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- PDB-4xln: Crystal structure of T. aquaticus transcription initiation comple... -

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Basic information

Entry
Database: PDB / ID: 4xln
TitleCrystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA
Components
  • (DNA (48-MER)) x 2
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA (5'-D(P*UP*CP*GP*A)-3')
  • RNA polymerase sigma factor SigA
Keywordstranscription/dna/rna / protein-DNA complex / Bacterial transcription initiation complex / transcription-dna-rna complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Enzyme I; Chain A, domain 2 / 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 / : / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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 / RNA polymerase Rpb2, domain 6 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsBae, B. / Darst, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053759 United States
CitationJournal: Elife / Year: 2015
Title: Structure of a bacterial RNA polymerase holoenzyme open promoter complex.
Authors: Bae, B. / Feklistov, A. / Lass-Napiorkowska, A. / Landick, R. / Darst, S.A.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 SigA
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 SigA
O: DNA (48-MER)
P: DNA (48-MER)
Q: RNA (5'-D(P*UP*CP*GP*A)-3')
R: DNA (48-MER)
S: DNA (48-MER)
T: RNA (5'-D(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)896,78524
Polymers896,47518
Non-polymers3106
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 SigA
O: DNA (48-MER)
P: DNA (48-MER)
Q: RNA (5'-D(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,39312
Polymers448,2379
Non-polymers1553
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 SigA
R: DNA (48-MER)
S: DNA (48-MER)
T: RNA (5'-D(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,39312
Polymers448,2379
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)289.259, 289.259, 536.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' or chain 'B' or (chain 'C' and (resseq...
211chain 'G' or chain 'H' or (chain 'I' and (resseq...
112chain 'C' and (resseq 22:130 or resseq 336:392)
212chain 'I' and (resseq 22:130 or resseq 336:392)
113chain 'C' and (resseq 143:324)
213chain 'I' and (resseq 143:324)
114(chain 'C' and resseq 703:830) or (chain 'F' and resseq 335:423)
214(chain 'I' and resseq 703:830) or (chain 'L' and resseq 335:423)
115(chain 'C' and resseq 1058:1119) or (chain 'D' and (resseq...
215(chain 'I' and resseq 1058:1119) or (chain 'J' and (resseq...

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(0.650278, -0.759629, 0.01014), (-0.759368, -0.650331, -0.02073), (0.022342, 0.00578, -0.999734)108.072998, 238.563004, 176.106003
2given(0.648974, -0.760745, 0.010046), (-0.760247, -0.648944, -0.029924), (0.029284, 0.011782, -0.999502)108.361, 239.156006, 174.477005
3given(0.647706, -0.761519, 0.023768), (-0.761147, -0.648137, -0.023955), (0.033647, -0.002575, -0.99943)107.815002, 238.722, 176.722
4given(0.660164, -0.750845, 0.020347), (-0.750249, -0.660461, -0.030305), (0.036193, 0.004741, -0.999334)104.751999, 240.774002, 175.389008
5given(0.6501, -0.759622, 0.018526), (-0.759106, -0.65035, -0.028341), (0.033577, 0.004361, -0.999427)107.302002, 239.261002, 175.835999
6given(0.666925, -0.744325, 0.034515), (-0.743227, -0.667816, -0.040435), (0.053147, 0.001315, -0.998586)101.734001, 242.960007, 175.184998
7given(0.642912, -0.765884, 0.009323), (-0.765637, -0.642952, -0.020325), (0.021561, 0.005929, -0.99975)109.478996, 237.677994, 176.201996
8given(0.650524, -0.759172, 0.02182), (-0.758482, -0.650873, -0.03271), (0.039035, 0.004729, -0.999227)107.126999, 239.490005, 175.513
9given(0.645266, -0.76395, -0.003383), (-0.763836, -0.645079, -0.020686), (0.013621, 0.015932, -0.99978)110.317001, 237.759995, 174.917999
10given(0.65635, -0.754049, 0.024797), (-0.753343, -0.656813, -0.032728), (0.040965, 0.002801, -0.999157)105.088997, 240.266998, 175.460999
Detailsbiological unit is a hetero 6-mer. There are 2 biological units in the asymmetric unit (chains ABCDEFOPQ and GHIJKLRST

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Components

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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: 34830.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 124930.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11642.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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DNA chain , 2 types, 4 molecules ORPS

#6: DNA chain DNA (48-MER)


Mass: 14878.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA non-template strand / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (48-MER)


Mass: 14831.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand / Source: (synth.) synthetic construct (others)

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Protein / RNA chain , 2 types, 4 molecules FLQT

#5: Protein RNA polymerase sigma factor SigA


Mass: 39864.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: sigA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EZJ8
#8: RNA chain RNA (5'-D(P*UP*CP*GP*A)-3')


Mass: 1240.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA transcript / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 6 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 6.26 Å3/Da / Density % sol: 80.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4→35 Å / Num. obs: 189134 / % possible obs: 99.1 % / Redundancy: 23.9 % / Biso Wilson estimate: 99.62 Å2 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.182 / Rrim(I) all: 0.268 / Χ2: 1.829 / Net I/av σ(I): 4.111 / Net I/σ(I): 2 / Num. measured all: 4528253
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
4-4.142.7172400.031.44491.3
4.14-4.3120.6188140.2111.5499.8
4.31-4.524.3188450.4111.559100
4.5-4.7425.3189450.5281.5881000.828
4.74-5.0426.3189160.571.6111000.718
5.04-5.4227.1189940.6171.6361000.621
5.42-5.9728190640.7111.6381000.492
5.97-6.8328.5191580.8611.6831000.315
6.83-8.5828.3192900.9841.9761000.1110.5860.597
8.58-3526.2198680.9983.11799.90.0310.1580.161

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→34.96 Å / SU ML: 0.83 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3149 9495 5.03 %
Rwork0.2804 --
obs0.2821 188749 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54236 4013 6 0 58255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00459727
X-RAY DIFFRACTIONf_angle_d0.85381560
X-RAY DIFFRACTIONf_dihedral_angle_d18.46123269
X-RAY DIFFRACTIONf_chiral_restr0.0589170
X-RAY DIFFRACTIONf_plane_restr0.00410000
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A15542X-RAY DIFFRACTIONPOSITIONAL
12G15542X-RAY DIFFRACTIONPOSITIONAL0.015
21C1279X-RAY DIFFRACTIONPOSITIONAL
22I1279X-RAY DIFFRACTIONPOSITIONAL0.007
31C1431X-RAY DIFFRACTIONPOSITIONAL
32I1431X-RAY DIFFRACTIONPOSITIONAL0.005
41C1714X-RAY DIFFRACTIONPOSITIONAL
42I1714X-RAY DIFFRACTIONPOSITIONAL0.027
51C5267X-RAY DIFFRACTIONPOSITIONAL
52I5267X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.04540.39152790.3915182X-RAY DIFFRACTION87
4.0454-4.09290.39742960.38245483X-RAY DIFFRACTION92
4.0929-4.14270.40512700.37195515X-RAY DIFFRACTION92
4.1427-4.19510.37373140.36085922X-RAY DIFFRACTION99
4.1951-4.25020.37133180.36995947X-RAY DIFFRACTION100
4.2502-4.30830.37512750.37456018X-RAY DIFFRACTION100
4.3083-4.36980.40082960.36755964X-RAY DIFFRACTION100
4.3698-4.43490.39143480.36785946X-RAY DIFFRACTION100
4.4349-4.5040.41623200.36785970X-RAY DIFFRACTION100
4.504-4.57770.37573250.35215978X-RAY DIFFRACTION100
4.5777-4.65650.37143110.35176018X-RAY DIFFRACTION100
4.6565-4.74090.35873250.33885954X-RAY DIFFRACTION100
4.7409-4.83190.38783240.34385995X-RAY DIFFRACTION100
4.8319-4.93030.38773180.3486006X-RAY DIFFRACTION100
4.9303-5.03720.38062960.34636003X-RAY DIFFRACTION100
5.0372-5.1540.40623120.33656000X-RAY DIFFRACTION100
5.154-5.28240.33183180.3236021X-RAY DIFFRACTION100
5.2824-5.42480.36573490.31445976X-RAY DIFFRACTION100
5.4248-5.58380.3183270.29376013X-RAY DIFFRACTION100
5.5838-5.76320.31612970.2846065X-RAY DIFFRACTION100
5.7632-5.96820.34483240.28076011X-RAY DIFFRACTION100
5.9682-6.20590.33393040.25926059X-RAY DIFFRACTION100
6.2059-6.48670.26363210.23516067X-RAY DIFFRACTION100
6.4867-6.82630.25853580.21516025X-RAY DIFFRACTION100
6.8263-7.25040.24573130.1966097X-RAY DIFFRACTION100
7.2504-7.80450.22743290.17366090X-RAY DIFFRACTION100
7.8045-8.57930.1983140.15016144X-RAY DIFFRACTION100
8.5793-9.79680.18583340.14936147X-RAY DIFFRACTION100
9.7968-12.2540.17363290.15566203X-RAY DIFFRACTION100
12.254-34.96080.30843510.26556435X-RAY DIFFRACTION100

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