[English] 日本語
Yorodumi
- PDB-4yg2: X-ray crystal structur of Escherichia coli RNA polymerase sigma70... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yg2
TitleX-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
KeywordsTRANSFERASE/TRANSCRIPTION / RNA polymerase / TRANSFERASE-TRANSCRIPTION 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 / : / : / : ...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 RNA polymerase / response to heat / protein dimerization activity / negative regulation of 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 sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 ...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 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 II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / : / 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 Alpha Subunit; Chain A, domain 2 / Helix Hairpins / 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 / 5' to 3' exonuclease, C-terminal subdomain / Helix non-globular / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb6 / Special / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A
Similarity search - Domain/homology
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 O157:H7 (bacteria)
Escherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.7 Å
AuthorsMurakami, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087350 United States
Citation
Journal: J. Biol. Chem. / Year: 2013
Title: X-ray crystal structure of Escherichia coli RNA polymerase sigma70 holoenzyme
Authors: Murakami, K.S.
#1: Journal: 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
SupersessionMar 18, 2015ID: 4IGC
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
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)920,17220
Polymers919,81412
Non-polymers3598
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)460,08610
Polymers459,9076
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38660 Å2
ΔGint-196 kcal/mol
Surface area159740 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)460,08610
Polymers459,9076
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37130 Å2
ΔGint-185 kcal/mol
Surface area153080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.308, 205.901, 309.185
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 O157:H7 (bacteria) / Strain: O157:H7 / Gene: rpoA, Z4665, ECs4160 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7Z6, 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 O157:H7 (bacteria) / Strain: O157:H7 / Gene: rpoB, Z5560, ECs4910 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8V4, 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 O157:H7 (bacteria) / Strain: O157:H7 / Gene: rpoC, Z5561, ECs4911 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8T8, 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 O157:H7 (bacteria) / Strain: O157:H7 / Gene: rpoZ, Z5075, ECs4524 / Plasmid: pACYCDuet-1_Ec_rpoZ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A802, 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 K12 (bacteria) / Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Plasmid: pGEMD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00579

-
Non-polymers , 2 types, 8 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 123448 / % possible obs: 96.8 % / Redundancy: 4.5 % / Net I/σ(I): 10.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementResolution: 3.7→29.978 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 6179 5.01 %
Rwork0.1914 --
obs0.1949 123398 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→29.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55733 0 8 0 55741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01356551
X-RAY DIFFRACTIONf_angle_d1.69776329
X-RAY DIFFRACTIONf_dihedral_angle_d18.08821815
X-RAY DIFFRACTIONf_chiral_restr0.078695
X-RAY DIFFRACTIONf_plane_restr0.00810012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.7420.40591830.32293529X-RAY DIFFRACTION88
3.742-3.78590.36612030.30353827X-RAY DIFFRACTION97
3.7859-3.8320.33932030.29553879X-RAY DIFFRACTION96
3.832-3.88040.38081970.3163796X-RAY DIFFRACTION95
3.8804-3.93130.46341960.36883667X-RAY DIFFRACTION92
3.9313-3.98510.37871940.28653704X-RAY DIFFRACTION92
3.9851-4.04190.32932020.24863875X-RAY DIFFRACTION97
4.0419-4.10210.31492030.23933848X-RAY DIFFRACTION97
4.1021-4.1660.32212050.22993877X-RAY DIFFRACTION97
4.166-4.23410.2872030.21673871X-RAY DIFFRACTION97
4.2341-4.30690.29462040.20863881X-RAY DIFFRACTION97
4.3069-4.3850.28512040.20123881X-RAY DIFFRACTION97
4.385-4.46910.24552040.1983892X-RAY DIFFRACTION97
4.4691-4.560.26692060.19493863X-RAY DIFFRACTION97
4.56-4.65880.26512040.18743870X-RAY DIFFRACTION97
4.6588-4.76670.24572060.18183898X-RAY DIFFRACTION97
4.7667-4.88550.25322080.18113927X-RAY DIFFRACTION97
4.8855-5.0170.24382070.17913925X-RAY DIFFRACTION98
5.017-5.16390.24412090.183937X-RAY DIFFRACTION98
5.1639-5.32960.27832100.17823940X-RAY DIFFRACTION98
5.3296-5.5190.25862110.17913968X-RAY DIFFRACTION98
5.519-5.73850.25932080.18033986X-RAY DIFFRACTION99
5.7385-5.99770.28672090.18463988X-RAY DIFFRACTION99
5.9977-6.31110.27162110.19674015X-RAY DIFFRACTION99
6.3111-6.70240.26452090.19244028X-RAY DIFFRACTION99
6.7024-7.21320.26512130.19094027X-RAY DIFFRACTION99
7.2132-7.92690.24912150.16724038X-RAY DIFFRACTION99
7.9269-9.04630.19782160.14284048X-RAY DIFFRACTION98
9.0463-11.29510.17272110.12944052X-RAY DIFFRACTION98
11.2951-29.97890.22852250.174182X-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)
10.423-0.33460.53550.2958-0.2990.7414-0.0559-1.10880.02710.954-0.01780.17870.78690.40290.00011.74060.06170.04711.35660.14861.033691.688510.23746.3268
21.44610.8029-0.66694.816-0.87763.391-0.0123-0.33920.37560.27210.1930.2702-0.4673-0.12580.00031.36720.17480.06281.3028-0.11821.0383101.920241.809334.2683
31.3542-0.3801-0.17811.18570.5711.32690.3127-1.1229-0.26021.3188-0.10810.28160.62770.7766-0.00151.84690.18250.19411.53130.10561.206990.277212.393945.1955
41.0462-0.9252-0.52530.879-0.66420.5338-0.2466-0.7751-0.17750.2630.3959-1.3104-0.30450.019-0.00081.90280.1105-0.1042.0344-0.09091.924366.449756.889623.3888
51.695-0.563-0.13560.2960.39780.5817-0.419-1.09720.2248-0.53780.05230.50580.337-0.73130.00131.1969-0.1856-0.02741.35510.1681.172775.031211.977430.5032
62.21260.301-0.84561.34541.04051.276-0.025-0.1337-0.36811.65250.3040.64170.8088-0.47360.00172.5488-0.28140.55471.97150.46642.010268.7014-21.668937.9901
71.8879-1.2810.39321.5156-0.27132.0446-0.1894-0.16040.50520.3923-0.35242.31570.4335-0.14220.05271.557-0.1470.51021.48460.26421.160975.01629.803432.9979
82.0470.7617-0.65912.5578-0.91172.14020.13110.28770.3122-0.1309-0.2903-0.1622-0.85450.7833-0.00021.0192-0.1685-0.13951.25470.0431.085132.490242.9228-9.2542
90.8825-0.15210.4661.73711.77471.33830.4830.2832-0.9221-1.4041-0.3847-0.92680.29690.19460.00052.64170.08420.42712.19150.13151.9193142.26629.3906-49.5409
101.11211.17320.20073.26922.36941.0904-0.34551.0325-0.034-1.24530.1758-0.0020.21150.34310.00121.1459-0.06280.05451.75760.17681.1409134.985930.3512-29.9446
111.77561.4664-0.54052.693-0.51033.6043-0.0620.4762-0.3054-0.41750.0545-0.19220.59310.37740.00130.57120.0601-0.0311.0290.03620.9067128.170520.6973-3.3212
121.6048-0.4944-0.18292.3797-0.77831.3601-0.1056-0.36410.45570.31950.1933-0.0246-0.3675-0.0209-0.00020.74770.0099-0.03011.1018-0.09130.7619111.50239.204615.2875
132.39280.97260.32051.56810.85121.07360.00650.37550.71090.22260.1022-0.25140.00760.5235-0.00011.3252-0.20880.13441.4184-0.03391.3329116.841960.203313.8004
142.0102-1.21130.8641.5014-0.83251.3611-0.0958-0.45150.0230.65360.083-0.14810.06190.1328-0.00030.85730.0282-0.01481.07240.06980.8662111.20118.267721.1924
152.01971.062-3.55082.5356-1.30433.25630.34460.10660.65330.0042-0.01420.1249-0.5044-0.2878-00.6449-0.0603-0.03530.8672-0.08590.941578.21729.9645-18.1078
162.61260.4117-0.90954.04620.36764.6576-0.08550.2596-0.1095-0.517-0.0129-0.0157-0.1807-0.3025-0.00050.76690.0907-0.01510.96320.13870.942888.681339.6522-45.9788
171.3923-0.17380.65771.0357-0.11360.99560.14160.2636-0.6156-0.2328-0.1150.15130.52990.05970.00010.95920.01820.12620.92680.00891.123789.8696-0.2243-10.7416
181.2105-1.2544-0.95563.98244.24125.8672-0.3822-0.8458-0.61471.44090.50610.61952.1728-0.6028-0.01530.6864-0.15380.06411.04910.10461.634160.404213.6456-2.9271
192.21710.39520.42880.20240.2340.35230.9404-0.8738-0.6355-0.5551-0.7187-0.499-1.4336-0.52760.25451.27780.2869-0.03531.035-0.31671.519941.966524.6215-16.9651
200.1382-0.88471.33342.2305-1.70320.6009-0.1731-0.11730.35770.4343-0.0959-0.1614-0.78220.0781-0.00072.40080.01650.5531.73270.07231.872696.424276.2282-66.9423
210.4220.2679-0.38081.0358-0.21060.0624-0.11630.4238-0.3527-1.8979-0.63592.0803-1.5075-0.7136-0.00343.08630.4271-0.58132.5407-0.09533.585574.896961.6737-83.7057
222.47150.2986-0.79682.82230.09343.28240.1383-0.20560.3105-0.0671-0.1798-0.6414-1.31240.8905-0.00041.1923-0.11940.21391.1639-0.01071.5745105.907260.4301-39.2799
230.275-0.7073-0.52261.73911.07540.55520.37890.63720.8517-0.8381-0.1294-0.5308-0.6357-0.59610.00011.34680.0803-0.02991.5860.00081.369457.356460.6145-2.0915
240.4106-0.41540.44520.2532-0.07040.23820.4754-0.32450.1332-0.279-0.25691.025-0.237-0.8011-0.00031.56750.2020.26491.68560.21182.2193-17.8849-19.198-21.4234
251.07410.1984-0.94094.11680.94682.1339-0.0266-0.4493-0.45310.7446-0.07120.50850.7067-0.53280.00061.5705-0.21020.26271.60530.26631.9965-12.5422-51.7335-34.4037
261.8312-1.12690.20685.0641.8691.30590.28-0.19730.0519-1.0325-0.50762.4503-0.6203-0.159-0.08661.65730.03350.81791.60670.28892.1686-16.4817-21.4285-20.6235
270.34790.0619-0.30580.61280.70120.96760.0573-1.2151-0.02760.3453-0.5269-2.19370.5926-0.77130.00551.45670.05780.14621.4690.04052.02173.0627-21.39-12.4618
280.94260.54330.51951.10150.1690.9085-0.0448-0.51831.00290.0297-0.21730.78420.1557-0.3858-0.00062.24010.39090.63541.9975-0.37412.38731.686912.5119-5.4272
291.2074-0.236-0.12481.197-1.41181.93771.4717-0.42720.79111.2542-1.051-1.28950.3356-0.6415-0.03551.9750.09540.92351.6412-0.18411.97631.3303-19.1253-11.8038
301.8771-0.7135-0.06581.7040.3891.72130.14420.719-0.4783-1.0365-0.4450.53850.5189-0.311802.32810.061-0.02481.5698-0.04281.412213.3074-56.1223-81.1024
314.03580.4103-1.50823.1260.00352.2045-0.0193-0.03420.5861-0.5699-0.1586-0.47620.32090.8177-0.00032.04820.0034-0.1161.7252-0.08071.414249.468-24.1302-105.464
321.58161.6126-1.86311.1027-1.44782.0326-0.10970.6994-0.26380.3722-0.13610.24860.3340.4496-0.00012.28330.0577-0.17591.6971-0.0411.45832.4797-44.8652-91.9238
331.3181-0.1881-1.15934.2691.54981.66110.06360.32760.2651-1.08940.1260.12750.0023-0.01930.00051.6985-0.0747-0.08241.41540.22991.330511.6508-33.5441-74.946
340.8399-0.7323-0.73172.57251.41672.1755-0.14160.1229-0.3046-0.29070.14140.94410.3223-0.6429-0.00021.4542-0.2082-0.08691.27420.25251.5720.7461-50.5397-51.3273
350.96720.7928-0.78542.7380.77941.2728-0.41811.42450.0998-0.8060.28161.150.1166-0.5581-0.00041.9824-0.1785-0.04842.62890.25252.054-0.7765-72.0341-56.3196
361.5058-0.39360.21621.5921-0.06691.5544-0.11970.46140.3069-0.32070.11430.6353-0.1448-0.78130.00061.41250.04330.1471.55410.29371.5509-3.197-29.2142-49.343
371.7076-1.4791-2.48533.51890.62082.5026-0.1398-0.2969-0.17960.6090.29950.18380.13030.4224-0.00071.3186-0.0220.12431.1864-0.06881.113445.5576-43.3614-35.6405
383.75550.3697-1.90983.0614-0.23115.2697-0.2125-0.3714-0.0472-0.2106-0.0916-0.0562-0.09140.38180.00071.24840.14980.03770.9798-0.06410.974265.949-54.1942-57.7346
391.6388-0.2977-0.2051.41160.09851.42170.030.1090.6778-0.08770.1437-0.1069-0.48470.196901.4655-0.06270.30521.0668-0.03691.372735.6285-12.7972-43.9911
401.23150.81211.06110.44330.80951.2113-0.6735-1.33840.4492.00080.84230.280.01450.1497-0.00041.77340.15530.22441.7038-0.26761.218439.8755-26.4098-13.4204
410.0470.07950.05780.03920.01850.00050.6185-0.6182-0.74450.72570.2022-0.39651.04680.6904-0.00612.7782-0.0567-0.50922.0081-0.31412.078755.9117-33.2383-3.1468
421.1925-2.08090.20832.08060.489-0.35710.2741-0.2528-0.2563-0.6872-0.38680.03650.5857-0.1419-0.00052.7996-0.11790.40621.6-0.00321.860381.7991-91.7352-74.3249
43-0.10150.19580.2650.2032-0.0815-0.32880.91641.2234-0.10632.0466-0.1188-2.4710.26030.78060.00032.99680.138-0.61052.7527-0.05813.7911105.354-77.0331-60.8192
441.98091.1018-1.74251.4075-0.92353.9103-0.81270.549-1.0605-0.47270.27970.29120.5493-0.77750.00041.9755-0.20450.14681.2206-0.07581.572351.932-74.6062-69.3741
451.19371.5645-0.95462.18870.00932.8788-0.3216-0.4521-0.60081.00840.26580.15931.23420.7192-0.00012.4136-0.09030.17531.63310.11061.513641.9553-72.8056-9.7247
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 'A' and (resid 234 through 325 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 49 )
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 179 )
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 233 )
8X-RAY DIFFRACTION8chain C and (resid 3 through 158 )
9X-RAY DIFFRACTION9chain C and (resid 159 through 370 )
10X-RAY DIFFRACTION10chain C and (resid 371 through 481 )
11X-RAY DIFFRACTION11chain C and (resid 482 through 703 )
12X-RAY DIFFRACTION12chain C and (resid 704 through 883 )
13X-RAY DIFFRACTION13chain C and (resid 884 through 1037 )
14X-RAY DIFFRACTION14chain C and (resid 1038 through 1252 )
15X-RAY DIFFRACTION15chain C and (resid 1253 through 1342 )
16X-RAY DIFFRACTION16chain 'D' and (resid 8 through 332 )
17X-RAY DIFFRACTION17chain 'D' and (resid 333 through 1376 )
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 60 )
19X-RAY DIFFRACTION19chain 'E' and (resid 61 through 90 )
20X-RAY DIFFRACTION20chain F and (resid 94 through 262 )
21X-RAY DIFFRACTION21chain F and (resid 263 through 354 )
22X-RAY DIFFRACTION22chain F and (resid 355 through 530 )
23X-RAY DIFFRACTION23chain F and (resid 531 through 612 )
24X-RAY DIFFRACTION24chain 'G' and (resid 7 through 49 )
25X-RAY DIFFRACTION25chain 'G' and (resid 50 through 179 )
26X-RAY DIFFRACTION26chain 'G' and (resid 180 through 233 )
27X-RAY DIFFRACTION27chain 'H' and (resid 6 through 49 )
28X-RAY DIFFRACTION28chain 'H' and (resid 50 through 179 )
29X-RAY DIFFRACTION29chain 'H' and (resid 180 through 233 )
30X-RAY DIFFRACTION30chain 'I' and (resid 3 through 158 )
31X-RAY DIFFRACTION31chain 'I' and (resid 159 through 370 )
32X-RAY DIFFRACTION32chain 'I' and (resid 371 through 481 )
33X-RAY DIFFRACTION33chain 'I' and (resid 482 through 703 )
34X-RAY DIFFRACTION34chain 'I' and (resid 704 through 883 )
35X-RAY DIFFRACTION35chain 'I' and (resid 884 through 1037 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1038 through 1252 )
37X-RAY DIFFRACTION37chain 'I' and (resid 1253 through 1342 )
38X-RAY DIFFRACTION38chain 'J' and (resid 16 through 332 )
39X-RAY DIFFRACTION39chain 'J' and (resid 333 through 1375 )
40X-RAY DIFFRACTION40chain 'K' and (resid 2 through 60 )
41X-RAY DIFFRACTION41chain 'K' and (resid 61 through 80 )
42X-RAY DIFFRACTION42chain 'L' and (resid 94 through 262 )
43X-RAY DIFFRACTION43chain 'L' and (resid 263 through 354 )
44X-RAY DIFFRACTION44chain 'L' and (resid 355 through 530 )
45X-RAY DIFFRACTION45chain 'L' and (resid 531 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://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