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- PDB-1qa4: HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1qa4
TitleHIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES
ComponentsProtein Nef
KeywordsVIRAL PROTEIN / HIV / AIDS / REGULATORY FACTOR / NEGATIVE FACTOR / NEF / MYRISTOYLATION / MYRISTYLATION
Function / homology
Function and homology information


negative regulation of glycoprotein biosynthetic process / 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 / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / thioesterase binding / CD4 receptor binding / MHC class I protein binding / host cell Golgi membrane / viral life cycle ...negative regulation of glycoprotein biosynthetic process / 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 / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / thioesterase binding / CD4 receptor binding / MHC class I protein binding / host cell Golgi membrane / viral life cycle / regulation of calcium-mediated signaling / SH3 domain binding / virion component / ATPase binding / symbiont-mediated suppression of host innate immune response / signaling receptor binding / protein kinase binding / GTP 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_oper_list / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_fragment / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein Nef


Theoretical massNumber of molelcules
Total (without water)5,8171
Polymers5,8171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Nef


Mass: 5817.458 Da / Num. of mol.: 1 / Fragment: ANCHOR DOMAIN, residues 2-57 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 (isolate NL4-3)
References: UniProt: P04324
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 1H

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Sample preparation

Sample conditionspH: 7.1 / Temperature: 285.0 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)).
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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