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- PDB-4jk2: X-ray crystal structure of Escherichia coli sigma70 holoenzyme in... -

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Basic information

Entry
Database: PDB / ID: 4jk2
TitleX-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)
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 / DNA-directed RNA polymerase complex / 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 / transcription cis-regulatory region binding / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
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 / 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 ...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 / 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 / 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 / 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 / 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, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-0O2 / : / 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: 4.201 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 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)920,75817
Polymers919,81412
Non-polymers9455
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)460,7219
Polymers459,9076
Non-polymers8143
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Unit cell
Length a, b, c (Å)185.323, 205.411, 309.581
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-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N5O20P5

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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: 3.2 Å3/Da / Density % sol: 61.6 %
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: 4.2→30 Å / Num. obs: 69537 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 %

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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
Starting model: 4IGC

4igc
PDB Unreleased entry


Resolution: 4.201→29.942 Å / SU ML: 0.71 / σ(F): 1.34 / Phase error: 34.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3219 3502 5.04 %
Rwork0.2443 --
obs0.2483 69477 80.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.201→29.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56075 0 44 0 56119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256931
X-RAY DIFFRACTIONf_angle_d0.48676832
X-RAY DIFFRACTIONf_dihedral_angle_d11.53622024
X-RAY DIFFRACTIONf_chiral_restr0.0198746
X-RAY DIFFRACTIONf_plane_restr0.00210069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.201-4.25880.33061320.29562467X-RAY DIFFRACTION77
4.2588-4.31950.40391410.31432656X-RAY DIFFRACTION82
4.3195-4.38380.34721390.32152673X-RAY DIFFRACTION83
4.3838-4.45210.38151470.32032707X-RAY DIFFRACTION83
4.4521-4.52480.37791430.29822730X-RAY DIFFRACTION83
4.5248-4.60260.35211450.29592725X-RAY DIFFRACTION84
4.6026-4.6860.36161370.28842729X-RAY DIFFRACTION84
4.686-4.77570.32721470.27672724X-RAY DIFFRACTION83
4.7757-4.87280.34171400.27152704X-RAY DIFFRACTION84
4.8728-4.97830.33581450.27542721X-RAY DIFFRACTION84
4.9783-5.09360.34891410.26932712X-RAY DIFFRACTION83
5.0936-5.22030.37761410.26822685X-RAY DIFFRACTION82
5.2203-5.36070.37821400.26432699X-RAY DIFFRACTION83
5.3607-5.51750.33141460.25692675X-RAY DIFFRACTION82
5.5175-5.69440.34251480.24772654X-RAY DIFFRACTION81
5.6944-5.89640.31511410.24982654X-RAY DIFFRACTION81
5.8964-6.13060.41331340.25872640X-RAY DIFFRACTION81
6.1306-6.4070.32721400.26392640X-RAY DIFFRACTION80
6.407-6.74110.44611470.24892594X-RAY DIFFRACTION79
6.7411-7.15810.32331340.24352614X-RAY DIFFRACTION79
7.1581-7.70210.3031410.22072576X-RAY DIFFRACTION78
7.7021-8.46120.31291380.19482557X-RAY DIFFRACTION77
8.4612-9.64960.25341430.182532X-RAY DIFFRACTION76
9.6496-12.0250.25191220.19172481X-RAY DIFFRACTION73
12.025-29.94290.29541300.2622426X-RAY DIFFRACTION70

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