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- PDB-6b9k: Solution NMR Structure of Unbound P18-I10 -

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Basic information

Entry
Database: PDB / ID: 6b9k
TitleSolution NMR Structure of Unbound P18-I10
ComponentsARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE
KeywordsPEPTIDE BINDING PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFlores-Solis, D. / McShan, A. / Sgourakis, N.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.
Authors: McShan, A.C. / Natarajan, K. / Kumirov, V.K. / Flores-Solis, D. / Jiang, J. / Badstubner, M. / Toor, J.S. / Bagshaw, C.R. / Kovrigin, E.L. / Margulies, D.H. / Sgourakis, N.G.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE


Theoretical massNumber of molelcules
Total (without water)1,0751
Polymers1,0751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1400 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE


Mass: 1075.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04578*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
132isotropic22D 1H-15N HSQC
142isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
lyophilized powder11.0 mM ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE, 90% H2O/10% D2OUnlabeled PeptideP18-I1090% H2O/10% D2O
lyophilized powder21.00 mM [U-99% 13C; U-99% 15N] ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE, 90% H2O/10% D2O13C and 15N labeled13C 15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILEnatural abundance1
1.00 mMARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 0.05 mM / Label: Unlabel / pH: 7.2 / PH err: 0.05 / Pressure: 1 atm / Temperature: 277 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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