[English] 日本語
Yorodumi
- PDB-3q23: X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q23
TitleX-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GMPCPP and Manganese: sustrate complex II
Components
  • DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
  • Virion RNA polymerase
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / TWO-METAL CATALYSIS / GMPCPP / GPCPP / DE NOVO TRANSCRIPTION INITIATION / NUCLEOTIDYLTRANSFERASE / INITIATION COMPLEX / DNA-HAIRPIN / VIRION RNA POLYMERASE / PHOSPHATE ION / RNA POLYMERASE / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / virion component / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain / Transcription Regulator spoIIAA / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGleghorn, M.L. / Murakami, K.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
Authors: Gleghorn, M.L. / Davydova, E.K. / Basu, R. / Rothman-Denes, L.B. / Murakami, K.S.
History
DepositionDec 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Virion RNA polymerase
C: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
B: Virion RNA polymerase
D: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,90014
Polymers268,4014
Non-polymers2,49910
Water47,3072626
1
A: Virion RNA polymerase
C: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,4507
Polymers134,2012
Non-polymers1,2495
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-16 kcal/mol
Surface area46200 Å2
MethodPISA
2
B: Virion RNA polymerase
D: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,4507
Polymers134,2012
Non-polymers1,2495
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-20 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.834, 111.861, 276.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein Virion RNA polymerase


Mass: 123193.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage N4 (virus) / Gene: gp50 / Plasmid: PKMK56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase
#2: DNA chain DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')


Mass: 11007.082 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Non-polymers , 4 types, 2636 molecules

#3: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O4P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2626 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25 % (DROP) 20% (RESERVOIR) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS-HCLTris11
2DIBASIC AMMONIUM CITRATE11
3AMMONIUM DIHYDROGEN MONOPHOSPHATE11
4PEG 335011
5TRIS-HCLTris12
6DIBASIC AMMONIUM CITRATE12
7AMMONIUM DIHYDROGEN MONOPHOSPHATE12
8PEG 335012

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.959997
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2006
RadiationMonochromator: Silicon(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959997 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 234419 / Num. obs: 234419 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.545 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.77 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 11758 5 %RANDOM
Rwork0.2 ---
all0.201 234301 --
obs0.201 234301 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.5 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16897 828 142 2626 20493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02218231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0662.04224868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.852187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60325.761769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.076153119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0381582
X-RAY DIFFRACTIONr_chiral_restr0.070.22843
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.29332
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.212643
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.277
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.511209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.819217525
X-RAY DIFFRACTIONr_scbond_it1.16338184
X-RAY DIFFRACTIONr_scangle_it1.8434.57343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 754 -
Rwork0.273 14513 -
obs--88.3 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more