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- PDB-1qa5: MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES -

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Entry
Database: PDB / ID: 1qa5
TitleMYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES
ComponentsPROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE-GLY2 TO TRP57))
KeywordsVIRAL PROTEIN / HIV / AIDS / REGULATORY FACTOR / NEGATIVE FACTOR / NEF / MYRISTOYLATION
Function / homology
Function and homology information


perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / host cell Golgi membrane / MHC class I protein binding ...perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / host cell Golgi membrane / MHC class I protein binding / regulation of calcium-mediated signaling / viral life cycle / virion component / SH3 domain binding / ATPase binding / signaling receptor binding / GTP binding / protein kinase binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
HIV 1 nef anchor domain / HIV 1 nef anchor domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsGeyer, M. / Kalbitzer, H.R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein.
Authors: Geyer, M. / Munte, C.E. / Schorr, J. / Kellner, R. / Kalbitzer, H.R.
#1: Journal: Protein Sci. / Year: 1997
Title: Refined solution structure and backbone dynamics of HIV-1 Nef.
Authors: Grzesiek, S. / Bax, A. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Tjandra, N. / Wingfield, P.T.
#2: Journal: Biochemistry / Year: 1997
Title: Solution structure of a polypeptide from the N terminus of the HIV protein Nef.
Authors: Barnham, K.J. / Monks, S.A. / Hinds, M.G. / Azad, A.A. / Norton, R.S.
#3: Journal: Structure / Year: 1997
Title: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling.
Authors: Arold, S. / Franken, P. / Strub, M.P. / Hoh, F. / Benichou, S. / Benarous, R. / Dumas, C.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain.
Authors: Lee, C.H. / Saksela, K. / Mirza, U.A. / Chait, B.T. / Kuriyan, J.
#5: Journal: Nat.Struct.Biol. / Year: 1996
Title: The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase.
Authors: Grzesiek, S. / Bax, A. / Clore, G.M. / Gronenborn, A.M. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Wingfield, P.T.
#6: Journal: Eur.J.Biochem. / Year: 1994
Title: A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease.
Authors: Freund, J. / Kellner, R. / Konvalinka, J. / Wolber, V. / Krausslich, H.G. / Kalbitzer, H.R.
History
DepositionApr 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 27, 2021Group: Data collection / Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.5Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

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Assembly

Deposited unit
A: PROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE-GLY2 TO TRP57))


Theoretical massNumber of molelcules
Total (without water)6,0281
Polymers6,0281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area310 Å2
ΔGint2 kcal/mol
Surface area6460 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 400TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN
RepresentativeModel #1

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Components

#1: Protein PROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE-GLY2 TO TRP57))


Mass: 6027.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 (isolate NL4-3)
Keywords: N-TERMINAL MYRISTOYLATION ON GLY-2 / References: UniProt: P04324

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 1H
NMR detailsText: THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE STRUCTURE OF THE MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT WELL DEFINED BY NMR ...Text: THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE STRUCTURE OF THE MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT WELL DEFINED BY NMR RESTRAINTS. ONLY TWO SECONDARY STRUCTURE ELEMENTS CAN BE OBSERVED: A FIRST HELIX IN THE POSITIVE CLUSTER REGION FROM PRO14 TO ARG22 AND A SECOND HELICAL REGION FROM ALA33 TO GLY41. ADDITIONALLY, THE N-TERMINAL MYRISTIC ACID RESIDUE CLOSELY INTERACTS WITH THE SIDE CHAIN OF TRP5 AND THEREBY FORMS A LOOP WITH GLY2, GLY3 AND LYS4 IN THE KINK REGION. TWO MODELS ARE PRESENTED TO DEMONSTRATE THE CONFORMATIONAL VARIETY OF THE STRUCTURES CALCULATED.

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Sample preparation

Sample conditionspH: 4.6 / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
AURELIA2Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerstructure calculation
X-PLOR3.851BRUNGERstructure calculation
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF ...Details: THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYR-2-57) SOLVED BY TWO-DIMENSIONAL HOMONUCLEAR NMR SPECTROSCOPY IS BASED ON 540 EXPERIMENTAL RESTRAINTS: 332 INTRARESIDUAL, 156 SEQUENTIAL AND MEDIUM RANGE (1<=|I-J|<=4), AND 10 LONG RANGE (|I-J|>=5) INTERPROTON DISTANCE RESTRAINTS; 42 TORSION ANGLE RESTRAINTS (PHI). NO RESTRAINTS FOR HYDROGEN BONDS WERE ADDED.
NMR ensembleConformer selection criteria: TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN
Conformers calculated total number: 400 / Conformers submitted total number: 2

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