[English] 日本語
Yorodumi
- PDB-6erq: Structure of the human mitochondrial transcription initiation com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6erq
TitleStructure of the human mitochondrial transcription initiation complex at the HSP promoter
Components
  • DNA-directed RNA polymerase, mitochondrial
  • Dimethyladenosine transferase 2, mitochondrial
  • Non-Template DNA
  • Template DNA
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION / Mitochondria / Initiation / Polymerase
Function / homology
Function and homology information


rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial respiratory chain complex assembly / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication ...rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial respiratory chain complex assembly / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial transcription / rRNA methylation / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol
Similarity search - Function
DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / : ...DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / : / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase, mitochondrial / Transcription factor A, mitochondrial / Dimethyladenosine transferase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsHillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.
Funding support Germany, United States, 6items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
German Research FoundationSPP1935 Germany
European Research Council693023 Germany
Volkswagen Foundation Germany
National Institutes of HealthRO1 GM104231 United States
Boehringer Ingelheim FondsPhD Student Fellowship Germany
CitationJournal: Cell / Year: 2017
Title: Structural Basis of Mitochondrial Transcription Initiation.
Authors: Hillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Transcription factor A, mitochondrial
D: Non-Template DNA
E: Template DNA
G: Transcription factor A, mitochondrial
H: Non-Template DNA
I: Template DNA
A: DNA-directed RNA polymerase, mitochondrial
B: DNA-directed RNA polymerase, mitochondrial
F: Dimethyladenosine transferase 2, mitochondrial
J: Dimethyladenosine transferase 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)453,22010
Polymers453,22010
Non-polymers00
Water00
1
C: Transcription factor A, mitochondrial
D: Non-Template DNA
E: Template DNA
A: DNA-directed RNA polymerase, mitochondrial
F: Dimethyladenosine transferase 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)226,6105
Polymers226,6105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-70 kcal/mol
Surface area85180 Å2
MethodPISA
2
G: Transcription factor A, mitochondrial
H: Non-Template DNA
I: Template DNA
B: DNA-directed RNA polymerase, mitochondrial
J: Dimethyladenosine transferase 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)226,6105
Polymers226,6105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15240 Å2
ΔGint-73 kcal/mol
Surface area83570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.620, 197.730, 134.340
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#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: 24516.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAM, TCF6, TCF6L2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: Q00059
#2: DNA chain Non-Template DNA


Mass: 15104.715 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain Template DNA


Mass: 15701.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein DNA-directed RNA polymerase, mitochondrial / MtRPOL


Mass: 127904.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLRMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O00411, DNA-directed RNA polymerase
#5: Protein Dimethyladenosine transferase 2, mitochondrial / Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial ...Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial 12S rRNA dimethylase 2 / Mitochondrial transcription factor B2 / mtTFB2 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 2


Mass: 43383.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFB2M, NS5ATP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q9H5Q4, Transferases; Transferring one-carbon groups; Methyltransferases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: L-Proline, PEG8000, BIS-TRIS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 4.5→49.58 Å / Num. obs: 31460 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 1 / Rrim(I) all: 0.087 / Net I/σ(I): 13.38
Reflection shellResolution: 4.5→4.61 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2303 / CC1/2: 0.502 / Rrim(I) all: 2.232 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model of the human mitochondrial IC on the LSP promoter

Resolution: 4.5→49.576 Å / SU ML: 0.92 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 44.2
RfactorNum. reflection% reflection
Rfree0.3334 1571 5 %
Rwork0.291 --
obs0.2932 31417 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.5→49.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23883 3724 0 0 27607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228593
X-RAY DIFFRACTIONf_angle_d0.51339445
X-RAY DIFFRACTIONf_dihedral_angle_d16.19316795
X-RAY DIFFRACTIONf_chiral_restr0.0544369
X-RAY DIFFRACTIONf_plane_restr0.0034417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-4.64520.42551420.40622701X-RAY DIFFRACTION99
4.6452-4.81110.44911410.41592694X-RAY DIFFRACTION99
4.8111-5.00350.41751420.39352704X-RAY DIFFRACTION99
5.0035-5.2310.42041420.38482692X-RAY DIFFRACTION98
5.231-5.50650.38251430.38632720X-RAY DIFFRACTION100
5.5065-5.8510.50621450.40132740X-RAY DIFFRACTION100
5.851-6.30190.43491410.38832696X-RAY DIFFRACTION100
6.3019-6.93460.36251450.36912741X-RAY DIFFRACTION100
6.9346-7.93450.3521420.33242698X-RAY DIFFRACTION98
7.9345-9.98320.27311430.23662724X-RAY DIFFRACTION100
9.9832-49.5790.27651450.21552736X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL11 (°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)
12.7701-1.3061-2.949410.0699-0.85893.6295-0.20142.01742.52.34390.3813-2.3594-1.11983.6050.00433.27510.28260.01443.74890.42413.789590.09649.0948-42.9345
2-0.1896-0.31720.0066-0.2945-0.6042-0.3921-1.5995.38190.4743-1.15420.0723-0.3175-1.78733.53390.02793.7770.0155-0.38465.6150.33185.114871.407947.1889-50.3278
32.79333.11470.90199.28767.48215.1762-0.2364-0.0971-1.381-3.511.9286-1.95410.30490.76140.00493.2211-0.07090.32074.39180.57843.403493.2519.0369-68.0437
40.5361-0.2127-0.15960.7476-0.64860.71094.27641.3933-0.45152.0442-2.8699-2.3682-0.3146-0.18450.00434.4927-0.0378-0.43944.91750.21544.004176.010411.9165-75.159
51.86790.55462.28640.44461.15573.1455-0.36351.85680.8845-3.665-2.7457-0.547-1.94973.51750.00054.4663-0.97620.91086.2913-0.09394.538294.728825.9518-68.6332
63.31891.5812-0.03280.6799-0.0772-0.028-0.41320.5123-6.22111.2144-1.28424.5619-1.93581.49930.00484.16391.160.0124.48820.00675.032482.26841.3101-42.5172
70.4778-0.7743-0.3051.11530.48990.17611.75347.49844.71-1.4684-2.9195-9.57371.1665-0.91250.00893.5910.30810.37494.52411.25724.919359.759434.6822-36.7017
82.01973.69042.94016.29438.48181.96756.60734.0019-4.07440.043-0.463-0.3222.55681.69698.71718.1225-1.58473.24824.8056-2.3766.207342.397340.2365-35.2078
94.2786-3.38422.00512.99958.98561.98024.8729-1.6855-2.1593-4.32330.52976.91713.92377.38314.08185.3951.8353-1.19794.55910.67526.334620.941340.5518-35.5677
100.23020.06350.2049-0.00640.07930.1339-2.54994.28492.5767-1.22143.66291.49971.1738.31570.00156.31841.2344-1.47198.8136-1.15316.292526.095342.5088-17.1521
110.5220.6913-0.6270.9830.1823.24120.91612.0603-6.9403-5.0337-1.2034-1.3907-5.98461.25950.07124.77010.819-0.48766.2004-3.04397.560322.244848.481-15.2194
127.0449-6.7112-2.62642.0255-1.80531.8168-2.06262.61014.0741-9.40565.562-5.21452.9689-4.25851.31814.2306-0.3585-0.66517.25730.04584.789228.64133.1166-30.4913
132.978-0.63122.51096.75077.09099.43770.5757-2.11783.32880.7819-1.6014-0.8711-0.69540.4497-0.00043.1761-0.1605-0.06544.46650.49424.761459.593438.4415-38.1538
143.4044-2.3364-0.93581.57972.29846.2617-0.20290.61510.4644-1.30231.8677-0.4294-1.2442.30180.00084.85920.7419-0.03784.79080.1813.349488.584125.1328-65.3245
155.61932.58917.4741.44171.8349.0095-0.48950.5911-1.1473-0.91510.5252-0.45640.0986-0.25950.00343.75730.3289-0.5844.49110.23885.202695.366-104.4426-23.8566
167.2575-7.46725.2029.7393-7.6095.8667-0.0752.07740.5684-2.69051.0131-0.73691.09553.50730.05993.2263-0.17221.12683.3552-0.54212.842978.5538-100.9585-50.4496
174.981-6.3881-0.47395.79223.96859.4766-0.58713.21881.06630.26921.17690.85991.8821-2.61220.14374.18390.19590.76032.7295-0.13683.843266.5608-114.23-62.2023
185.1095-3.8356-4.89034.60450.77736.97190.7525-2.40262.1018-0.9006-1.3152-1.79733.3962-0.2011-0.00074.26770.0055-0.05924.9337-0.55445.111176.2703-106.2427-60.164
190.029-0.0641-0.66550.9542-0.24181.30290.0991-2.1117-1.9513-1.3786-0.3884-2.4709-4.6991-1.08720.00264.5209-0.21680.16435.32850.23545.261885.107-103.0572-27.3088
201.5070.57540.79150.54880.29370.3537-3.40420.95082.2146-4.68313.2984-3.69284.4838-2.1124-0.00475.6873-0.95580.29783.86930.68494.870873.1906-81.4307-22.2158
213.92711.83315.56510.79532.31934.861-1.0818-2.04531.1751.76780.70590.4681-0.6285-3.0618-0.00036.1209-0.10070.19244.0796-0.19264.981768.4257-51.6377-11.125
222.0106-7.447-2.34453.1870.97710.2924-5.8725-4.667711.5788-2.72318.9875-2.27544.6793-0.2687-0.10186.5127-0.0695-1.05733.6522-0.97956.776669.4597-42.85244.1661
231.96661.91069.21942.77933.65942.07847.07155.55560.52562.0899-0.1789-3.9832-1.26996.88250.86746.8582-2.58991.37957.2936-0.47294.92160.2591-52.4688-14.9123
246.5798-3.5652-3.1812.38281.02250.1889-1.96120.1123-2.6370.71490.96731.8984-0.31031.36650.00134.7925-0.02530.15614.5922-0.08135.210680.8889-92.5407-30.9046
254.020.01451.12415.3032-0.09730.26133.7312-0.63732.0165-6.6057-0.6258-4.45990.26261.1370.23235.5477-1.1179-0.21773.7792-0.17553.652568.586-104.2097-65.2416
264.806-4.7978-7.46640.26272.79858.27340.1604-1.00562.30050.79981.0197-0.6824-0.74231.00770.00123.615-0.0116-0.3223.9511-0.33492.748673.694212.4894-31.2296
276.8185-4.6944-5.77425.64160.63936.3856-1.7438-1.9963-1.53021.27681.3514-0.21831.39731.06570.00043.82790.6491-0.30373.61770.28942.129358.0696-4.3489-11.3372
282.56050.0134-2.13295.33920.62853.3178-0.07650.1789-0.7819-0.5249-0.2121-0.158-0.03260.1672-0.00072.7780.377-0.13013.2323-0.05862.590641.95184.1184-44.6019
298.7186-1.28150.34151.3287-2.41376.3734-0.10260.1161-0.45060.09770.26791.4738-0.4133-0.6888-02.79520.2628-0.18582.80910.06543.836716.8061-0.7783-37.4784
301.6197-0.70440.43316.5394-0.80571.7456-0.7544-0.6103-0.08170.11290.38521.5139-0.4696-0.7554-03.5970.57510.3544.21640.31823.639314.305214.3263-19.8259
311.5413-1.3281-0.25172.6251-0.34833.8543-0.24180.05890.11970.8940.09270.77040.65150.207303.7228-0.3746-0.02843.43160.64783.083640.9452-91.8807-21.5341
325.886-0.4669-2.85655.2373-0.66125.71680.26590.40280.19710.4440.06511.26730.07860.0827-0.00033.4285-0.1794-0.10512.7623-0.08943.188243.0696-71.8579-36.2936
332.1664-0.1079-2.56673.23710.74972.56510.38070.2231.48460.42410.39721.241-0.9051-1.232-0.00013.29120.0549-0.01043.16750.55014.196526.793-44.7091-27.1177
342.4484-0.40920.21886.76561.042-1.83381.2372-0.22791.13380.6078-0.56881.1168-1.3706-0.282-0.00014.2138-0.00540.22073.42-0.21823.214438.6676-48.1694-8.5757
351.71270.76850.47670.4741-0.46081.9075-1.82930.17240.9676-1.238-2.0021-0.3372-1.4508-1.5136-0.09874.454-0.040.93383.9929-0.4715.71219.660369.968-44.3887
360.4829-0.5634-0.06382.7897-1.47890.9101-0.335-1.19721.0811-0.4731-2.65736.3543-3.7133-2.28170.00263.99870.74940.44844.9921-0.62045.388212.951963.1052-47.3815
372.10911.72452.19182.60421.71292.3348-3.9876-1.67721.77580.69397.67890.4133-1.691-2.39150.00415.11690.56510.91865.10690.16384.8267.587263.3679-42.8216
380.9284-0.04390.91810.0317-0.27952.5286-1.56190.8334-0.1773-5.20051.25850.33412.9436-7.91760.00483.36960.45120.60443.54950.85193.268510.573942.9612-44.2961
391.87692.0951-3.53683.1052-3.60865.04311.16412.0781-0.12690.32081.36450.3028-0.9766-0.3684-0.00032.7796-0.2873-0.1474.48730.12744.090519.68352.6813-53.0651
402.4309-2.2972-2.49945.12298.53098.07220.6292-0.64522.13980.58850.6063-0.4529-0.99930.2412-0.00043.5312-0.35340.74473.3067-0.07164.436731.321349.656-56.6981
419.21041.6983-5.75152.16957.90634.142.3884-2.4711-0.0973-1.38873.2742-6.82113.02523.13117.23864.2834-0.2146-0.13294.42581.18073.354544.094433.7764-63.6552
423.18690.914-1.06545.584-3.27952.76792.10861.27791.0954-0.11980.49230.20331.8748-1.9144-0.00014.062-0.16360.14714.11740.87013.145237.814937.1628-65.2979
431.9484.5177-3.88731.98111.97858.7893-3.1904-4.7141-2.9729-1.1451-4.3918-8.7417-1.2695-1.0335-2.53973.9784-1.1069-0.31865.4644-1.50226.114495.1118-32.2991-18.3234
440.9010.4142-0.65991.78081.43092.02983.5491-4.08326.1451-2.3249-0.16122.9911-0.9422-4.88450.02782.97140.1059-0.17684.573-1.18774.607687.6542-27.3283-22.731
452.126-0.5733-2.63783.4721-0.91894.68063.5761-7.9675.72855.025-4.5721-2.5927-2.65687.9913-1.41354.3303-1.53420.4253.4012-1.94964.250185.2655-22.6434-18.1864
463.3282-0.55074.53380.6589-0.05476.9381.40950.39680.49471.3708-0.5965-0.5592-5.611-2.3610.00084.6740.09780.64853.074-0.3865.109375.0233-27.4949-32.219
471.6561-2.2358-1.35422.57430.36363.49361.4786-2.1712-0.131-1.5174-0.17151.32791.539-1.5428-0.00042.6281-0.5603-0.44552.7048-0.47683.423781.7939-40.3751-28.805
489.12630.8481-6.23959.63941.76054.68491.5327-0.611.639-0.2844-0.1184-4.03953.0778-0.0853-03.812-0.6153-0.49743.0894-0.37014.020586.0527-45.8233-34.9356
494.1482-1.73813.99191.0722-2.78156.14221.12920.9283-0.68650.4691-1.3921-2.39442.0799-0.25020.00043.7893-1.01560.06272.4882-0.50372.764173.1795-59.2756-43.6438
504.71574.0759-4.09974.7383-5.90357.3229-1.05372.66840.4772-1.06821.60770.64960.6668-0.39670.00033.0090.1730.02872.6759-0.04442.770874.9744-55.9628-47.5538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 43 through 92 )
2X-RAY DIFFRACTION2chain 'C' and (resid 93 through 151 )
3X-RAY DIFFRACTION3chain 'C' and (resid 152 through 234 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'D' and (resid 6 through 15 )
6X-RAY DIFFRACTION6chain 'D' and (resid 16 through 25 )
7X-RAY DIFFRACTION7chain 'D' and (resid 26 through 30 )
8X-RAY DIFFRACTION8chain 'D' and (resid 31 through 35 )
9X-RAY DIFFRACTION9chain 'D' and (resid 36 through 44 )
10X-RAY DIFFRACTION10chain 'D' and (resid 45 through 50 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 5 )
12X-RAY DIFFRACTION12chain 'E' and (resid 6 through 15 )
13X-RAY DIFFRACTION13chain 'E' and (resid 16 through 30 )
14X-RAY DIFFRACTION14chain 'E' and (resid 31 through 50 )
15X-RAY DIFFRACTION15chain 'G' and (resid 43 through 122 )
16X-RAY DIFFRACTION16chain 'G' and (resid 123 through 169 )
17X-RAY DIFFRACTION17chain 'G' and (resid 170 through 234 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 15 )
19X-RAY DIFFRACTION19chain 'H' and (resid 16 through 25 )
20X-RAY DIFFRACTION20chain 'H' and (resid 26 through 30 )
21X-RAY DIFFRACTION21chain 'H' and (resid 31 through 50 )
22X-RAY DIFFRACTION22chain 'I' and (resid 1 through 5 )
23X-RAY DIFFRACTION23chain 'I' and (resid 6 through 15 )
24X-RAY DIFFRACTION24chain 'I' and (resid 16 through 40 )
25X-RAY DIFFRACTION25chain 'I' and (resid 41 through 50 )
26X-RAY DIFFRACTION26chain 'A' and (resid 122 through 309 )
27X-RAY DIFFRACTION27chain 'A' and (resid 310 through 378 )
28X-RAY DIFFRACTION28chain 'A' and (resid 379 through 645 )
29X-RAY DIFFRACTION29chain 'A' and (resid 646 through 906 )
30X-RAY DIFFRACTION30chain 'A' and (resid 907 through 1230 )
31X-RAY DIFFRACTION31chain 'B' and (resid 122 through 423 )
32X-RAY DIFFRACTION32chain 'B' and (resid 424 through 677 )
33X-RAY DIFFRACTION33chain 'B' and (resid 678 through 972 )
34X-RAY DIFFRACTION34chain 'B' and (resid 973 through 1230 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 89 )
36X-RAY DIFFRACTION36chain 'F' and (resid 90 through 107 )
37X-RAY DIFFRACTION37chain 'F' and (resid 108 through 153 )
38X-RAY DIFFRACTION38chain 'F' and (resid 154 through 168 )
39X-RAY DIFFRACTION39chain 'F' and (resid 169 through 238 )
40X-RAY DIFFRACTION40chain 'F' and (resid 239 through 330 )
41X-RAY DIFFRACTION41chain 'F' and (resid 331 through 353 )
42X-RAY DIFFRACTION42chain 'F' and (resid 354 through 392 )
43X-RAY DIFFRACTION43chain 'J' and (resid 72 through 89 )
44X-RAY DIFFRACTION44chain 'J' and (resid 90 through 107 )
45X-RAY DIFFRACTION45chain 'J' and (resid 108 through 153 )
46X-RAY DIFFRACTION46chain 'J' and (resid 154 through 189 )
47X-RAY DIFFRACTION47chain 'J' and (resid 190 through 238 )
48X-RAY DIFFRACTION48chain 'J' and (resid 239 through 316 )
49X-RAY DIFFRACTION49chain 'J' and (resid 317 through 353 )
50X-RAY DIFFRACTION50chain 'J' and (resid 354 through 392 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more