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Title :   CRYSTAL STRUCTURE OF THE RNA-DEPENDENT RNA POLYMERASE 3D FROM HUMAN RHINOVIRUS SEROTYPE 14

Authors :   R. A. Love, K. A. Maegley, X. Yu, R. A. Ferre, L. K. Lingardo, W. Diehl, H. E. Parge, P. S. Dragovich, S. A. Fuhrman

Date :   13 Oct 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

Keywords :   Rna-Dependent Rna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Love, K. A. Maegley, X. Yu, R. A. Ferre, L. K. Lingardo, W. Diehl, H. E. Parge, P. S. Dragovich, S. A. Fuhrman
The Crystal Structure Of The Rna-Dependent Rna Polymerase From Human Rhinovirus: A Dual-Function Target For Common Cold Antiviral Therapy
Structure V. 12 1533 2004
PubMed-ID: 15296746 | Reference-DOI: 10.1016/J.STR.2004.05.024
(for further references see the PDB file header)

Molecule 1 - GENOME POLYPROTEIN
	Chains	:	A
	EC Number	:	2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(D3)
	Expression System Taxid	:	562
	Fragment	:	RNA-DIRECTED RNA POLYMERASE
	Gene	:	P3D
	Organism Scientific	:	HUMAN RHINOVIRUS 14
	Organism Taxid	:	12131

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SM	1	Ligand/Ion	SAMARIUM (III) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:233 , ASP A:327 , ASP A:328 , HOH A:902 , HOH A:903	BINDING SITE FOR RESIDUE SM A 901

(no "SS Bond" information available for 1XR5)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:118	-	Pro A:119

(no "SAP(SNP)/Variant" information available for 1XR5)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RDRP_SSRNA_POS	PS50507	RdRp of positive ssRNA viruses catalytic domain profile.	POLG_HRV14	1946-2060	1	A:227-341

(no "Exon" information available for 1XR5)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:460
 aligned with POLG_HRV14 | P03303 from UniProtKB/Swiss-Prot  Length:2179

    Alignment length:460
                                  1729      1739      1749      1759      1769      1779      1789      1799      1809      1819      1829      1839      1849      1859      1869      1879      1889      1899      1909      1919      1929      1939      1949      1959      1969      1979      1989      1999      2009      2019      2029      2039      2049      2059      2069      2079      2089      2099      2109      2119      2129      2139      2149      2159      2169      2179
          POLG_HRV14   1720 GQVIARHKVREFNINPVNTPTKSKLHPSVFYDVFPGDKEPAVLSDNDPRLEVKLTESLFSKYKGNVNTEPTENMLVAVDHYAGQLLSLDIPTSELTLKEALYGVDGLEPIDITTSAGFPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSVDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGVLTGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFVCLEKVLTKLGFAGSSLIQSICNTHHIFRDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDKLKILAYGDDLIVSYPYELDPQVLATLGKNYGLTITPPDKSETFTKMTWENLTFLKRYFKPDQQFPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNEFIQKIRTTDIGKCLILPEYSVLRRRWLDLF 2179
               SCOP domains d1xr5a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1xr5A02 A:213-242,A:291-366   ------------------------------------------------1xr5A02 A:213-242,A:291-366  [code=3.30.70.270, no name defined]            -------1xr5A03 A:374-460  [code=1.20.960.20, no name defined]                                  CATH domains
               Pfam domains ----------------RdRP_1-1xr5A01 A:17-459                                                                                                                                                                                                                                                                                                                                                                                                                                    - Pfam domains
         Sec.struct. author .eeeeeehhhhhh............ee.hhhh......ee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhh.hhhhhh......hhhhhhhhhhhh....eeeee...eehhhhhhh....eeee.hhhhhhhhh..hhhhhhhhhhh...........hhhhhh.hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhheeee....eeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeee.....hhhhhhhhhh.....ee.....................eeee.......eeee.hhhhhhhhhhee....hhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDRP_SSRNA_POS  PDB: A:227-341 UniProt: 1946-2060                                                                  ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xr5 A    1 GQVIARHKVREFNINPVNTPTKSKLHPSVFYDVFPGDKEPAVLSDNDPRLEVKLTESLFSKYKGNVNTEPTENMLVAVDHYAGQLLSLDIPTSELTLKEALYGVDGLEPIDITTSAGFPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSVDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGVLTGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFVCLEKVLTKLGFAGSSLIQSICNTHHIFRDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDKLKILAYGDDLIVSYPYELDPQVLATLGKNYGLTITPPDKSETFTKMTWENLTFLKRYFKPDQQFPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNEFIQKIRTTDIGKCLILPEYSVLRRRWLDLF  460
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: RNA-dependent RNA-polymerase (253)

Protein domain: Viral RNA polymerase (148)

Human rhinovirus 14, HRV-14 [TaxId: 12131] (1)

d1xr5a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.270, no name defined] (278)

Human rhinovirus 14. Organism_taxid: 12131. (1)

1xr5A02

A:213-242,A:291-366

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Mitochondrial Import Receptor Subunit Tom20; Chain A (25)

Homologous Superfamily: [code=1.20.960.20, no name defined] (24)

Human rhinovirus 14. Organism_taxid: 12131. (1)

1xr5A03

A:374-460

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RdRP (210)

Family: RdRP_1 (44)

Human rhinovirus 14 (HRV-14) (1)

RdRP_1-1xr5A01

A:17-459

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (POLG_HRV14 | P03303)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0017111	nucleoside-triphosphatase activity	Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0018144	RNA-protein covalent cross-linking	The formation of a covalent cross-link between RNA and a protein.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039520	induction by virus of host autophagy	Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0039664	lysis of host organelle involved in viral entry into host cell	The viral-induced lysis of an organelle (endosome, lysosome, or caveosome) that is involved in the uptake of a virus into a host cell. Occurs once the virus is within the organelle, and results in transfer of the viral contents from the organelle compartment into the cytoplasm.
	GO:0039707	pore formation by virus in membrane of host cell	The aggregation, arrangement and bonding together of a set of components by a virus to form a pore complex in a membrane of a host organism.
	GO:0044694	pore-mediated entry of viral genome into host cell	Injection by a non-enveloped virus of the viral genome into the host cytoplasm through creation of a pore or channel in the host cell membrane(s). Usually mediated by a viral pore-forming peptide associated with the viral capsid or bacteriophage tail.
	GO:0039690	positive stranded viral RNA replication	A viral genome replication process where the template genome is positive stranded, single stranded RNA ((+)ssRNA). Replication of the positive strand leads to dsRNA formation, which in turn is transcribed into positive single stranded RNA.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0039540	suppression by virus of host RIG-I activity	Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0039544	suppression by virus of host RIG-I activity by RIG-I proteolysis	The chemical reactions and pathways performed by a virus resulting in the hydrolysis of the host RIG-I protein (also known as DDX58) by cleavage of peptide bonds, thereby inhibiting RIG-I signal transduction.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039522	suppression by virus of host mRNA export from nucleus	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of movement of mRNA from the nucleus to the cytoplasm in the host organism.
	GO:0039611	suppression by virus of host translation initiation factor activity	Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0039618	T=pseudo3 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with pseudo T=3 symmetry. The T=pseudo3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044161	host cell cytoplasmic vesicle	A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.
	GO:0044162	host cell cytoplasmic vesicle membrane	The lipid bilayer surrounding a host cell cytoplasmic vesicle.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0044385	integral to membrane of host cell	Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric/Biological Unit
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	1xr5
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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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