[English] 日本語
Yorodumi
- PDB-4k50: Rhinovirus 16 polymerase elongation complex (r1_form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k50
TitleRhinovirus 16 polymerase elongation complex (r1_form)
Components
  • RNA (33-MER)
  • RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
  • RNA polymerase 3D-POL
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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / 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
ACETATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 polymerase 3D-POL
B: RNA (33-MER)
C: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
E: RNA polymerase 3D-POL
F: RNA (33-MER)
G: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
I: RNA polymerase 3D-POL
J: RNA (33-MER)
K: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
M: RNA polymerase 3D-POL
N: RNA (33-MER)
O: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,43838
Polymers272,76712
Non-polymers1,67126
Water7,350408
1
A: RNA polymerase 3D-POL
B: RNA (33-MER)
C: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,73411
Polymers68,1923
Non-polymers5428
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-59 kcal/mol
Surface area25780 Å2
MethodPISA
2
E: RNA polymerase 3D-POL
F: RNA (33-MER)
G: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5469
Polymers68,1923
Non-polymers3546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-47 kcal/mol
Surface area25660 Å2
MethodPISA
3
I: RNA polymerase 3D-POL
J: RNA (33-MER)
K: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78912
Polymers68,1923
Non-polymers5979
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-48 kcal/mol
Surface area25890 Å2
MethodPISA
4
M: RNA polymerase 3D-POL
N: RNA (33-MER)
O: RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3696
Polymers68,1923
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-45 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 113.893, 122.600
Angle α, β, γ (deg.)90.010, 90.490, 90.000
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules AEIM

#1: Protein
RNA polymerase 3D-POL / Genome polyprotein


Mass: 52344.035 Da / Num. of mol.: 4 / Fragment: unp residues 1694-2153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus A16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q82122, RNA-directed RNA polymerase

-
RNA chain , 2 types, 8 molecules BFJNCGKO

#2: RNA chain
RNA (33-MER)


Mass: 11283.772 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: RNA chain
RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')


Mass: 4563.828 Da / Num. of mol.: 4 / Source method: obtained synthetically

-
Non-polymers , 4 types, 434 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M ammonium sulfate, 0.08 M sodium acetate, pH 4.6, 20% (w/v) PEG 4000, and 20% (v/v) glycerol and directly frozen , VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
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: 2.93→49.07 Å / Num. obs: 61473 / % possible obs: 98.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 1.98 % / Rmerge(I) obs: 0.108 / Χ2: 1.02 / Net I/σ(I): 5.1 / Scaling rejects: 919
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.93-3.031.980.4381.61228361651.2498.3
3.03-3.161.970.362.11226661591.2198.4
3.16-3.31.980.2912.61212960911.198.6
3.3-3.471.970.2562.91221961521.0698.6
3.47-3.691.970.2063.7122856189198.5
3.69-3.981.970.1624.71212961160.9798.4
3.98-4.381.970.1236.31230262000.9398.7
4.38-5.011.980.1067.31227461520.9298.8
5.01-6.311.990.1097.11235761820.9498.7
6.31-49.071.990.05913.11216260670.8897.1

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.9.1Ldata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→45.303 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / SU ML: 0.44 / σ(F): 1.96 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 3069 5.01 %
Rwork0.1907 --
obs0.1935 61310 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.75 Å2 / Biso mean: 37.7811 Å2 / Biso min: 9.47 Å2
Refinement stepCycle: LAST / Resolution: 2.93→45.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14740 3928 111 408 19187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919579
X-RAY DIFFRACTIONf_angle_d1.18727362
X-RAY DIFFRACTIONf_chiral_restr0.0523173
X-RAY DIFFRACTIONf_plane_restr0.0072784
X-RAY DIFFRACTIONf_dihedral_angle_d15.7887792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.93-2.97580.38081300.31992667279798
2.9758-3.02460.37251220.30632596271898
3.0246-3.07670.42971420.30082677281998
3.0767-3.13270.35641360.28372658279498
3.1327-3.19290.31781530.26172626277998
3.1929-3.25810.3781450.25392616276198
3.2581-3.32890.31921450.24262670281598
3.3289-3.40630.30911470.24282652279998
3.4063-3.49140.27141450.22012633277898
3.4914-3.58580.31031480.21862694284299
3.5858-3.69130.2621360.20662608274498
3.6913-3.81040.22561000.18452750285098
3.8104-3.94650.24961540.1792584273898
3.9465-4.10440.2231360.16452666280298
4.1044-4.2910.211580.15292614277299
4.291-4.51710.18751360.14492699283598
4.5171-4.79980.17921430.13952632277599
4.7998-5.16990.19121440.14432675281999
5.1699-5.68930.21621530.15082622277599
5.6893-6.51050.22121350.16452673280899
6.5105-8.19460.18361310.15942658278998
8.1946-45.30850.1731300.15832571270195

+
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