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- PDB-1m9c: X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal doma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m9c | ||||||
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Title | X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex. | ||||||
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![]() | Isomerase/Viral protein / CAPSID / HIV-1 / CYCLOPHILIN A / ISOMERASE / ROTAMASE / Isomerase-Viral protein COMPLEX | ||||||
Function / homology | ![]() negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / host cell cytoplasm / positive regulation of MAPK cascade / response to hypoxia / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / host cell nucleus / Neutrophil degranulation / structural molecule activity / virion membrane / protein-containing complex / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Howard, B.R. / Vajdos, F.F. / Li, S. / Sundquist, W.I. / Hill, C.P. | ||||||
![]() | ![]() Title: Structural insights into the catalytic mechanism of cyclophilin A Authors: Howard, B.R. / Vajdos, F.F. / Li, S. / Sundquist, W.I. / Hill, C.P. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Complex "A" consists of chains B and C; Complex "B" consists of chains A and D. | ||||||
Remark 999 | SEQUENCE According to the authors, this apparent conflict is due to the use of HIV-1 strain NL4-3 ...SEQUENCE According to the authors, this apparent conflict is due to the use of HIV-1 strain NL4-3 which has a histidine at residue 120. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.4 KB | Display | ![]() |
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Full document | ![]() | 461.5 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m9dC ![]() 1m9eC ![]() 1m9fC ![]() 1m9xC ![]() 1m9yC ![]() 1ak4S ![]() 1m96 S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 1997 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→38 Å / Num. all: 38057 / Num. obs: 31588 / % possible obs: 83 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.55 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1153 / Rsym value: 0.195 / % possible all: 60 |
Reflection | *PLUS Lowest resolution: 38 Å / % possible obs: 83 % / Num. measured all: 89358 |
Reflection shell | *PLUS % possible obs: 60 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AK4 Resolution: 2→37.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.916 / SU ML: 0.252 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.315 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS But not output to the coordinate file.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.841 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 38 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.03 Å |