0.4437	-0.6309	-0.364	0.8915	0.5524	0.1959	-0.041	0.0304	0.4669	-0.0109	0.6184	55.1358	32.6484	5.5613
18	1.3727	0.0376	2.7095	2.4245	2.8305	8.7594	0.0963	0.7495	0.1341	-0.5713	-0.5674	-1.1058	-0.4657	0.7797	0.3272	0.0259	0.0877	0.0371	0.4372	0.0287	0.7653	59.9836	20.6683	7.3257
19	7.9394	4.4202	-2.0824	3.0968	-0.1082	2.3517	1.187	-0.5585	-3.514	0.246	-1.4625	-2.0781	0.6877	0.4807	0.2601	0.4883	0.2673	-0.0429	0.5167	0.1816	1.5836	62.5701	9.0214	9.0249
20	5.3616	-0.9099	-0.2467	0.1603	0.1929	1.8099	1.0562	1.0793	-1.0902	-1.6856	-0.656	0.4112	-0.4659	0.2348	-0.5139	0.5359	0.223	-0.1706	0.481	-0.1984	1.0624	55.8005	10.8777	3.1496
21	3.381	0.0574	-5.3522	0.1263	0.1497	9.9082	0.1633	1.3616	-0.376	-0.4145	-0.2148	-0.4636	-0.0516	-1.4382	0.3441	0.4845	-0.0562	0.0457	0.9694	-0.4609	0.6795	37.5027	18.323	-3.4283
22	2.4852	-1.8959	-1.3669	6.3149	-1.0488	7.5827	0.5616	0.1804	-0.1714	0.7214	0.4349	-0.2142	-0.7792	-0.255	-0.6523	0.4079	0.0639	-0.023	0.262	-0.0368	0.298	42.4167	25.2478	15.0422
23	8.8352	6.2749	-6.2085	5.2793	-2.4155	8.8995	1.173	-0.9609	-1.0843	1.8595	-1.798	0.3547	-0.7731	-0.0628	0.5013	1.1317	0.0303	0.2529	0.4327	0.0802	0.4543	37.5725	20.7869	29.0811
24	5.802	-1.0899	2.2951	4.3373	1.2367	1.499	-1.072	-0.276	0.5491	1.5543	0.3306	0.0805	-0.292	0.2959	0.8506	0.7099	-0.0965	-0.1496	0.3157	0.1011	0.4806	49.4622	5.0222	29.0288
25	0.7978	-0.2175	0.5963	2.8387	0.1267	0.4275	-0.4312	0.4898	0.0462	-2.2666	0.0881	-0.0449	-0.8122	0.0383	0.288	0.9656	0.076	-0.1285	0.4278	-0.0825	0.271	45.7395	-11.4417	28.6214
26	2.4354	1.9755	-2.4077	5.6764	-3.7289	3.1791	-0.4631	1.1964	0.2241	-1.532	1.1554	-0.2624	1.4694	-1.0611	-0.4933	1.3258	0.2419	-0.0646	0.82	-0.0925	0.2171	41.5962	-10.4736	14.0264
27	3.8076	-0.3254	-3.5121	4.1713	-3.0953	6.7269	1.7346	0.9771	-0.8796	0.1017	-1.027	0.5227	0.4451	1.6836	-0.6617	0.7904	0.117	-0.3078	0.9983	-0.4938	0.5552	47.6776	-17.1672	14.2534
28	6.4272	4.2313	7.0241	8.1021	5.9081	8.0387	-2.3659	0.0651	0.0745	-1.7762	1.1433	-0.5324	-6.0934	-0.4277	1.3983	1.9093	0.28	-0.1571	0.3544	-0.1049	0.161	43.4863	-4.508	23.2347
29	7.8635	3.2043	0.2298	3.6544	3.8246	9.4771	0.8017	-0.2959	1.017	-1.6882	-1.2774	0.2543	-3.0489	0.1101	0.3649	0.9642	0.0076	-0.0251	0.2393	-0.0292	0.3106	44.8101	4.8754	36.9223
30	5.7476	0.0242	4.8466	0.8071	0.2894	7.4648	0.4623	0.0393	-0.9368	0.7506	0.1687	1.6586	0.27	-0.0934	-0.9777	0.5877	-0.1337	-0.1386	0.0766	0.0375	0.5277	48.8696	16.5676	28.3413
31	4.6983	-6.0862	-0.8911	8.6885	3.2156	6.7525	0.9665	0.6509	-0.7245	-0.498	-0.3611	0.6245	-1.1097	-1.2872	-0.5948	0.3756	0.1527	-0.0369	0.4621	0.1504	0.4956	35.1931	21.351	18.9332
32	5.5625	-3.8148	-1.0093	5.4852	-2.3076	4.9593	-0.1331	0.8831	-0.1369	-0.8581	0.021	0.4435	1.0545	0.3671	0.0056	0.3077	0.0865	-0.0459	0.3363	-0.0417	0.3073	37.4185	29.1539	7.1115
33	4.2778	1.3176	0.9606	5.0144	5.8003	6.9918	1.111	0.7331	-0.6812	-0.8576	-1.2801	0.1281	0.4135	-0.9081	0.3869	0.5202	0.0331	-0.0535	0.7346	-0.3702	0.5956	46.0138	17.6129	-0.3169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:7)
2	X-RAY DIFFRACTION	2	(chain A and resid 8:19)
3	X-RAY DIFFRACTION	3	(chain A and resid 20:31)
4	X-RAY DIFFRACTION	4	(chain A and resid 32:39)
5	X-RAY DIFFRACTION	5	(chain A and resid 40:48)
6	X-RAY DIFFRACTION	6	(chain A and resid 49:63)
7	X-RAY DIFFRACTION	7	(chain A and resid 64:72)
8	X-RAY DIFFRACTION	8	(chain A and resid 73:77)
9	X-RAY DIFFRACTION	9	(chain A and resid 78:85)
10	X-RAY DIFFRACTION	10	(chain A and resid 86:91)
11	X-RAY DIFFRACTION	11	(chain A and resid 92:99)
12	X-RAY DIFFRACTION	12	(chain A and resid 100:106)
13	X-RAY DIFFRACTION	13	(chain A and resid 107:116)
14	X-RAY DIFFRACTION	14	(chain A and resid 117:137)
15	X-RAY DIFFRACTION	15	(chain A and resid 138:149)
16	X-RAY DIFFRACTION	16	(chain A and resid 150:162)
17	X-RAY DIFFRACTION	17	(chain A and resid 163:167)
18	X-RAY DIFFRACTION	18	(chain A and resid 168:179)
19	X-RAY DIFFRACTION	19	(chain A and resid 180:185)
20	X-RAY DIFFRACTION	20	(chain A and resid 186:191)
21	X-RAY DIFFRACTION	21	(chain B and resid 1:4)
22	X-RAY DIFFRACTION	22	(chain B and resid 5:10)
23	X-RAY DIFFRACTION	23	(chain B and resid 11:14)
24	X-RAY DIFFRACTION	24	(chain B and resid 15:20)
25	X-RAY DIFFRACTION	25	(chain B and resid 21:24)
26	X-RAY DIFFRACTION	26	(chain B and resid 25:28)
27	X-RAY DIFFRACTION	27	(chain C and resid 1:4)
28	X-RAY DIFFRACTION	28	(chain C and resid 5:8)
29	X-RAY DIFFRACTION	29	(chain C and resid 9:12)
30	X-RAY DIFFRACTION	30	(chain C and resid 13:16)
31	X-RAY DIFFRACTION	31	(chain C and resid 17:20)
32	X-RAY DIFFRACTION	32	(chain C and resid 21:24)
33	X-RAY DIFFRACTION	33	(chain C and resid 25:28)

-
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