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Yorodumi- PDB-1k5m: Crystal Structure of a Human Rhinovirus Type 14:Human Immunodefic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k5m | ||||||
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Title | Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2 | ||||||
Components |
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Keywords | VIRUS / engineered rhinovirus / HIV-1 V3 loop / beta turns / Icosahedral virus | ||||||
Function / homology | Function and homology information lysis of host organelle involved in viral entry into host cell / Dectin-2 family / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 ...lysis of host organelle involved in viral entry into host cell / Dectin-2 family / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 / host cell endosome membrane / 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 / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human rhinovirus 14 Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ding, J. / Smith, A.D. / Geisler, S.C. / Ma, X. / Arnold, G.F. / Arnold, E. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1 Authors: Ding, J. / Smith, A.D. / Geisler, S.C. / Ma, X. / Arnold, G.F. / Arnold, E. #1: Journal: J.Virol. / Year: 1998 Title: Human rhinovirus type 14:human immunodeficiency virus type 1 (HIV-1) V3 loop chimeras from a combinational library induce potent neutralizing antibody responses against HIV-1 Authors: Smith, A.D. / Geisler, S.C. / Chen, A.A. / Resnick, D.A. / Roy, B.M. / Lewi, P.J. / Arnold, E. / Arnold, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k5m.cif.gz | 189.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5m.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k5m_validation.pdf.gz | 606.7 KB | Display | wwPDB validaton report |
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Full document | 1k5m_full_validation.pdf.gz | 624.3 KB | Display | |
Data in XML | 1k5m_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 1k5m_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5m ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5m | HTTPS FTP |
-Related structure data
Related structure data | 4rhvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-COAT PROTEIN ... , 3 types, 3 molecules ACD
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
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#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
-Protein , 1 types, 1 molecules B
#2: Protein | Mass: 30097.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE CHIMERA CONSISTS OF THE HRV14 COAT PROTEIN VP2 (P1B) AND RESIDUES 314-325 OF HIV-1 gp120. Source: (gene. exp.) Human rhinovirus 14, (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate MN) Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Gene: env / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303, UniProt: P05877 |
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-Non-polymers , 2 types, 638 molecules
#5: Chemical | ChemComp-SPH / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.2 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 513239 / Num. obs: 513239 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4 / Num. unique all: 46826 / % possible all: 82.7 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 92.4 % / Num. measured all: 7100958 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 81.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Wild-type HRV14 structure coordinates (PDB entry 4RHV) Resolution: 2.7→50 Å / Isotropic thermal model: isotropic Cross valid method: The free R-factor was calculated in early stages of model building and refinement to monitor the progress. Due to the strong interdependency of structure factors in the presence ...Cross valid method: The free R-factor was calculated in early stages of model building and refinement to monitor the progress. Due to the strong interdependency of structure factors in the presence of high NCS, the free R-factor did not provide any useful information. Therefore, in the later stages of structure refinement, all data were included and no free R factor was calculated. σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.4 Å2 | |||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 / Rfactor all: 0.22 | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor all: 0.287 |