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- PDB-1hqm: CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUD... -

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Basic information

Entry
Database: PDB / ID: 1hqm
TitleCRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION
Components(DNA-directed RNA polymerase subunit ...) x 4
KeywordsTRANSFERASE / DNA-directed RNA polymerase
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity ...DNA-directed RNA polymerase complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
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 / Molybdopterin biosynthesis moea protein, domain 2 / : / 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 ...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 / Molybdopterin biosynthesis moea protein, domain 2 / : / 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 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 / 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 Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
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 aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.3 Å
AuthorsMinakhin, L. / Bhagat, S. / Brunning, A. / Campbell, E.A. / Darst, S.A. / Ebright, R.H. / Severinov, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.
Authors: Minakhin, L. / Bhagat, S. / Brunning, A. / Campbell, E.A. / Darst, S.A. / Ebright, R.H. / Severinov, K.
History
DepositionDec 18, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 7, 2001ID: 1DDQ
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,9387
Polymers347,8485
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29570 Å2
ΔGint-199 kcal/mol
Surface area122460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.760, 200.760, 292.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

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


Mass: 34955.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: 124930.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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: 141365.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.24 Å3/Da / Density % sol: 70.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Zhang, G., (1999) Cell, 98, 811.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
240-45 %satammonium sulfate1reservoir
30.1 MTris-HCl1
420 mM1MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9372 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 1998
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9372 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. all: 124136 / Num. obs: 102412 / % possible obs: 82.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 0.51 % / Rmerge(I) obs: 0.455 / % possible all: 50.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.36 4156 random
Rwork0.3 --
all0.3 83551 -
obs0.3 82246 -
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21252 0 2 0 21254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.69
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.28 / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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