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- PDB-1m4p: Structure of the Tsg101 UEV domain in complex with a HIV-1 PTAP "... -

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Basic information

Entry
Database: PDB / ID: 1m4p
TitleStructure of the Tsg101 UEV domain in complex with a HIV-1 PTAP "late domain" peptide, DYANA Ensemble
Components
  • Gag Polyprotein
  • Tumor Susceptibility gene 101 protein
KeywordsPEPTIDE BINDING PROTEIN / Tsg101 UEV domain / virus budding / vacuolar protein sorting / late domain
Function / homology
Function and homology information


positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of exosomal secretion / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / viral release from host cell / autophagosome maturation / keratinocyte differentiation / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / HCMV Late Events / ubiquitin binding / macroautophagy / regulation of cell growth / Late endosomal microautophagy / Budding and maturation of HIV virion / protein modification process / calcium-dependent protein binding / late endosome membrane / transcription corepressor activity / late endosome / early endosome membrane / early endosome / regulation of cell cycle / endosome / endosome membrane / negative regulation of cell population proliferation / cell division / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Gag protein p6 / Gag protein p6 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Tumor susceptibility gene 101 protein / Gag protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPornillos, O. / Alam, S.L. / Davis, D.R. / Sundquist, W.I.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein
Authors: Pornillos, O. / Alam, S.L. / Davis, D.R. / Sundquist, W.I.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor Susceptibility gene 101 protein
B: Gag Polyprotein


Theoretical massNumber of molelcules
Total (without water)17,5992
Polymers17,5992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Tumor Susceptibility gene 101 protein


Mass: 16633.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tumor susceptibility gene 101 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99816
#2: Protein/peptide Gag Polyprotein


Mass: 965.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: Gag / Plasmid: pAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9IF21

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.2Gntert, P., Mumenthaler, C. & Wthrich, K.structure solution
DYANA1.2Gntert, P., Mumenthaler, C. & Wthrich, K.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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