[English] 日本語
Yorodumi
- PDB-5uac: Escherichia coli RNA polymerase and Rifampin complex, wild-type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uac
TitleEscherichia coli RNA polymerase and Rifampin complex, wild-type
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
Keywordstransferase/transferase inhibitor / inhibitor / antibiotic / tuberculosis / rifampin / rifamycin / RNA polymerase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain ...RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RIFAMPICIN / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsMolodtsov, V. / Scharf, N.T. / Stefan, M.A. / Garcia, G.A. / Murakami, K.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087350 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI110780 United States
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis.
Authors: Molodtsov, V. / Scharf, N.T. / Stefan, M.A. / Garcia, G.A. / Murakami, K.S.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)920,94719
Polymers919,81412
Non-polymers1,1337
Water00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,88510
Polymers459,9076
Non-polymers9784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37810 Å2
ΔGint-193 kcal/mol
Surface area155030 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,0629
Polymers459,9076
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36800 Å2
ΔGint-188 kcal/mol
Surface area153950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.958, 204.430, 313.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABGHCIDJEK

#1: Protein
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase

-
Protein , 1 types, 2 molecules FL

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 70352.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Production host: Escherichia coli (E. coli) / References: UniProt: P00579

-
Non-polymers , 3 types, 7 molecules

#6: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6299 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6299 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 119630 / % possible obs: 100 % / Redundancy: 8.2 % / Net I/σ(I): 9.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YG2

4yg2


Resolution: 3.8→29.982 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 1991 1.67 %
Rwork0.2483 --
obs0.2491 119413 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→29.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54984 0 65 0 55049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01755850
X-RAY DIFFRACTIONf_angle_d1.56475384
X-RAY DIFFRACTIONf_dihedral_angle_d16.65334553
X-RAY DIFFRACTIONf_chiral_restr0.0788584
X-RAY DIFFRACTIONf_plane_restr0.0139878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.89480.36191280.34618125X-RAY DIFFRACTION98
3.8948-3.99990.37221530.34648296X-RAY DIFFRACTION100
3.9999-4.11730.3721350.32488341X-RAY DIFFRACTION100
4.1173-4.24990.37491430.30628327X-RAY DIFFRACTION100
4.2499-4.40130.3371450.29698332X-RAY DIFFRACTION100
4.4013-4.5770.30591310.28418346X-RAY DIFFRACTION100
4.577-4.78450.3391440.26968336X-RAY DIFFRACTION100
4.7845-5.03560.28681520.26758354X-RAY DIFFRACTION100
5.0356-5.34940.331390.26748399X-RAY DIFFRACTION100
5.3494-5.75980.32631420.26958392X-RAY DIFFRACTION100
5.7598-6.33450.33011420.27148433X-RAY DIFFRACTION100
6.3345-7.23980.32461420.25448455X-RAY DIFFRACTION100
7.2398-9.07920.27051430.21558531X-RAY DIFFRACTION100
9.0792-29.98330.2341520.19358755X-RAY DIFFRACTION100
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)
12.46382.3551-1.17383.5299-1.49632.40180.4441-0.7404-0.03831.032-0.2002-0.4523-0.45010.2253-0.24151.78330.0409-0.07591.6263-0.16221.3904103.00733.395839.1829
22.91382.0152-0.53394.1118-1.28211.3116-0.2472-0.58670.9286-0.4780.0640.38110.6263-0.35920.32351.7972-0.00450.05381.5318-0.28971.12795.958535.474129.3392
34.80292.02541.13333.90910.76032.18790.1234-1.38680.07022.1116-0.65350.4161.0588-0.09420.49372.35410.10980.29231.9075-0.12981.204790.102212.859745.9658
47.59813.3754-0.54957.40721.55114.0455-0.2706-0.52830.4153-0.8778-0.20660.60530.4188-0.46470.37321.409-0.1544-0.06791.42770.01941.142977.040812.884930.0125
50.4147-0.44680.36923.49241.02350.9178-0.83270.6557-0.37292.63860.23641.2312.31-0.28390.75763.4137-0.16690.86041.62070.32462.327275.5558-21.896739.9583
65.06013.17580.64288.5168-0.36041.4848-0.60982.2297-0.2393-2.55341.5657-0.2913-0.10981.3767-0.88432.8985-0.16690.6082.1420.34011.018972.5266-27.757529.7595
72.63030.8970.98086.76693.40965.93090.5585-2.2497-0.93962.4278-0.86371.18412.9208-3.25990.14272.964-0.39570.70032.44280.47191.739164.4839-17.606742.4868
83.72091.99140.77376.99263.44147.2974-0.4159-0.6768-0.33520.182-0.6806-0.27830.3337-1.3181.10182.1550.17180.32571.79320.15182.563759.619-18.268836.5542
92.06223.5557-0.36872.0015-3.56732.0257-1.2494-0.3791-3.24720.14-0.5039-0.82171.1467-2.37591.59231.9527-0.40920.38161.60110.30922.048462.8837-26.799127.6133
108.5291-1.6599-4.78769.83762.36312.9118-3.59330.2093-2.13380.62831.46540.0050.4721.01031.88983.4609-0.3120.2932.03780.66911.424865.6926-28.098639.5187
113.782-0.59390.89354.30141.90811.1807-0.09810.7339-1.04930.0223-0.57770.533-0.066-0.13750.61441.7549-0.13640.36071.7423-0.13281.154479.2857-6.232835.3385
123.171-1.20771.69875.50241.42582.6076-0.3239-1.1050.2374-0.8696-0.48180.98031.4204-0.52720.63211.4153-0.38480.30781.70280.06761.245676.223111.214134.1655
133.7567-0.0616-0.83134.2982-1.43754.63390.47510.51660.4822-0.0347-0.8235-0.9127-1.08350.88810.3121.1384-0.127-0.15461.24150.13991.4954136.545443.7612-8.0234
142.9855-0.2446-1.61122.65340.4815.5228-0.08211.2028-0.7171-1.92760.3542-1.26140.0512-0.0722-0.16441.9533-0.18630.38821.8582-0.22571.636138.196611.1347-39.239
154.52260.597-1.32212.22191.98292.209-0.21112.8733-2.2408-0.88680.9929-1.7136-0.21610.7578-0.55822.3632-0.20010.93283.0501-0.9483.1504151.4845-3.3753-53.3905
162.59130.5685-0.55612.41720.07442.5068-0.06370.29170.0056-0.3514-0.0524-0.48020.14850.56580.0980.90760.0481-0.07261.19050.10731.1569131.694225.8902-7.8325
171.82520.4111-0.04681.6920.11760.91680.0272-0.33390.52620.5076-0.0313-0.1889-0.21660.19290.00911.2034-0.02520.02541.3618-0.08441.1299114.151338.880417.0639
180.77430.08260.45971.4019-0.67132.90890.0909-0.23680.15920.0716-0.17280.1562-0.1137-0.04850.18640.9984-0.07720.10321.3224-0.01751.151486.52626.3999-8.2009
193.23110.546-1.4924.0853-0.69944.4569-0.01950.542-0.142-0.6891-0.0711-0.0426-0.1818-0.14070.12780.97350.03120.01791.13530.17261.118989.685939.7952-47.1996
200.8989-0.7079-0.25921.2604-0.63815.26930.10660.2379-0.0108-0.32080.01010.2636-0.28630.1446-0.13091.1062-0.1121-0.05781.1752-0.0331.098688.558130.1248-10.5771
211.5987-0.06440.93371.2974-0.56830.78830.146-0.0097-0.50940.0454-0.0513-0.03180.5560.0633-0.08761.22870.04030.18861.11210.02151.069893.5476-3.13410.5507
223.3828-0.0545-0.41776.33241.21564.24590.20211.0675-0.4967-1.1751-0.4314-0.37910.70810.26950.29631.22090.13980.1561.25790.01310.988391.3165-0.8116-35.6477
232.0262.31931.13652.0207-1.37226.7815-1.25180.28260.23521.5570.92842.60790.0215-1.5130.32931.38210.12140.38371.4336-0.01742.010668.30125.472-4.3739
244.2721.5661-0.59233.3604-1.75765.02050.707-0.68050.62920.24340.44541.1978-0.2582-1.1246-0.82741.35380.00190.12831.7269-0.23562.213461.146915.9751-2.7923
252.5582-0.21931.10283.1452-1.18132.59310.22880.1748-0.3437-1.2353-0.0554-0.59910.01051.02120.30112.32440.13960.31881.8856-0.0631.93343.881323.9424-17.036
266.7412-0.7721.46723.8096-1.61155.36060.50431.82510.30170.56640.0790.4667-1.52210.5598-0.57422.24820.29820.34052.14620.21011.6967111.088458.5011-65.0636
274.1574-1.838-0.58364.4865-2.99245.4252-0.4589-0.1499-0.6284-0.4628-0.4947-0.41040.1961-0.97970.9393.6728-0.04860.36962.64030.24252.434887.307578.9372-70.5052
285.93341.7111-1.72663.4773-2.71549.2543-3.125-2.20871.3138-1.5462-0.2183-0.39720.32930.33783.35263.00570.5592-0.26124.0185-0.63593.162572.138958.7825-88.9618
292.440.0028-2.9391.728-0.08284.18630.4189-0.1260.3795-0.2879-0.1558-0.3177-0.9570.306-0.24991.59470.0189-0.08181.3534-0.02561.686592.663860.4528-28.8891
302.18250.98841.70391.27490.93382.48880.04010.23430.04450.3907-0.10540.5153-0.5811-1.5721-0.10041.69760.03630.42472.21540.20352.451-15.8883-19.7958-22.13
311.0753-0.98460.9932.66261.07942.26110.0325-0.3122-0.30430.188-0.33510.6890.555-0.65330.12932.0597-0.47630.58311.5838-0.03712.5206-13.7147-51.9051-37.0471
322.2055-3.8448-0.72576.04881.73521.4138-0.27530.78970.55980.6676-0.0125-0.71370.2863-0.35540.28421.749-0.18770.46431.84410.12362.9321-7.5752-34.0916-26.9876
330.56351.37260.88372.74021.89831.36740.544-0.50820.31830.603-0.89831.31950.7064-0.2240.30071.8443-0.20910.80741.88230.21162.4919-12.8276-28.5061-19.5663
341.58562.610.64914.1801-0.56661.43610.1365-0.66090.13710.0525-0.1865-0.925-0.4119-0.53240.03471.70190.06620.53441.9613-0.32052.27873.4981-10.9686-11.8228
352.4961-0.58991.93373.8759-0.63441.1030.3323-0.74970.6826-0.23350.0799-0.3923-0.4608-0.1937-0.43142.267-0.08730.76871.9721-0.55792.69185.01579.8341-4.5333
363.2127-1.51270.71084.2888-0.08074.2550.7768-0.75521.1206-0.30140.9415-0.1547-0.7773-1.1365-1.51212.1359-0.02570.90341.9441-0.12892.17293.059-21.0408-11.1846
371.89560.1899-1.33610.8541-0.13882.27180.07630.59570.032-0.361-0.07940.20950.1650.0241-0.01231.90.0533-0.1142.05210.14061.904625.0138-37.198-86.8525
382.44210.0240.00621.1599-0.30651.05350.21070.4805-0.0312-0.14610.02370.72850.4947-0.5604-0.24281.4913-0.21270.12281.57830.00481.77179.4455-46.3324-48.4642
394.9330.1116-2.12533.8562-0.15656.863-0.14090.2203-0.2458-0.2579-0.1552-0.3145-0.32450.21450.26641.17090.0310.04431.0095-0.23271.078168.8277-53.9867-58.1778
403.0453-1.6096-1.57981.03920.5670.6059-0.52840.5266-0.5080.27030.04020.65210.2915-0.14990.3521.6033-0.38780.16831.3032-0.06341.660538.4072-41.0381-46.0958
411.6744-0.81620.48252.3195-0.35560.9132-0.256-0.15390.30560.52860.14330.763-0.2397-0.04820.09861.5582-0.10560.37881.1854-0.12411.790921.7069-12.9637-36.0251
422.84450.54340.83750.4557-0.01441.3212-0.02790.54650.9676-0.13250.03110.0733-0.45260.3080.0011.6453-0.12310.21811.28290.10431.633449.5055-9.5313-50.4781
435.6963-1.34531.27479.1435-0.47841.9519-2.5409-1.2297-1.0905-0.27622.2031-3.17220.31840.21590.5022.87490.23490.62371.9807-0.13992.764342.1814-25.7065-14.2297
442.38431.1515-1.10771.16790.60762.62231.27160.48080.78691.36731.18791.2335-1.5244-1.1312-2.43063.2488-0.01340.22092.78080.71253.49858.0902-32.7851-4.0278
453.1843-1.42921.94285.9754-1.18793.42680.68810.9049-0.1196-1.6492-1.56550.48390.51461.11190.85382.6976-0.00190.44412.3449-0.25052.08173.48-72.4677-85.1569
463.8552-3.57040.15756.10430.56343.50730.9061-1.292-0.5115-0.7723-1.1323-0.2275-0.4850.10920.31322.48930.08550.47842.98920.15032.924989.6284-94.2727-68.3586
471.9484-0.30261.53293.09894.43872.01534.2529-0.02790.89091.04180.4653-1.68521.8512-0.8993-4.45924.08470.0634-0.36093.48670.21373.4145112.4103-73.7708-61.7897
482.40910.7813-3.2840.8066-1.26075.6949-0.46590.9723-0.7332-0.46330.03840.49280.8445-1.00890.46011.9228-0.2486-0.14311.563-0.37831.963551.9572-72.71-61.9404
493.668-0.1060.54713.9593-1.06374.2038-0.45450.1613-0.0379-0.4377-0.0837-0.50660.61620.5040.40761.9877-0.33930.47841.82530.39992.393542.7699-75.6468-10.3361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 234 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 48 )
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 68 )
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 106 )
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 136 )
10X-RAY DIFFRACTION10chain 'B' and (resid 137 through 146 )
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 190 )
12X-RAY DIFFRACTION12chain 'B' and (resid 191 through 232 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 142 )
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 254 )
15X-RAY DIFFRACTION15chain 'C' and (resid 255 through 345 )
16X-RAY DIFFRACTION16chain 'C' and (resid 346 through 804 )
17X-RAY DIFFRACTION17chain 'C' and (resid 805 through 1212 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1213 through 1342 )
19X-RAY DIFFRACTION19chain 'D' and (resid 8 through 307 )
20X-RAY DIFFRACTION20chain 'D' and (resid 308 through 393 )
21X-RAY DIFFRACTION21chain 'D' and (resid 394 through 914 )
22X-RAY DIFFRACTION22chain 'D' and (resid 915 through 1376 )
23X-RAY DIFFRACTION23chain 'E' and (resid 2 through 16 )
24X-RAY DIFFRACTION24chain 'E' and (resid 17 through 60 )
25X-RAY DIFFRACTION25chain 'E' and (resid 61 through 90 )
26X-RAY DIFFRACTION26chain 'F' and (resid 94 through 135 )
27X-RAY DIFFRACTION27chain 'F' and (resid 136 through 291 )
28X-RAY DIFFRACTION28chain 'F' and (resid 292 through 354 )
29X-RAY DIFFRACTION29chain 'F' and (resid 355 through 612 )
30X-RAY DIFFRACTION30chain 'G' and (resid 8 through 49 )
31X-RAY DIFFRACTION31chain 'G' and (resid 50 through 150 )
32X-RAY DIFFRACTION32chain 'G' and (resid 151 through 200 )
33X-RAY DIFFRACTION33chain 'G' and (resid 201 through 231 )
34X-RAY DIFFRACTION34chain 'H' and (resid 6 through 69 )
35X-RAY DIFFRACTION35chain 'H' and (resid 70 through 186 )
36X-RAY DIFFRACTION36chain 'H' and (resid 187 through 232 )
37X-RAY DIFFRACTION37chain 'I' and (resid 3 through 787 )
38X-RAY DIFFRACTION38chain 'I' and (resid 788 through 1342 )
39X-RAY DIFFRACTION39chain 'J' and (resid 16 through 307 )
40X-RAY DIFFRACTION40chain 'J' and (resid 308 through 376 )
41X-RAY DIFFRACTION41chain 'J' and (resid 377 through 703 )
42X-RAY DIFFRACTION42chain 'J' and (resid 704 through 1375 )
43X-RAY DIFFRACTION43chain 'K' and (resid 2 through 60 )
44X-RAY DIFFRACTION44chain 'K' and (resid 61 through 80 )
45X-RAY DIFFRACTION45chain 'L' and (resid 94 through 135 )
46X-RAY DIFFRACTION46chain 'L' and (resid 136 through 291 )
47X-RAY DIFFRACTION47chain 'L' and (resid 292 through 354 )
48X-RAY DIFFRACTION48chain 'L' and (resid 355 through 562 )
49X-RAY DIFFRACTION49chain 'L' and (resid 563 through 613 )

+
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://pdbjlvh1.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