1RA6

Poliovirus Polymerase Full Length Apo Structure

> Summary

Summary for 1RA6

Related1RDR 1RA7 1RAJ 1TQL
DescriptorGenome polyprotein, fragment RNA-directed RNA polymerase (E.C.2.7.7.48)
Functional Keywordsnucleotidyltransferase, poliovirus, 3d, rna-dependent, polymerase, n-terminus, transferase
Biological sourceHuman poliovirus 1
Cellular locationProtein VP2: Virion. Protein VP3: Virion. Protein VP1: Virion. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3B: Virion (Potential). Picornain 3C: Host cytoplasm (Potential). RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential) P03300
Total number of polymer chains1
Total molecular weight53468.87
Authors
Thompson, A.A.,Peersen, O.B. (deposition date: 2003-10-31, release date: 2004-08-17, modification date: 2011-07-13)
Primary citation
Thompson, A.A.,Peersen, O.B.
Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase.
Embo J., 23:3462-3471, 2004
PubMed: 15306852
DOI: 10.1038/sj.emboj.7600357
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.243160.2%2.0%7.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1ra6
no rotation
Molmil generated image of 1ra6
rotated about x axis by 90°
Molmil generated image of 1ra6
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AGenome polyproteinpolymer46152988.51
UniProt (P03300)
Pfam (PF00680)
Human poliovirus 1P3D
ACETIC ACIDnon-polymer60.18
waterwater18.0297

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight52988.5
Non-Polymers*Number of molecules8
Total molecular weight480.4
All*Total molecular weight53468.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2 Å)

Cell axes127.590127.590112.971
Cell angles90.0090.00120.00
SpacegroupP 65
Resolution limits30.00 - 2.00
the highest resolution shell value2.070 - 2.000
R-work0.23100
the highest resolution shell value0.393
R-free0.24700
the highest resolution shell value0.394
RMSD bond length0.007
RMSD bond angle1.300

Data Collection Statistics

Resolution limits30.00 - 2.00
the highest resolution shell value -
Number of reflections67110
Rmerge_l_obs0.054
the highest resolution shell value0.456
Completeness96.3
Redundancy3.5
the highest resolution shell value3.1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7289

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0044162cellular_componenthost cell cytoplasmic vesicle membrane
A0044385cellular_componentintegral to membrane of host cell
A0016020cellular_componentmembrane
A0039618cellular_componentT=pseudo3 icosahedral viral capsid
A0005524molecular_functionATP binding
A0004197molecular_functioncysteine-type endopeptidase activity
A0005216molecular_functionion channel activity
A0003723molecular_functionRNA binding
A0003724molecular_functionRNA helicase activity
A0003968molecular_functionRNA-directed RNA polymerase activity
A0005198molecular_functionstructural molecule activity
A0075509biological_processendocytosis involved in viral entry into host cell
A0039520biological_processinduction by virus of host autophagy
A0039707biological_processpore formation by virus in membrane of host cell
A0044694biological_processpore-mediated entry of viral genome into host cell
A0039690biological_processpositive stranded viral RNA replication
A0051259biological_processprotein oligomerization
A0018144biological_processRNA-protein covalent cross-linking
A0039522biological_processsuppression by virus of host mRNA export from nucleus
A0039544biological_processsuppression by virus of host RIG-I activity by RIG-I proteolysis
A0039611biological_processsuppression by virus of host translation initiation factor activity
A0006351biological_processtranscription, DNA-templated
A0001172biological_processtranscription, RNA-templated
A0039694biological_processviral RNA genome replication
A0019062biological_processvirion attachment to host cell
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17BINDING SITE FOR RESIDUE ACY A 901
ChainResidue
ASER28
AILE401
ATRP403
ATHR404
ATHR410
AHIS413
AHOH

AC24BINDING SITE FOR RESIDUE ACY A 902
ChainResidue
AASP71
ALYS311
AASP349
ATYR350

AC32BINDING SITE FOR RESIDUE ACY A 903
ChainResidue
ALYS375
ALEU417

AC45BINDING SITE FOR RESIDUE ACY A 904
ChainResidue
ATYR334
AHIS336
APRO440
AARG443
AHOH

AC51BINDING SITE FOR RESIDUE ACY A 906
ChainResidue
AHIS270

AC62BINDING SITE FOR RESIDUE ACY A 907
ChainResidue
AHOH
AHOH

AC75BINDING SITE FOR RESIDUE ACY A 908
ChainResidue
AALA357
ASER360
AASN370
AHOH
AHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ACY_1ra6_A_90111ACETIC ACID binding site
ChainResidueligand
ASER28-PHE30ACY: ACETIC ACID
AILE401ACY: ACETIC ACID
ATRP403-THR404ACY: ACETIC ACID
AASP406ACY: ACETIC ACID
AASN409-THR410ACY: ACETIC ACID
AHIS413-VAL414ACY: ACETIC ACID

ACY_1ra6_A_9025ACETIC ACID binding site
ChainResidueligand
AILE67ACY: ACETIC ACID
AASP71ACY: ACETIC ACID
ALYS311ACY: ACETIC ACID
AASP349-TYR350ACY: ACETIC ACID

ACY_1ra6_A_9075ACETIC ACID binding site
ChainResidueligand
APRO222ACY: ACETIC ACID
ATRP368ACY: ACETIC ACID
APHE378ACY: ACETIC ACID
AALA380ACY: ACETIC ACID
AILE388ACY: ACETIC ACID

ACY_1ra6_A_9064ACETIC ACID binding site
ChainResidueligand
AASP266-TYR267ACY: ACETIC ACID
AHIS270ACY: ACETIC ACID
ACAS281ACY: ACETIC ACID

ACY_1ra6_A_9088ACETIC ACID binding site
ChainResidueligand
AALA357-ASP358ACY: ACETIC ACID
ASER360ACY: ACETIC ACID
ATHR362ACY: ACETIC ACID
AGLU364-VAL366ACY: ACETIC ACID
AASN370ACY: ACETIC ACID

ACY_1ra6_A_9037ACETIC ACID binding site
ChainResidueligand
ALYS375ACY: ACETIC ACID
AMET392ACY: ACETIC ACID
AGLU396-ILE397ACY: ACETIC ACID
ASER400ACY: ACETIC ACID
ALEU417ACY: ACETIC ACID
ALEU420ACY: ACETIC ACID

ACY_1ra6_A_9055ACETIC ACID binding site
ChainResidueligand
APHE377ACY: ACETIC ACID
AARG379ACY: ACETIC ACID
AVAL391ACY: ACETIC ACID
APRO393ACY: ACETIC ACID
AASN424ACY: ACETIC ACID

ACY_1ra6_A_9042ACETIC ACID binding site
ChainResidueligand
APRO440ACY: ACETIC ACID
AARG443ACY: ACETIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI13For picornain 2A activity (By similarity).
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI23For picornain 3C activity (Potential).
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI71ATP (Potential).
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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