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- PDB-2r04: STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CA... -
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Basic information
Entry | Database: PDB / ID: 2r04 | ||||||||||||
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Title | STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES | ||||||||||||
![]() | (HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ...) x 4 | ||||||||||||
![]() | VIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus | ||||||||||||
Function / homology | ![]() lysis of host organelle 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 / 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 ...lysis of host organelle 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 / 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 / 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 / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() | ||||||||||||
![]() | Badger, J. / Smith, T.J. / Rossmann, M.G. | ||||||||||||
![]() | ![]() Title: Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses. Authors: Badger, J. / Minor, I. / Oliveira, M.A. / Smith, T.J. / Rossmann, M.G. #1: ![]() Title: The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure Authors: Arnold, E. / Rossmann, M.G. #2: ![]() Title: Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms Authors: Arnold, E. / Rossmann, M.G. #3: ![]() Title: Three-Dimensional Structures of Drug-Resistant Mutants of Human Rhinovirus 14 Authors: Badger, J. / Krishnaswamy, S. / Kremer, M.J. / Oliveira, M.A. / Rossmann, M.G. / Heinz, B.A. / Rueckert, R.R. / Dutko, F.J. / Mckinlay, M.A. #4: ![]() Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14 Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A. #5: ![]() Title: The Structure Determination of a Common Cold Virus, Human Rhinovirus 14 Authors: Arnold, E. / Vriend, G. / Luo, M. / Griffith, J.P. / Kamer, G. / Erickson, J.W. / Johnson, J.E. / Rossmann, M.G. #6: ![]() Title: Implications of the Picornavirus Capsid Structure for Polyprotein Structure Authors: Arnold, E. / Luo, M. / Vriend, G. / Rossmann, M.G. / Palmenberg, A.C. / Parks, G.D. / Nicklin, M.J.H. / Wimmer, E. #7: ![]() Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J. #8: ![]() Title: The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Vriend, G. #9: ![]() Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G. #10: ![]() Title: Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14 Authors: Arnold, E. / Erickson, J.W. / Fout, G.S. / Frankenberger, E.A. / Hecht, H.-J. / Luo, M. / Rossmann, M.G. / Rueckert, R.R. #11: ![]() Title: Picornaviruses of Two Different Genera Have Similar Structures Authors: Luo, M. / Arnold, E. / Erickson, J.W. / Rossmann, M.G. / Boege, U. / Scraba, D.G. #12: ![]() Title: Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals Authors: Erickson, J.W. / Frankenberger, E.A. / Rossmann, M.G. / Fout, G.S. / Medappa, K.C. / Rueckert, R.R. | ||||||||||||
History |
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Remark 700 | SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE ...SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. THUS SHEETS B11 AND B12 DIFFER ONLY IN STRAND 4, SHEETS B12 AND B22 DIFFER ONLY IN STRAND 4, AND SHEETS B13 AND B23 DIFFER IN STRANDS 1 AND 4 (DOUBLY BIFURCATED). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.6 KB | Display | ![]() |
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PDB format | ![]() | 117.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1r08C ![]() 2r06C ![]() 2r07C ![]() 2rm2C ![]() 2rr1C ![]() 2rs1C ![]() 2rs3C ![]() 2rs5C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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4 | ![]()
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6 | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 2 83 IS A CIS PROLINE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 2 types, 5 molecules ![](data/chem/img/W71.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-W71 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Arnold, E., (1984) J.Mol.Biol., 177, 417. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 194573 / Observed criterion σ(I): 2 / Num. measured all: 275570 / Rmerge(I) obs: 0.136 |
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Processing
Software | Name: REAL-SPACE / Version: REFINEMENT / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refinement | *PLUS Rfactor obs: 0.196 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |