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- PDB-1s0v: Structural basis for substrate selection by T7 RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 1s0v
TitleStructural basis for substrate selection by T7 RNA polymerase
Components
  • 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
  • 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
  • 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
  • DNA-directed RNA polymerasePolymerase
KeywordsTransferase/DNA-RNA HYBRID / T7 RNA polymerase / DNA / RNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / Transferase-DNA-RNA COMPLEX / Transferase-DNA-RNA HYBRID complex
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal ...T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Helix Hairpins / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA / DNA (> 10) / RNA / RNA (> 10) / T7 RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTemiakov, D. / Patlan, V. / Anikin, M. / McAllister, W.T. / Yokoyama, S. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural basis for substrate selection by t7 RNA polymerase.
Authors: Temiakov, D. / Patlan, V. / Anikin, M. / McAllister, W.T. / Yokoyama, S. / Vassylyev, D.G.
#1: Journal: Nature / Year: 2002
Title: Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
Authors: Tahirov, T.H. / Temiakov, D. / Anikin, M. / Patlan, V. / G Vassylyev, D. / McAllister, W.T. / Yokoyama, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex
Authors: Temiakov, D. / Tahirov, T.H. / Anikin, M. / McAllister, W.T. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 23, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
E: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
F: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
G: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
H: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
I: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
J: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
K: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
L: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
M: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
N: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
O: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
P: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
A: DNA-directed RNA polymerase
B: DNA-directed RNA polymerase
C: DNA-directed RNA polymerase
D: DNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,70828
Polymers445,49316
Non-polymers2,21512
Water17,997999
1
E: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
F: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
G: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
A: DNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9277
Polymers111,3734
Non-polymers5543
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
I: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
J: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
B: DNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9277
Polymers111,3734
Non-polymers5543
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
L: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
M: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
C: DNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9277
Polymers111,3734
Non-polymers5543
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
N: 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'
O: 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'
P: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'
D: DNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9277
Polymers111,3734
Non-polymers5543
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.133, 87.703, 206.531
Angle α, β, γ (deg.)91.93, 91.02, 110.66
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 8 molecules EHKNGJMP

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


Mass: 5541.591 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA Template strand
#3: DNA chain
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'


Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA Non-template strand

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RNA chain / Protein , 2 types, 8 molecules FILOABCD

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


Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: RNA transcript
#4: Protein
DNA-directed RNA polymerase / Polymerase / 2.7.7.6


Mass: 98984.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 1 / Production host: Escherichia coli (E. coli) / Strain (production host): dcat4 / References: UniProt: P00573, DNA-directed RNA polymerase

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Non-polymers , 3 types, 1011 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 3.28 Å3/Da / Density % sol: 62.22 %
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Temiakov, D., (2003) Acta Crystallogr.,Sect.D, 59, 185.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG80001reservoir
310 %glycerol1reservoir
45 mMbeta-mercaptoethanol1reservoir
5100 mMTris1reservoirpH8.1

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 106154 / Num. obs: 94902 / % possible obs: 89.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1
Reflection shellResolution: 3→3.11 Å / % possible all: 83.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 229915 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 83.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H83

1h83


Resolution: 3.2→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.307 3685 RANDOM
Rwork0.255 --
all0.255 87784 -
obs0.255 73174 -
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26984 2784 132 999 30899
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.022
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.1
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg1.46

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