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- PDB-5ip9: Structure of RNA Polymerase II-TFIIF complex -

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Basic information

Entry
Database: PDB / ID: 5ip9
TitleStructure of RNA Polymerase II-TFIIF complex
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
KeywordsTRANSCRIPTION / transcription
Function / homologyDNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit 2 ...DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit 2 / Pol II subunit B9, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 2 superfamily / Transcription initiation factor IIF, alpha subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerases M / 15 Kd subunits signature. / HRDC-like superfamily / Transcription Factor IIF, Rap30/Rap74, interaction / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase RBP11 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 6 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / RNA polymerase Rpb3/Rpb11 dimerisation domain / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb4 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb3/RpoA insert domain / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / Zinc finger TFIIS-type signature. / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase Rpb1, domain 4 / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.9 Å resolution
AuthorsPlaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P.
CitationJournal: Nature / Year: 2016
Title: Transcription initiation complex structures elucidate DNA opening.
Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2016 / Release: May 11, 2016
RevisionDateData content typeGroupProviderType
1.0May 11, 2016Structure modelrepositoryInitial release
1.1May 25, 2016Structure modelDatabase references
1.2Jun 8, 2016Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Q: PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,98322
Polyers498,43613
Non-polymers5489
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)66670
ΔGint (kcal/M)-326
Surface area (Å2)151010
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)222.820, 392.730, 283.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC 2 2 21

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191690.375 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138806.109 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 29921.785 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P16370
#4: Protein/peptide DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20433
#7: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P34087
#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 13942.714 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P27999
#11: Protein/peptide DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13113.989 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 24985.895 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20434
#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 10046.682 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20435
#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16394.166 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20436
#10: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 7647.000 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22139
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 5252.261 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40422

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Protein/peptide , 1 types, 1 molecules Q

#13: Protein/peptide PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG


Mass: 2102.603 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P41895*PLUS

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 6.22 / Density percent sol: 80.22 %
Crystal growTemp: 295 K / Method: vapor diffusion, hanging drop
Details: peg 6000, sodium acetate, ammonium acetate, hepes, tcep

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91889 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Collection date: Jul 3, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91889 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 99.89 Å2 / D resolution high: 3.45 Å / D resolution low: 5 Å / Number obs: 112721 / Observed criterion sigma I: -3 / CC half: 0.997 / Rmerge I obs: 0.206 / NetI over sigmaI: 9.19 / Redundancy: 7.5 % / Percent possible obs: 99.9
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsDiffraction IDPercent possible all
4.0113.4503.5400.6301100.000
2.8273.5403.6400.870199.900
1.8813.6403.7401.3001100.000
1.4373.7403.8601.6901100.000
1.0313.8603.9802.3701100.000
0.6783.9804.1203.4501100.000
0.4894.1204.2804.8001100.000
0.3354.2804.4506.7701100.000
0.2714.4504.6508.3301100.000
0.2204.6504.8809.9601100.000
0.2034.8805.14010.7301100.000
0.1875.1405.45011.1801100.000
0.1685.4505.83012.2301100.000
0.1445.8306.30014.2301100.000
0.1136.3006.90016.8101100.000
0.0806.9007.71021.020199.900
0.0567.7108.91026.7201100.000
0.0448.91010.91034.460199.900
0.03810.91015.43038.350199.900
0.03215.43042.410195.900

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.20data extraction
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PO2
Correlation coeff Fo to Fc: 0.9248 / Correlation coeff Fo to Fc free: 0.8954 / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall SU R free Blow DPI: 0.383
Displacement parametersB iso max: 3 Å2 / B iso mean: 130.08 Å2 / B iso min: 2 Å2 / Aniso B11: 3.8406 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 25.5238 Å2 / Aniso B23: 0 Å2 / Aniso B33: -29.3644 Å2
Least-squares processR factor R free: 0.1937 / R factor R work: 0.1622 / R factor obs: 0.1628 / Highest resolution: 3.9 Å / Lowest resolution: 48.93 Å / Number reflection R free: 2265 / Number reflection obs: 112717 / Percent reflection R free: 2.01 / Percent reflection obs: 99.97
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refine hist #finalHighest resolution: 3.9 Å / Lowest resolution: 48.93 Å / B iso mean ligand: 124.4 / Number residues total: 3950
Number of atoms included #finalProtein: 31330 / Nucleic acid: 0 / Ligand: 9 / Solvent: 0 / Total: 31339
Refine LS restraints
Refine IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11507SINUSOIDAL2.000
X-RAY DIFFRACTIONt_trig_c_planes859HARMONIC2.000
X-RAY DIFFRACTIONt_gen_planes4553HARMONIC5.000
X-RAY DIFFRACTIONt_it31891HARMONIC20.000
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5.000
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4206SEMIHARMONIC5.000
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1.000
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37326SEMIHARMONIC4.000
X-RAY DIFFRACTIONt_bond_d31891HARMONIC2.0000.010
X-RAY DIFFRACTIONt_angle_deg43050HARMONIC2.0001.260
X-RAY DIFFRACTIONt_omega_torsion2.740
X-RAY DIFFRACTIONt_other_torsion23.940
Refine LS shellHighest resolution: 3.9 Å / R factor R free: 0.2915 / R factor R work: 0.2272 / R factor all: 0.2283 / Lowest resolution: 4 Å / Number reflection R free: 155 / Number reflection R work: 8085 / Number reflection all: 8240 / Total number of bins used: 20 / Percent reflection R free: 1.88 / Percent reflection obs: 99.94
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
18.68561.44800.55322.3303-0.35122.1122-0.01150.6308-0.77180.0160-0.0786-0.08900.4862-0.31550.0901-0.3162-0.04260.13010.19650.0098-0.353398.481331.7277-37.8527
21.10780.74080.28383.7726-0.76811.6918-0.03650.35780.3214-0.0055-0.17160.2615-0.1290-0.19630.2081-0.48780.1722-0.05050.17200.3727-0.068991.513359.4881-40.8573
30.31860.21600.48410.4974-0.18081.27150.03880.09010.15920.2445-0.0949-0.09700.10540.07770.0561-0.1770-0.02910.0095-0.07290.0643-0.0512125.829036.63345.1955
41.2563-0.7988-0.35392.6085-0.40750.0000-0.07090.07120.44470.7812-0.15230.1204-0.21450.12020.22320.1958-0.06950.2098-0.2727-0.29320.0029103.532069.365825.3714
52.24220.68990.67660.96000.09980.19300.1942-0.04910.33810.1459-0.1143-0.18950.0129-0.0452-0.0799-0.4100-0.08990.0864-0.19520.15950.3081140.072066.8794-2.6252
65.7121-3.82180.38721.7538-0.65150.5359-0.2432-0.15230.72800.11760.1192-0.57190.0082-0.06800.1240-0.49630.07820.0295-0.4866-0.17370.9119101.9540104.57000.3650
70.12090.11280.74181.29230.30740.34460.09230.33600.6415-0.0812-0.1882-0.05390.1441-0.08590.0960-0.37960.06980.1375-0.07200.19850.2408118.987059.1296-18.4193
80.4066-1.2007-0.05730.4765-0.26800.00000.0649-0.1617-0.12580.09110.11571.0227-0.0720-0.1231-0.1806-0.43490.05020.3111-0.19780.03600.714666.765644.520910.4976
94.67740.36921.77984.9706-1.03922.0022-0.10210.1098-0.2219-0.16740.22880.24960.0008-0.0229-0.1267-0.48990.23080.1678-0.4411-0.17860.536566.646383.6992-5.8316
101.7099-0.25991.18710.00000.29721.0085-0.12320.20220.3413-0.19470.28600.7447-0.06110.2323-0.1628-0.20160.05910.1810-0.21320.03050.355375.072651.69421.5771
110.0124-1.81580.52950.6168-1.03871.1777-0.1397-0.28390.39090.3910-0.08380.40430.0397-0.20540.2236-0.19710.26220.4559-0.1886-0.15080.443869.355168.351326.2079
120.0000-1.1113-0.34321.2727-0.69900.2832-0.0844-0.15170.15270.39670.24430.13310.0109-0.0367-0.1599-0.0265-0.02920.3595-0.1470-0.1200-0.062793.035142.363023.3411
130.07310.88601.73462.93930.61063.9570-0.22680.0563-0.0141-0.67600.51070.6559-0.01220.4150-0.28390.0393-0.23220.0848-0.22290.0202-0.012786.738317.0139-0.4611
140.4005-0.06100.00010.1217-0.21421.29610.04580.12070.23930.17500.05810.11700.1720-0.0242-0.1039-0.07260.02010.1315-0.08960.0028-0.1789108.541038.39802.0771
151.2011-0.00130.11191.1303-0.08130.1989-0.0697-0.2970-0.24620.75720.05070.05660.20650.05930.01910.3289-0.00440.1892-0.03720.1795-0.4998110.558016.446236.2838
160.1493-0.0894-0.11831.0362-0.10204.3608-0.04900.3411-0.03560.18510.1054-0.02640.06130.5630-0.0564-0.40820.15760.07230.3883-0.0920-0.3327135.865029.8736-65.5017
171.2184-0.27910.02763.86080.11600.34380.05790.18030.5267-0.4658-0.1345-0.1336-0.05530.13980.0766-0.3138-0.06980.0802-0.34430.44410.5299126.935092.7723-25.3168
181.3690-0.10840.09435.9984-0.54832.53070.05110.13000.15670.15300.0540-0.51060.20680.2566-0.1051-0.42510.07600.06700.10920.1417-0.0852139.693038.7219-19.8766
190.21330.16141.39870.97291.55365.29450.00420.0553-0.24240.13710.09150.11470.46640.3482-0.0957-0.27750.24640.13660.24780.0089-0.1799126.307023.3184-59.6886
202.28311.64831.44263.9300-1.00101.4855-0.1879-0.32750.41720.5085-0.1378-0.6469-0.24890.29690.3257-0.0316-0.3091-0.45590.0424-0.0660-0.1398152.249052.354036.3730
210.6906-1.51061.47771.4295-2.21162.1602-0.15310.15080.41430.7644-0.05110.4612-0.02180.18340.20410.01170.27390.2978-0.3725-0.26680.651376.888499.312614.1705
223.66681.0445-0.60380.72650.41830.5738-0.03650.09650.29370.61010.08520.28830.11690.2386-0.04870.27220.05260.4208-0.13380.0531-0.268791.164825.841437.5209
231.12610.53620.58082.0994-1.35930.0000-0.06620.3737-0.25480.4154-0.1259-0.31960.11450.20300.19220.10540.1733-0.0821-0.01920.1129-0.3388131.963017.398128.2003
241.46961.44491.26523.22281.18663.54590.12140.0711-0.41330.4871-0.26331.39150.5542-0.04500.1419-0.1156-0.25340.2418-0.25570.22060.457776.35199.64979.1671
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A3A811{ A|3 - A|81 }
2A82A3232{ A|82 - A|323 }
3A324A6593{ A|324 - A|659 }
4A660A8314{ A|660 - A|831 }
5A832A11275{ A|832 - A|1127 }
6A1128A13296{ A|1128 - A|1329 }
7A1330A14547{ A|1330 - A|1454 }
8B20B2348{ B|20 - B|234 }
9B235B3929{ B|235 - B|392 }
10B393B53910{ B|393 - B|539 }
11B540B73511{ B|540 - B|735 }
12B736B84112{ B|736 - B|841 }
13B842B97413{ B|842 - B|974 }
14B975B122414{ B|975 - B|1224 }
15C3C26815{ C|3 - C|268 }
16D4D22116{ D|4 - D|221 }
17E2E21517{ E|2 - E|215 }
18F72F15518{ F|72 - F|155 }
19G1G17119{ G|1 - G|171 }
20H2H14620{ H|2 - H|146 }
21I2I12021{ I|2 - I|120 }
22J1J6522{ J|1 - J|65 }
23K2K11423{ K|2 - K|114 }
24L25L7024{ L|25 - L|70 }

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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. See below links for details.
  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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.

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

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