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- PDB-1j8n: Solution structure of beta3-analogue peptide corresponding to the... -
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Basic information
Entry | Database: PDB / ID: 1j8n | |||||||||
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Title | Solution structure of beta3-analogue peptide corresponding to the gp41 600-612 loop of HIV. | |||||||||
![]() | HIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala | |||||||||
![]() | VIRAL PROTEIN / beta peptide / gp41 / cyclic peptide | |||||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | |||||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics, energy minimization | |||||||||
![]() | Phan Chan Du, A. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S. | |||||||||
![]() | ![]() Title: Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein. Authors: Du, A.P. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 93.6 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1im7C ![]() 1j8zC ![]() 1j9vC ![]() 1jaaC ![]() 1jarC ![]() 1jc8C ![]() 1jcpC ![]() 1jd8C ![]() 1jdkC 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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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1393.694 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PARENT SEQUENCE IWGCSGKLICTTA OCCURS IN HIV GP41 PROTEIN. This analogue contains a modified residue BSE which is a beta3-Ser (i.e. with an additional CH2 between NH and Calpha). References: UniProt: P12488 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. NOESY EXPERIMENTS WITH MIXING TIMES FROM 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST CONDITIONS IN ORDER TO AVOID SPIN DIFFUSION. |
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Sample preparation
Details |
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Sample conditions | Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics, molecular dynamics, energy minimization Software ordinal: 1 Details: 50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR ...Details: 50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER MODULE OF MSI SOFTWARE. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 27 |