[English] 日本語
Yorodumi
- PDB-4k4z: Coxsackievirus B3 polymerase elongation complex (r2_Mg_form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k4z
TitleCoxsackievirus B3 polymerase elongation complex (r2_Mg_form)
Components
  • RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
  • RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
  • RNA-dependent RNA polymerase
KeywordsTransferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / Transferase-rna complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsGong, P. / Peersen, O.B.
CitationJournal: Plos One / Year: 2013
Title: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
Authors: Gong, P. / Kortus, M.G. / Nix, J.C. / Davis, R.E. / Peersen, O.B.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2May 20, 2015Group: Structure summary
Revision 1.3Feb 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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: RNA-dependent RNA polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
E: RNA-dependent RNA polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
I: RNA-dependent RNA polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
K: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
M: RNA-dependent RNA polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
H: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
O: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,11920
Polymers275,02216
Non-polymers974
Water22,8071266
1
E: RNA-dependent RNA polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7805
Polymers68,7554
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA-dependent RNA polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7805
Polymers68,7554
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: RNA-dependent RNA polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
K: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7805
Polymers68,7554
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: RNA-dependent RNA polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
O: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7805
Polymers68,7554
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.641, 60.633, 194.680
Angle α, β, γ (deg.)89.98, 89.92, 78.68
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules AEIM

#1: Protein
RNA-dependent RNA polymerase


Mass: 53624.203 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1724-2185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus B3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q66338, UniProt: Q5UEA2*PLUS, RNA-directed RNA polymerase

-
RNA chain , 3 types, 12 molecules BFJNCGKODLHP

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


Mass: 7629.574 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: RNA chain
RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')


Mass: 4526.756 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: RNA chain
RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')


Mass: 2974.854 Da / Num. of mol.: 4 / Source method: obtained synthetically

-
Non-polymers , 2 types, 1270 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1266 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: sitting drop, temperature 289K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→45.6 Å / Num. obs: 140661 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 1.95 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.7
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.5 / % possible all: 97.1

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.9.4Ddata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→45.58 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.96 / Phase error: 29.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 7082 5.05 %
Rwork0.204 --
obs0.206 140232 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.96 Å2
Refinement stepCycle: LAST / Resolution: 2.17→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14756 2877 4 1266 18903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818339
X-RAY DIFFRACTIONf_angle_d1.10225462
X-RAY DIFFRACTIONf_dihedral_angle_d13.5597164
X-RAY DIFFRACTIONf_chiral_restr0.0482902
X-RAY DIFFRACTIONf_plane_restr0.0062738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.19470.38662570.32064341X-RAY DIFFRACTION97
2.1947-2.22050.39872310.31844433X-RAY DIFFRACTION97
2.2205-2.24760.38582140.3094515X-RAY DIFFRACTION96
2.2476-2.2760.36592270.30814289X-RAY DIFFRACTION96
2.276-2.3060.31282270.28674398X-RAY DIFFRACTION97
2.306-2.33760.3072480.274520X-RAY DIFFRACTION97
2.3376-2.3710.31582440.27034234X-RAY DIFFRACTION97
2.371-2.40630.32912590.25534536X-RAY DIFFRACTION97
2.4063-2.44390.32822400.26974354X-RAY DIFFRACTION97
2.4439-2.4840.36172310.27314451X-RAY DIFFRACTION97
2.484-2.52680.30892360.25534507X-RAY DIFFRACTION98
2.5268-2.57280.28952070.24714396X-RAY DIFFRACTION98
2.5728-2.62230.30172590.25764427X-RAY DIFFRACTION98
2.6223-2.67580.3012350.24674432X-RAY DIFFRACTION98
2.6758-2.73390.29922310.23624502X-RAY DIFFRACTION98
2.7339-2.79750.26022370.22864409X-RAY DIFFRACTION98
2.7975-2.86750.31452380.22684522X-RAY DIFFRACTION98
2.8675-2.9450.28372290.23834378X-RAY DIFFRACTION98
2.945-3.03160.27382630.22974566X-RAY DIFFRACTION98
3.0316-3.12950.29582410.22274352X-RAY DIFFRACTION98
3.1295-3.24130.22792260.21534469X-RAY DIFFRACTION98
3.2413-3.3710.25252290.20084526X-RAY DIFFRACTION98
3.371-3.52440.22292540.18384385X-RAY DIFFRACTION98
3.5244-3.71010.1942440.17344428X-RAY DIFFRACTION98
3.7101-3.94250.22332310.16394475X-RAY DIFFRACTION98
3.9425-4.24670.18772260.16264502X-RAY DIFFRACTION98
4.2467-4.67360.1572330.14514519X-RAY DIFFRACTION98
4.6736-5.3490.20132170.17314451X-RAY DIFFRACTION99
5.349-6.73570.20972510.19584496X-RAY DIFFRACTION98
6.7357-45.5920.20422170.17844337X-RAY DIFFRACTION95

+
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://pdbjlvh1.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