[English] 日本語
Yorodumi
- PDB-4yfx: Escherichia coli RNA polymerase in complex with Myxopyronin B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yfx
TitleEscherichia coli RNA polymerase in complex with Myxopyronin B
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
Keywordstranscription/transcription inhibitor / switch region / squaramide / transcription-transcription inhibitor complex
Function / homology
Function and homology information


sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat ...sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region ...Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Sigma-70 factors family signature 1. / 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 / Helix Hairpins / 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 / 5' to 3' exonuclease, C-terminal subdomain / Beta Complex / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / 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 / 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 / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Myxopyronin B / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.844 Å
AuthorsMolodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
CitationJournal: J.Med.Chem. / Year: 2015
Title: X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
Authors: Molodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references / Non-polymer description
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

-
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)920,55519
Polymers919,81412
Non-polymers7427
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)460,49310
Polymers459,9076
Non-polymers5874
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Unit cell
Length a, b, c (Å)188.520, 205.177, 310.140
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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoA, EcE24377A_3778 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZSI4, 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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoB, EcE24377A_4528 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZUK1, 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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoC, EcE24377A_4529 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZUK2, 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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoZ, EcE24377A_4152 / Plasmid: pACYCDuet-1_Ec_rpoZ / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZTK1, 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 / Plasmid: pGEMD / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P00579

-
Non-polymers , 3 types, 7 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-4C4 / Myxopyronin B


Mass: 431.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33NO6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7 / Details: 0.1M HEPES-HCL , 0.2M CaACETATE, 15% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 106246 / % possible obs: 93.8 % / Redundancy: 4.3 % / Net I/σ(I): 9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGC

4igc
PDB Unreleased entry


Resolution: 3.844→29.947 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2999 1854 1.75 %
Rwork0.2356 --
obs0.2368 105840 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.844→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55318 0 37 0 55355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01456160
X-RAY DIFFRACTIONf_angle_d2.14675803
X-RAY DIFFRACTIONf_dihedral_angle_d19.40121648
X-RAY DIFFRACTIONf_chiral_restr0.0848641
X-RAY DIFFRACTIONf_plane_restr0.019938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8436-3.94730.37241170.34616456X-RAY DIFFRACTION75
3.9473-4.06320.4331440.34817973X-RAY DIFFRACTION93
4.0632-4.1940.37991360.29488141X-RAY DIFFRACTION95
4.194-4.34340.42421480.29188122X-RAY DIFFRACTION95
4.3434-4.51680.28241370.27198133X-RAY DIFFRACTION95
4.5168-4.72160.3711560.25398123X-RAY DIFFRACTION94
4.7216-4.96950.34921340.24498117X-RAY DIFFRACTION94
4.9695-5.27930.35151410.25478117X-RAY DIFFRACTION94
5.2793-5.68430.34671470.25488127X-RAY DIFFRACTION94
5.6843-6.25160.39371520.26838099X-RAY DIFFRACTION94
6.2516-7.14550.3531390.25718166X-RAY DIFFRACTION93
7.1455-8.96240.25151460.21058156X-RAY DIFFRACTION93
8.9624-29.94760.21081570.1748256X-RAY DIFFRACTION92
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5698-1.4542-0.52371.5974-0.0571.37-0.2398-0.93321.12051.2411-0.16150.3293-1.5391-0.35350.00912.00560.0318-0.3631.6468-0.26031.3499-92.5871-9.675446.1817
22.96273.50622.71077.72440.62123.76670.3252-0.5758-0.59210.3068-0.0499-1.14880.6795-0.39380.00031.4248-0.0004-0.09981.47490.14981.3561-102.686-41.440934.7311
32.88351.1270.58861.8598-1.42482.90190.5745-2.55720.37811.8255-0.5266-0.4326-0.5004-0.7081-0.0191.82120.0193-0.20441.6289-0.04441.7489-91.0407-12.003645.0733
41.9473-0.5935-0.60871.09480.4921.7295-0.7914-0.5447-0.0564-1.48530.696-1.50650.40061.1445-0.00191.31620.00270.11361.7051-0.00981.6766-76.1172-11.759130.2649
51.6518-0.06231.67883.8587-1.33462.1545-0.0829-0.47780.07292.26470.08280.3872-2.17390.5620.0013.0647-0.2731-0.67181.9752-0.17312.3344-69.293221.879236.9554
61.6884-1.74010.01946.08270.22643.03990.11390.0463-0.9352-0.593-0.3854-2.0113-1.18030.41250.09691.5917-0.4142-0.42151.6632-0.03131.7581-75.8217-9.582832.8059
71.67330.47950.9535.18593.39793.58560.08260.1358-0.27570.3826-0.77731.1660.6922-0.6758-0.00631.0301-0.08710.19911.7206-0.05571.2568-132.6485-43.3391-8.7299
81.45021.2117-0.27263.176-1.07012.8329-0.13750.01571.336-1.4604-0.14320.989-0.4594-0.436-0.00012.6098-0.1121-0.63181.9932-0.03842.2512-143.4368-10.2047-49.4436
90.06160.48652.47163.1593-0.62363.2740.10080.36690.006-1.2068-0.01910.1028-0.15420.118101.39-0.05790.09451.8099-0.00541.4705-135.775-31.0241-29.4977
101.49361.83531.08324.46222.38823.31760.22540.45410.2123-0.3148-0.40690.2704-0.5843-0.4053-0.00630.78680.050.04461.60730.03051.1184-128.9301-20.7727-3.1005
111.2311-0.389-0.0174.01231.43571.96460.1682-0.368-0.51360.2271-0.041-0.06820.2405-0.12301.1338-0.08260.04491.44530.1730.8862-112.3389-39.170415.6048
123.54570.6675-0.02092.6349-0.52070.06280.2395-0.4281-0.83710.4406-0.25150.30340.1789-0.1057-01.4457-0.3054-0.08891.9567-0.03851.4275-117.6014-60.123514.0624
132.1731-0.3382-0.81242.4750.49171.46660.0229-0.72640.14450.7470.03680.44990.0725-0.01810.00020.9871-0.0143-0.01861.44970.00371.0994-112.0425-18.274421.2816
142.34761.89693.31454.22942.25063.90350.65010.0755-0.81230.1139-0.3585-0.58990.6971-0.030.00040.79450.06270.07811.26440.17811.1586-79.1397-30.2822-17.8432
153.73130.90281.39273.5218-0.22015.2909-0.18580.61210.2504-0.36160.05270.0131-0.3363-0.1014-0.00021.11490.07740.07981.50090.0291.2195-90.457-39.3633-45.212
162.0976-0.3981-0.47691.7080.46991.39160.23370.66120.7875-0.3628-0.2158-0.183-0.6387-0.05880.01571.17420.0039-0.01521.31440.24131.4463-91.0624-0.126-10.8013
170.79051.1852-0.32761.5475-0.20660.0076-0.1907-0.34420.74910.5130.455-0.6772-0.45830.32050.00031.10430.0229-0.04191.83650.2332.1065-61.4065-13.9531-2.5998
180.2726-0.23220.02340.1287-0.26940.14821.4833-0.05490.0984-0.8733-0.4911-0.71510.3967-1.11280.00242.31190.0494-0.29091.84580.3682.0217-42.6841-24.6654-16.8072
190.70940.6388-2.98973.19552.17612.2638-0.93890.7543-0.99140.6607-0.6644-0.14172.0058-0.6073-0.00053.42850.31450.07243.0217-0.30462.4931-97.8476-75.6521-68.5761
20-0.2228-0.0509-0.05690.74390.74420.07630.69241.2953-0.1968-0.3625-1.2034-0.9676-0.02560.7931-0.01313.8028-0.11410.64734.0813-0.35913.6135-75.4458-60.2917-81.2763
211.99940.5251.30862.0616-1.53093.3312-0.12160.33530.1354-0.58010.04280.62810.847-0.2668-0.00551.59460.0124-0.03151.68780.07961.8132-107.3179-60.0012-38.3258
223.54161.1884-0.75561.9195-0.72610.6402-0.6758-0.0203-0.67730.75790.0225-0.58550.80570.52-0.00071.68620.0935-0.05321.60440.26671.8919-58.801-60.4769-3.9142
230.9978-0.022-0.44880.99060.88790.5631-0.74310.41080.5864-1.4566-0.4792-0.8198-0.3626-1.7222-0.04652.68150.3187-0.77782.28090.1483.104116.667818.7127-21.7436
240.7150.920.34983.29580.39492.02710.0844-0.5621-0.04470.7782-0.0137-0.47940.15910.092402.4295-0.0077-1.01412.0342-0.53273.399711.615151.3116-34.7254
251.1119-0.37020.47750.3273-0.55270.4277-0.61580.5278-0.26890.8625-0.187-1.791-0.1967-1.0132-0.02193.37360.3216-0.90981.9346-0.21063.004715.156221.1162-20.6982
260.61880.0089-0.85480.1291-0.11360.6171-0.0689-0.41680.32240.88190.41164.17540.74421.27910.013.550.4726-0.46121.8544-0.06172.9275-4.299321.3378-12.9526
271.7462-0.0829-0.61610.2085-0.51390.29571.35350.4468-0.4157-0.5196-0.94-0.20331.08380.73130.07934.22430.4211-0.86672.43230.63362.8343-3.1676-12.6674-5.5994
283.22710.623-0.64162.8023-0.9741.9191.0126-2.3127-0.77321.26751.79362.0318-0.3953-0.07553.32184.13010.4451-1.91062.03160.98212.2196-2.595619.1403-11.9105
294.2827-0.78252.2220.85270.19424.5488-0.02730.49780.977-0.6721-0.3608-0.9815-0.82880.4779-0.00052.1702-0.04020.13991.50070.17332.0755-13.985455.6891-81.0459
303.99580.64872.8454.42330.98364.0547-0.12370.2548-0.56440.2470.16520.36540.4781-0.3083-0.00021.7999-0.08590.23421.81380.31561.4392-49.712123.9581-106.265
314.06813.30323.18382.57851.54313.2257-0.43850.21760.3303-0.34530.28610.1631-0.53040.184301.8396-0.12180.0871.66570.10111.4333-32.918744.5621-92.4017
321.9027-0.96121.49396.4121-1.0123.2805-0.07710.2044-0.1634-0.33-0.06730.01850.19010.31010.00361.7075-0.0598-0.12121.40880.11741.7269-12.585633.0136-75.1142
331.2194-1.4867-0.24613.1931-0.36974.47050.23420.0360.47390.55840.0593-0.9132-0.70281.085901.7597-0.0815-0.33631.7029-0.09152.2135-1.716550.1153-51.661
343.40930.54880.87054.2367-1.10510.24090.32481.7674-0.2352-0.7147-0.0818-1.280.09140.3643-0.00142.50610.0801-0.0772.6473-0.42022.55870.301771.5052-56.5546
351.56750.4472-0.46662.10940.60413.0845-0.3154-0.2816-0.10980.33880.3826-1.40510.60131.0630.00022.06940.1476-0.55811.65760.00532.11212.069628.7681-49.4712
361.2556-2.73692.64274.1092-1.4682.4658-0.1981-0.21970.31480.95830.0767-0.5981-0.0332-0.9584-0.00082.2567-0.4694-0.10241.43090.13771.5546-46.823343.5035-35.8559
376.0951-0.13892.65463.4822-0.17315.88470.10480.3323-0.11770.3847-0.42180.13080.4563-0.6942-0.00031.5728-0.06080.11781.65410.14161.4199-65.941854.1289-58.5203
381.7912-0.7133-0.23961.3560.24341.3471-0.16530.0075-0.62290.43780.11030.10080.8966-0.4489-0.00042.8275-0.3185-0.12651.45610.25911.6476-36.999312.9447-44.0513
390.26910.26-0.360.0534-0.26860.13480.4684-1.8594-1.92361.06221.47140.01981.5678-2.92870.00533.9218-0.5117-0.49113.12391.18943.3369-40.908626.7705-13.7451
400.0324-0.1278-0.09460.47820.04810.14561.12641.4056-0.7494-0.36792.8022-0.0416-0.028-0.09410.01015.71430.09680.88023.5051-0.73063.2285-56.612133.5082-3.5779
412.0899-0.1003-0.63673.4448-1.77620.60690.6028-0.44451.91-0.5264-0.60220.1755-1.2159-0.08580.00023.2199-0.0112-0.72422.5759-0.19173.6937-82.188191.1495-75.7644
42-0.11310.30070.02430.0109-0.1820.24050.67080.6587-1.61940.50160.16382.46840.10790.38540.00144.1467-0.27970.373.36140.24474.7866-103.500275.9543-61.819
433.70020.71261.32931.27161.0012.4023-0.4838-0.33220.8459-0.5392-0.0449-0.262-0.5861-0.2611-0.00022.2152-0.1739-0.04581.80460.36592.1267-51.595973.659-70.2855
440.91740.70750.43781.1277-0.08251.1317-0.018-0.83910.0974-0.26240.81530.08210.0003-0.76390.00132.4779-0.2748-0.18421.91880.13722.2762-42.370372.251-11.0559
451.6571-0.8439-1.64220.41790.5431.28350.0588-0.76130.0683-0.26980.1476-0.7363-0.82441.1969-03.2946-0.9-0.66392.81690.01042.6869-54.35075.710759.8467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 179 )
3X-RAY DIFFRACTION3chain A and (resid 180 through 233 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 49 )
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 179 )
6X-RAY DIFFRACTION6chain 'B' and (resid 180 through 233 )
7X-RAY DIFFRACTION7chain C and (resid 3 through 158 )
8X-RAY DIFFRACTION8chain C and (resid 159 through 370 )
9X-RAY DIFFRACTION9chain C and (resid 371 through 481 )
10X-RAY DIFFRACTION10chain C and (resid 482 through 703 )
11X-RAY DIFFRACTION11chain C and (resid 704 through 883 )
12X-RAY DIFFRACTION12chain C and (resid 884 through 1037 )
13X-RAY DIFFRACTION13chain C and (resid 1038 through 1252 )
14X-RAY DIFFRACTION14chain C and (resid 1253 through 1342 )
15X-RAY DIFFRACTION15chain 'D' and (resid 8 through 332 )
16X-RAY DIFFRACTION16chain 'D' and (resid 333 through 1376 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 60 )
18X-RAY DIFFRACTION18chain 'E' and (resid 61 through 90 )
19X-RAY DIFFRACTION19chain F and (resid 95 through 262 )
20X-RAY DIFFRACTION20chain F and (resid 263 through 354 )
21X-RAY DIFFRACTION21chain F and (resid 355 through 530 )
22X-RAY DIFFRACTION22chain F and (resid 531 through 609 )
23X-RAY DIFFRACTION23chain 'G' and (resid 7 through 49 )
24X-RAY DIFFRACTION24chain 'G' and (resid 50 through 179 )
25X-RAY DIFFRACTION25chain 'G' and (resid 180 through 233 )
26X-RAY DIFFRACTION26chain 'H' and (resid 6 through 49 )
27X-RAY DIFFRACTION27chain 'H' and (resid 50 through 179 )
28X-RAY DIFFRACTION28chain 'H' and (resid 180 through 233 )
29X-RAY DIFFRACTION29chain 'I' and (resid 3 through 158 )
30X-RAY DIFFRACTION30chain 'I' and (resid 159 through 370 )
31X-RAY DIFFRACTION31chain 'I' and (resid 371 through 481 )
32X-RAY DIFFRACTION32chain 'I' and (resid 482 through 703 )
33X-RAY DIFFRACTION33chain 'I' and (resid 704 through 883 )
34X-RAY DIFFRACTION34chain 'I' and (resid 884 through 1037 )
35X-RAY DIFFRACTION35chain 'I' and (resid 1038 through 1252 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1253 through 1342 )
37X-RAY DIFFRACTION37chain 'J' and (resid 16 through 332 )
38X-RAY DIFFRACTION38chain 'J' and (resid 333 through 1375 )
39X-RAY DIFFRACTION39chain 'K' and (resid 2 through 60 )
40X-RAY DIFFRACTION40chain 'K' and (resid 61 through 80 )
41X-RAY DIFFRACTION41chain 'L' and (resid 95 through 262 )
42X-RAY DIFFRACTION42chain 'L' and (resid 263 through 354 )
43X-RAY DIFFRACTION43chain 'L' and (resid 355 through 530 )
44X-RAY DIFFRACTION44chain 'L' and (resid 531 through 609 )
45X-RAY DIFFRACTION45chain 'B' and (resid 246 through 317 )

+
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