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Open data
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Basic information
Entry | Database: PDB / ID: 2m8l | ||||||
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Title | HIV capsid dimer structure | ||||||
![]() | Capsid protein p24 | ||||||
![]() | VIRAL PROTEIN / capsid / HIV / dimer | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / ![]() | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Deshmukh, L. / Schwieters, C.D. / Grishaev, A. / Clore, G. / Ghirlando, R. | ||||||
![]() | ![]() Title: Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution. Authors: Deshmukh, L. / Schwieters, C.D. / Grishaev, A. / Ghirlando, R. / Baber, J.L. / Clore, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 13 MB | Display | ![]() |
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PDB format | ![]() | 11 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.8 KB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 907.7 KB | Display | |
Data in CIF | ![]() | 1.1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein | Mass: 25630.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment |
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NMR experiment |
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Sample preparation
Details | Contents: 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 308 K |
-Data collection
NMR spectrometer |
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Soln scatter | Type: x-ray / Conc. range: 3.25 - 6.5 / Detector type: PILATUS 2M / Sample pH: 6.5 / Source beamline: 12-ID-B / Source class: synchrotron / Source type: APS / Temperature: 298 K |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: This is an ensemble refinement. The MODEL entries appear in groups of 5, representing 20 ensembles. Xplor-NIH Ensemble Calculation This file contains 20 ensembles of size 5 Ensemble 1: MODEL ...Details: This is an ensemble refinement. The MODEL entries appear in groups of 5, representing 20 ensembles. Xplor-NIH Ensemble Calculation This file contains 20 ensembles of size 5 Ensemble 1: MODEL 1, weight: 0.207 MODEL 2, weight: 0.204 MODEL 3, weight: 0.201 MODEL 4, weight: 0.197 MODEL 5, weight: 0.191 Ensemble 2: MODEL 6, weight: 0.225 MODEL 7, weight: 0.214 MODEL 8, weight: 0.203 MODEL 9, weight: 0.190 MODEL 10, weight: 0.168 Ensemble 3: MODEL 11, weight: 0.202 MODEL 12, weight: 0.201 MODEL 13, weight: 0.200 MODEL 14, weight: 0.199 MODEL 15, weight: 0.198 Ensemble 4: MODEL 16, weight: 0.283 MODEL 17, weight: 0.243 MODEL 18, weight: 0.203 MODEL 19, weight: 0.162 MODEL 20, weight: 0.109 Ensemble 5: MODEL 21, weight: 0.200 MODEL 22, weight: 0.200 MODEL 23, weight: 0.200 MODEL 24, weight: 0.200 MODEL 25, weight: 0.200 Ensemble 6: MODEL 26, weight: 0.209 MODEL 27, weight: 0.206 MODEL 28, weight: 0.201 MODEL 29, weight: 0.196 MODEL 30, weight: 0.187 Ensemble 7: MODEL 31, weight: 0.203 MODEL 32, weight: 0.202 MODEL 33, weight: 0.201 MODEL 34, weight: 0.199 MODEL 35, weight: 0.196 Ensemble 8: MODEL 36, weight: 0.190 MODEL 37, weight: 0.194 MODEL 38, weight: 0.198 MODEL 39, weight: 0.204 MODEL 40, weight: 0.214 Ensemble 9: MODEL 41, weight: 0.200 MODEL 42, weight: 0.200 MODEL 43, weight: 0.200 MODEL 44, weight: 0.200 MODEL 45, weight: 0.200 Ensemble 10: MODEL 46, weight: 0.200 MODEL 47, weight: 0.200 MODEL 48, weight: 0.200 MODEL 49, weight: 0.200 MODEL 50, weight: 0.200 Ensemble 11: MODEL 51, weight: 0.203 MODEL 52, weight: 0.202 MODEL 53, weight: 0.200 MODEL 54, weight: 0.199 MODEL 55, weight: 0.197 Ensemble 12: MODEL 56, weight: 0.200 MODEL 57, weight: 0.200 MODEL 58, weight: 0.200 MODEL 59, weight: 0.200 MODEL 60, weight: 0.200 Ensemble 13: MODEL 61, weight: 0.200 MODEL 62, weight: 0.200 MODEL 63, weight: 0.200 MODEL 64, weight: 0.200 MODEL 65, weight: 0.200 Ensemble 14: MODEL 66, weight: 0.179 MODEL 67, weight: 0.186 MODEL 68, weight: 0.196 MODEL 69, weight: 0.208 MODEL 70, weight: 0.232 Ensemble 15: MODEL 71, weight: 0.200 MODEL 72, weight: 0.200 MODEL 73, weight: 0.200 MODEL 74, weight: 0.200 MODEL 75, weight: 0.200 Ensemble 16: MODEL 76, weight: 0.200 MODEL 77, weight: 0.200 MODEL 78, weight: 0.200 MODEL 79, weight: 0.200 MODEL 80, weight: 0.200 Ensemble 17: MODEL 81, weight: 0.200 MODEL 82, weight: 0.200 MODEL 83, weight: 0.200 MODEL 84, weight: 0.200 MODEL 85, weight: 0.199 Ensemble 18: MODEL 86, weight: 0.200 MODEL 87, weight: 0.200 MODEL 88, weight: 0.200 MODEL 89, weight: 0.200 MODEL 90, weight: 0.200 Ensemble 19: MODEL 91, weight: 0.201 MODEL 92, weight: 0.201 MODEL 93, weight: 0.200 MODEL 94, weight: 0.200 MODEL 95, weight: 0.198 Ensemble 20: MODEL 96, weight: 0.200 MODEL 97, weight: 0.200 MODEL 98, weight: 0.200 MODEL 99, weight: 0.200 MODEL 100, weight: 0.200 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 480 / Conformers submitted total number: 100 |