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- PDB-4g7h: Crystal structure of Thermus thermophilus transcription initiatio... -

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Basic information

Entry
Database: PDB / ID: 4g7h
TitleCrystal structure of Thermus thermophilus transcription initiation complex
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'
  • 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / TRANSFERASE/DNA / protein-DNA complex / transcription initiation complex / RNAP-promoter complex / RNAP-promoter open complex / open complex / RPo / RNA polymerase / transcription initiation / transcription Initiation factor sigma A / promoter DNA / nucleoid / TRANSFERASE-DNA 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 / metal ion binding / cytoplasm
Similarity search - Function
Ribonucleotide Reductase Protein R1; domain 1 - #90 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Molybdopterin biosynthesis moea protein, domain 2 / : ...Ribonucleotide Reductase Protein R1; domain 1 - #90 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Molybdopterin biosynthesis moea protein, domain 2 / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Ribonucleotide Reductase Protein R1; domain 1 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Barwin-like endoglucanases / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / 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: 2.9 Å
AuthorsZhang, Y. / Ebright, R.H.
CitationJournal: Science / Year: 2012
Title: Structural basis of transcription initiation.
Authors: Zhang, Y. / Feng, Y. / Chatterjee, S. / Tuske, S. / Ho, M.X. / Arnold, E. / Ebright, R.H.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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_ref_seq_dif.details / _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: 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
G: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'
H: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor
Q: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'
R: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)886,68930
Polymers886,18416
Non-polymers50514
Water9,260514
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
G: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'
H: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,34515
Polymers443,0928
Non-polymers2527
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52330 Å2
ΔGint-227 kcal/mol
Surface area141520 Å2
MethodPISA
2
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor
Q: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'
R: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,34515
Polymers443,0928
Non-polymers2527
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52660 Å2
ΔGint-235 kcal/mol
Surface area141040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.560, 104.570, 297.550
Angle α, β, γ (deg.)90.00, 98.32, 90.00
Int Tables number4
Space group name H-MP1211
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 'C' and ((resseq 260:760))
211chain 'M' and ((resseq 260:760))
112chain 'D' and ((resseq 100:215))
212chain 'N' and ((resseq 100:215))
113chain 'D' and ((resseq 340:950))
213chain 'N' and ((resseq 340:950))
114chain 'E'
214chain 'O'
115chain 'C' and ((resseq 820:1118))
215chain 'M' and ((resseq 820:1118))

NCS ensembles :
ID
1
2
3
4
5

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Components

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

#1: Protein
DNA-directed RNA polymerase subunit alpha / 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / 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 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNA polymerase beta-prime subunit / RNAP subunit beta' / RNA polymerase subunit beta' / ...RNA polymerase beta-prime subunit / 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 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / 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 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules FP

#5: Protein RNA polymerase sigma factor / RNA polymerase principle sigma factor / sigma A


Mass: 50769.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoD, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1

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DNA chain , 2 types, 4 molecules GQHR

#6: DNA chain 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*G)-3'


Mass: 5821.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: template strand
#7: DNA chain 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'


Mass: 8421.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nontemplate strand

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Non-polymers , 3 types, 528 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 100 mM Tris-HCl, pH 8.7, 200 mM potassium chloride, 50 mM magnesium chloride, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 250138 / Num. obs: 249337 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.667 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IW7

1iw7


Resolution: 2.9→49.27 Å / SU ML: 0.38 / σ(F): 0.82 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 2204 0.88 %
Rwork0.188 --
obs0.1884 249046 99.48 %
all-249053 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6203 Å20 Å26.6393 Å2
2--24.6399 Å20 Å2
3----19.0196 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55246 1646 14 514 57420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00558086
X-RAY DIFFRACTIONf_angle_d0.98978906
X-RAY DIFFRACTIONf_dihedral_angle_d16.36322558
X-RAY DIFFRACTIONf_chiral_restr0.0748882
X-RAY DIFFRACTIONf_plane_restr0.00510066
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C3949X-RAY DIFFRACTIONPOSITIONAL
12M3949X-RAY DIFFRACTIONPOSITIONAL0.097
21D931X-RAY DIFFRACTIONPOSITIONAL
22N931X-RAY DIFFRACTIONPOSITIONAL0.118
31D4784X-RAY DIFFRACTIONPOSITIONAL
32N4784X-RAY DIFFRACTIONPOSITIONAL0.152
41E761X-RAY DIFFRACTIONPOSITIONAL
42O761X-RAY DIFFRACTIONPOSITIONAL0.155
51C2334X-RAY DIFFRACTIONPOSITIONAL
52M2334X-RAY DIFFRACTIONPOSITIONAL0.07
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9630.40211360.30915254X-RAY DIFFRACTION99
2.963-3.0320.33971400.285815217X-RAY DIFFRACTION99
3.032-3.10780.29381300.27215277X-RAY DIFFRACTION99
3.1078-3.19180.32861380.26315279X-RAY DIFFRACTION99
3.1918-3.28570.29461360.25315355X-RAY DIFFRACTION99
3.2857-3.39170.30071380.232915347X-RAY DIFFRACTION99
3.3917-3.51290.24541400.215515336X-RAY DIFFRACTION99
3.5129-3.65350.28451370.204915401X-RAY DIFFRACTION100
3.6535-3.81970.24281370.193315423X-RAY DIFFRACTION100
3.8197-4.0210.21151380.175215455X-RAY DIFFRACTION100
4.021-4.27280.18561350.161615437X-RAY DIFFRACTION100
4.2728-4.60250.17991390.149715467X-RAY DIFFRACTION100
4.6025-5.06530.20171400.148915545X-RAY DIFFRACTION100
5.0653-5.79720.18641390.165315602X-RAY DIFFRACTION100
5.7972-7.30010.21361410.175815619X-RAY DIFFRACTION100
7.3001-49.27670.16871400.15715828X-RAY DIFFRACTION99

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