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- PDB-4jk1: X-ray crystal structure of Escherichia coli sigma70 holoenzyme in... -

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Basic information

Entry
Database: PDB / ID: 4jk1
TitleX-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp)
Components(Escherichia coli RNA polymerase ...) x 5
KeywordsTRANSCRIPTION / TRANSFERASE / DNA
Function / homology
Function and homology information


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / 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
Sigma-70 factor, region 1.1 / Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / 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 ...Sigma-70 factor, region 1.1 / Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / 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 / Annexin V; domain 1 / 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. / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / : / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / Helix non-globular / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / 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 Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / 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
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / : / 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: 3.9 Å
AuthorsMurakami, K.S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Differential regulation by ppGpp versus pppGpp in Escherichia coli.
Authors: Mechold, U. / Potrykus, K. / Murphy, H. / Murakami, K.S. / Cashel, M.
History
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Escherichia coli RNA polymerase alpha subunit
B: Escherichia coli RNA polymerase alpha subunit
C: Escherichia coli RNA polymerase beta subunit
D: Escherichia coli RNA polymerase beta' subunit
E: Escherichia coli RNA polymerase omega subunit
X: Escherichia coli RNA polymerase sigma70 subunit
F: Escherichia coli RNA polymerase alpha subunit
G: Escherichia coli RNA polymerase alpha subunit
H: Escherichia coli RNA polymerase beta subunit
I: Escherichia coli RNA polymerase beta' subunit
J: Escherichia coli RNA polymerase omega subunit
Y: Escherichia coli RNA polymerase sigma70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)920,67817
Polymers919,81412
Non-polymers8655
Water00
1
A: Escherichia coli RNA polymerase alpha subunit
B: Escherichia coli RNA polymerase alpha subunit
C: Escherichia coli RNA polymerase beta subunit
D: Escherichia coli RNA polymerase beta' subunit
E: Escherichia coli RNA polymerase omega subunit
X: Escherichia coli RNA polymerase sigma70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,6419
Polymers459,9076
Non-polymers7343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41040 Å2
ΔGint-163 kcal/mol
Surface area167450 Å2
MethodPISA
2
F: Escherichia coli RNA polymerase alpha subunit
G: Escherichia coli RNA polymerase alpha subunit
H: Escherichia coli RNA polymerase beta subunit
I: Escherichia coli RNA polymerase beta' subunit
J: Escherichia coli RNA polymerase omega subunit
Y: Escherichia coli RNA polymerase sigma70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,0388
Polymers459,9076
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36690 Å2
ΔGint-163 kcal/mol
Surface area158390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.567, 203.817, 307.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Escherichia coli RNA polymerase ... , 5 types, 12 molecules ABFGCHDIEJXY

#1: Protein
Escherichia coli RNA polymerase alpha subunit / 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 (E. coli) / Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Plasmid: pGEMABC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Protein Escherichia coli RNA polymerase beta subunit / 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 (E. coli) / Strain: K12
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Plasmid: pGEMABC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: Protein Escherichia coli RNA polymerase beta' subunit / 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 (E. coli) / Strain: K12 / Gene: rpoC, tabB, b3988, JW3951 / Plasmid: pGEMABC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: Protein Escherichia coli RNA polymerase omega subunit / 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 (E. coli) / Strain: K-12 substr. MDS42 / Gene: rpoZ, ECMDS42_3083 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: H0QDQ9, UniProt: P0A800*PLUS, DNA-directed RNA polymerase
#5: Protein Escherichia coli RNA polymerase sigma70 subunit / Sigma-70


Mass: 70352.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Plasmid: pGEMD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00579

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Non-polymers , 2 types, 5 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Hepes-HCl (pH 7.0), 0.2 M CaAcetate, ~15 % PEG400, 10 mM Tri(2-carboxyethyl)phosphine (TCEP), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2012
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.9→30 Å / Num. obs: 96273 / % possible obs: 87.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→29.839 Å / SU ML: 0.73 / σ(F): 1.37 / Phase error: 35.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3198 4725 4.98 %RANDOM
Rwork0.2517 ---
obs0.2551 94874 89.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→29.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56075 0 40 0 56115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256927
X-RAY DIFFRACTIONf_angle_d0.48976825
X-RAY DIFFRACTIONf_dihedral_angle_d11.62822018
X-RAY DIFFRACTIONf_chiral_restr0.0358746
X-RAY DIFFRACTIONf_plane_restr0.00210069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.94420.39881030.39562164X-RAY DIFFRACTION65
3.9442-3.99050.40511190.36432310X-RAY DIFFRACTION70
3.9905-4.03910.44071250.36222445X-RAY DIFFRACTION74
4.0391-4.09010.3991440.33762549X-RAY DIFFRACTION77
4.0901-4.14380.38481390.33412632X-RAY DIFFRACTION80
4.1438-4.20040.39281450.33292669X-RAY DIFFRACTION81
4.2004-4.26020.32751390.32282784X-RAY DIFFRACTION84
4.2602-4.32360.37511370.31292852X-RAY DIFFRACTION85
4.3236-4.3910.3471550.31162909X-RAY DIFFRACTION87
4.391-4.46270.33551580.29892922X-RAY DIFFRACTION88
4.4627-4.53940.34451590.28562991X-RAY DIFFRACTION90
4.5394-4.62170.34251590.28223027X-RAY DIFFRACTION90
4.6217-4.71020.31631580.26853035X-RAY DIFFRACTION92
4.7102-4.8060.34851670.27043088X-RAY DIFFRACTION93
4.806-4.91010.341560.26093119X-RAY DIFFRACTION93
4.9101-5.02380.37251630.26253081X-RAY DIFFRACTION93
5.0238-5.14880.32021700.25293120X-RAY DIFFRACTION93
5.1488-5.28720.31791640.26193143X-RAY DIFFRACTION94
5.2872-5.44190.31391670.26523160X-RAY DIFFRACTION95
5.4419-5.61650.34341650.26243194X-RAY DIFFRACTION95
5.6165-5.81580.37111690.25013175X-RAY DIFFRACTION95
5.8158-6.04680.37351710.25943191X-RAY DIFFRACTION95
6.0468-6.31950.34131710.25783249X-RAY DIFFRACTION96
6.3195-6.64920.33121650.25343273X-RAY DIFFRACTION97
6.6492-7.06060.3381690.25433252X-RAY DIFFRACTION96
7.0606-7.59750.3391730.22273281X-RAY DIFFRACTION97
7.5975-8.34680.28921750.19823316X-RAY DIFFRACTION97
8.3468-9.52010.25751780.18313348X-RAY DIFFRACTION98
9.5201-11.86750.22431780.19163365X-RAY DIFFRACTION97
11.8675-29.83990.32371840.25773505X-RAY DIFFRACTION98

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