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- PDB-2ppb: Crystal structure of the T. thermophilus RNAP polymerase elongati... -

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Basic information

Entry
Database: PDB / ID: 2ppb
TitleCrystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
Components
  • (DNA-directed RNA polymerase ...) x 4
  • DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')
  • RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')
KeywordsTRANSFERASE/DNA/RNA / RNA POLYMERASE / ELONGATION COMPLEX / TEMPLATE DNA / NON-TEMPLATE DNA / RNA TRANSCRIPT / NTP SUBSTRATE / ANTIBIOTIC STREPTOLYDIGIN / TRANSFERASE-DNA-RNA COMPLEX
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc 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 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / Molybdopterin biosynthesis moea protein, domain 2 / RNA polymerase Rpb1 funnel domain ...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 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / Molybdopterin biosynthesis moea protein, domain 2 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Enzyme I; Chain A, domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Wheat Germ Agglutinin (Isolectin 2); domain 1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / STREPTOLYDIGIN / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVassylyev, D.G. / Vassylyeva, M.N. / Artsimovitch, I. / Landick, R.
CitationJournal: Nature / Year: 2007
Title: Structural basis for substrate loading in bacterial RNA polymerase.
Authors: Vassylyev, D.G. / Vassylyeva, M.N. / Zhang, J. / Palangat, M. / Artsimovitch, I. / Landick, R.
History
DepositionApr 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_conn.ptnr2_label_seq_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
G: DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')
H: RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')
I: DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')
X: DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')
Y: RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')
Z: DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')
A: DNA-directed RNA polymerase alpha chain
B: DNA-directed RNA polymerase alpha chain
C: DNA-directed RNA polymerase beta chain
D: DNA-directed RNA polymerase beta' chain
E: DNA-directed RNA polymerase omega chain
K: DNA-directed RNA polymerase alpha chain
L: DNA-directed RNA polymerase alpha chain
M: DNA-directed RNA polymerase beta chain
N: DNA-directed RNA polymerase beta' chain
O: DNA-directed RNA polymerase omega chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,74928
Polymers789,17816
Non-polymers2,57112
Water44,4972470
1
G: DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')
H: RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')
I: DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')
A: DNA-directed RNA polymerase alpha chain
B: DNA-directed RNA polymerase alpha chain
C: DNA-directed RNA polymerase beta chain
D: DNA-directed RNA polymerase beta' chain
E: DNA-directed RNA polymerase omega chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,87414
Polymers394,5898
Non-polymers1,2856
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')
Y: RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')
Z: DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')
K: DNA-directed RNA polymerase alpha chain
L: DNA-directed RNA polymerase alpha chain
M: DNA-directed RNA polymerase beta chain
N: DNA-directed RNA polymerase beta' chain
O: DNA-directed RNA polymerase omega chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,87414
Polymers394,5898
Non-polymers1,2856
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.379, 155.379, 496.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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DNA chain , 2 types, 4 molecules GXIZ

#1: DNA chain DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')


Mass: 7001.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA TEMPLATE STRAND
#3: DNA chain DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')


Mass: 4323.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA NON-TEMPLATE STRAND

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RNA chain , 1 types, 2 molecules HY

#2: RNA chain RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')


Mass: 5184.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA TRANSCRIPT

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

#4: Protein
DNA-directed RNA polymerase alpha chain / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase 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: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase beta chain / RNAP beta subunit / Transcriptase beta chain / RNA polymerase 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
#6: Protein DNA-directed RNA polymerase beta' chain / RNAP beta' subunit / Transcriptase beta' chain / RNA polymerase beta' subunit


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
#7: Protein DNA-directed RNA polymerase omega chain / RNAP omega subunit / Transcriptase omega chain / RNA polymerase omega subunit


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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Non-polymers , 5 types, 2482 molecules

#8: Chemical ChemComp-STD / STREPTOLYDIGIN / 2-PYRROLIDINEACETAMIDE / PORTAMYCIN


Mass: 600.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H44N2O9 / Comment: antibiotic*YM
#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.: 4 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2470 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% MPD, 0.1M NA CACODYLATE, 0.2M MG ACETATE, 2MM AMPCPP, 2MM STD, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 6.50, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NA CACODYLATE11
3MG ACETATE11
4AMPCPP11
5MPD12
6NA CACODYLATE12
7MG ACETATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 25, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 207148 / Num. obs: 207148 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.2 / Num. unique all: 16469 / Rsym value: 0.439 / % possible all: 70.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5I

2o5i


Resolution: 3→40 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THEREFORE, SOME REFLECTIONS WERE LOST DUE TO THE DETWINNING PROCEDURE AND ARE MISSING IN THE DEPOSITED SF FILE, WHEREAS THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED ATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 11916 5.1 %RANDOM
Rwork0.234 ---
all0.243 207148 --
obs0.234 207148 87.8 %-
Displacement parametersBiso mean: 55.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47168 2168 156 2470 51962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.84
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.314 910 3.9 %
Rwork0.284 16469 -
obs-16469 70.1 %

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