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Yorodumi- PDB-2me3: HIV-1 gp41 clade C Membrane Proximal External Region peptide in D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2me3 | ||||||
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Title | HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle | ||||||
Components | Envelope glycoprotein gp160 | ||||||
Keywords | MEMBRANE PROTEIN / MPER / viral fusion / helix-hinge-helix | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model5 | ||||||
Authors | Sun, Z.J. / Wagner, G. / Reinherz, E.L. / Kim, M. / Song, L. / Choi, J. / Cheng, Y. / Chowdhury, B. / Bellot, G. / Shih, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Disruption of Helix-Capping Residues 671 and 674 Reveals a Role in HIV-1 Entry for a Specialized Hinge Segment of the Membrane Proximal External Region of gp41. Authors: Sun, Z.Y. / Cheng, Y. / Kim, M. / Song, L. / Choi, J. / Kudahl, U.J. / Brusic, V. / Chowdhury, B. / Yu, L. / Seaman, M.S. / Bellot, G. / Shih, W.M. / Wagner, G. / Reinherz, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2me3.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2me3.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 2me3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2me3_validation.pdf.gz | 516.8 KB | Display | wwPDB validaton report |
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Full document | 2me3_full_validation.pdf.gz | 594.1 KB | Display | |
Data in XML | 2me3_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2me3_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/2me3 ftp://data.pdbj.org/pub/pdb/validation_reports/me/2me3 | HTTPS FTP |
-Related structure data
Related structure data | 2me1C 2me2C 2me4C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3514.016 Da / Num. of mol.: 1 Fragment: membrane proximal external region (UNP residues 636-662) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade C, DU151.2 isolate / Gene: env / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q202K4 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: MODELS SUPERIMPOSED FROM RESIDUE 666 TO RESIDUE 672. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structure models were calculated using TENSO module incorporating RDC restraints during the high temperature torsion angle dynamics annealing stage, and planeDisPot module incorporating EPR ...Details: Structure models were calculated using TENSO module incorporating RDC restraints during the high temperature torsion angle dynamics annealing stage, and planeDisPot module incorporating EPR depth restraints during the subsequent low temperature Cartesian coordinate dynamics annealing stage. | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 382 / NOE intraresidue total count: 137 / NOE long range total count: 12 / NOE medium range total count: 111 / NOE sequential total count: 122 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 22 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 4 ° / Maximum upper distance constraint violation: 0.28 Å |