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- PDB-5i2d: Crystal structure of T. thermophilus TTHB099 class II transcripti... -

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Basic information

Entry
Database: PDB / ID: 5i2d
TitleCrystal structure of T. thermophilus TTHB099 class II transcription activation complex: TAP-RPo
Components
  • (DNA (72-MER)) x 2
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA (5'-R(*UP*CP*GP*A)-3')
  • RNA polymerase sigma factor SigA
  • Transcriptional regulator, Crp familyTranscriptional regulation
KeywordsTRANSCRIPTION/DNA/RNA / Transcription / RNA polymerase / Catabolite activator protein / cAMP receptor protein / 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 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding ...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 / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding / protein homodimerization activity / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / 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 ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / 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 / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / 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 / RmlC-like jelly roll fold / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / Transcriptional regulator LdrP / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.405 Å
AuthorsFeng, Y. / Zhang, Y. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041376 United States
CitationJournal: Science / Year: 2016
Title: Structural basis of transcription activation.
Authors: Feng, Y. / Zhang, Y. / Ebright, R.H.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transcriptional regulator, Crp family
H: Transcriptional regulator, Crp family
I: DNA (72-MER)
J: DNA (72-MER)
K: RNA (5'-R(*UP*CP*GP*A)-3')
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit alpha
N: DNA-directed RNA polymerase subunit beta
O: DNA-directed RNA polymerase subunit beta'
P: DNA-directed RNA polymerase subunit omega
Q: RNA polymerase sigma factor SigA
R: Transcriptional regulator, Crp family
S: Transcriptional regulator, Crp family
T: DNA (72-MER)
U: DNA (72-MER)
V: RNA (5'-R(*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,047,02028
Polymers1,046,70922
Non-polymers3106
Water0
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
G: Transcriptional regulator, Crp family
H: Transcriptional regulator, Crp family
I: DNA (72-MER)
J: DNA (72-MER)
K: RNA (5'-R(*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,51014
Polymers523,35511
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72170 Å2
ΔGint-297 kcal/mol
Surface area169120 Å2
MethodPISA
2
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit alpha
N: DNA-directed RNA polymerase subunit beta
O: DNA-directed RNA polymerase subunit beta'
P: DNA-directed RNA polymerase subunit omega
Q: RNA polymerase sigma factor SigA
R: Transcriptional regulator, Crp family
S: Transcriptional regulator, Crp family
T: DNA (72-MER)
U: DNA (72-MER)
V: RNA (5'-R(*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,51014
Polymers523,35511
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71970 Å2
ΔGint-300 kcal/mol
Surface area169120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.487, 105.446, 374.585
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABLMCNDOEP

#1: Protein
DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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Protein , 2 types, 6 molecules FQGHRS

#5: Protein RNA polymerase sigma factor SigA


Mass: 50769.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: sigA, TTHA0532 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW1
#6: Protein
Transcriptional regulator, Crp family / Transcriptional regulation


Mass: 24344.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHB099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W63

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DNA chain , 2 types, 4 molecules ITJU

#7: DNA chain DNA (72-MER)


Mass: 22234.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#8: DNA chain DNA (72-MER)


Mass: 22341.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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RNA chain , 1 types, 2 molecules KV

#9: RNA chain RNA (5'-R(*UP*CP*GP*A)-3')


Mass: 1240.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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Non-polymers , 2 types, 6 molecules

#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#11: 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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES, pH 7.6, 0.1 M MgCl2, and 6% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4.4→49.31 Å / Num. obs: 71660 / % possible obs: 98.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 8.182
Reflection shellResolution: 4.4→4.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G7H

4g7h


Resolution: 4.405→49.31 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.37
RfactorNum. reflection% reflection
Rfree0.284 1794 2.5 %
Rwork0.2414 --
obs0.2425 71660 85.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.405→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61280 5596 6 0 66882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00368624
X-RAY DIFFRACTIONf_angle_d0.66293906
X-RAY DIFFRACTIONf_dihedral_angle_d18.40526856
X-RAY DIFFRACTIONf_chiral_restr0.04810608
X-RAY DIFFRACTIONf_plane_restr0.00311318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4051-4.52410.38691020.33744110X-RAY DIFFRACTION67
4.5241-4.65710.30721300.31114682X-RAY DIFFRACTION76
4.6571-4.80730.36621230.29794928X-RAY DIFFRACTION79
4.8073-4.9790.27721330.27855087X-RAY DIFFRACTION83
4.979-5.17810.3181290.27855196X-RAY DIFFRACTION83
5.1781-5.41350.29881400.26415220X-RAY DIFFRACTION84
5.4135-5.69850.32891470.25715371X-RAY DIFFRACTION86
5.6985-6.0550.30871350.26735487X-RAY DIFFRACTION88
6.055-6.52150.33971420.26235615X-RAY DIFFRACTION90
6.5215-7.1760.34691460.25165842X-RAY DIFFRACTION93
7.176-8.21030.29441540.20816014X-RAY DIFFRACTION96
8.2103-10.32840.20751620.19636200X-RAY DIFFRACTION98
10.3284-49.31320.24641510.21736114X-RAY DIFFRACTION94

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