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- PDB-3obu: Crystal structure of the Tsg101 UEV domain in complex with a HIV-... -

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Basic information

Entry
Database: PDB / ID: 3obu
TitleCrystal structure of the Tsg101 UEV domain in complex with a HIV-1 PTAP peptide
Components
  • Gag polyprotein
  • Tumor susceptibility gene 101 protein
KeywordsPROTEIN TRANSPORT / Protein tranport / ubiquitin / HIV-1 Gag
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 / ubiquitin binding / HCMV Late Events / macroautophagy / regulation of cell growth / Late endosomal microautophagy / Budding and maturation of HIV virion / protein modification process / host multivesicular body / calcium-dependent protein binding / late endosome membrane / transcription corepressor activity / late endosome / viral nucleocapsid / early endosome membrane / early endosome / endosome / regulation of cell cycle / endosome membrane / viral translational frameshifting / negative regulation of cell population proliferation / cell division / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / nucleolus / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / RNA binding / extracellular exosome / zinc ion binding / membrane / 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 / gag protein p24 N-terminal domain / Ubiquitin-conjugating enzyme/RWD-like / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Gag polyprotein / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIm, Y.J. / Hurley, J.H.
CitationJournal: Structure / Year: 2010
Title: Crystallographic and Functional Analysis of the ESCRT-I /HIV-1 Gag PTAP Interaction.
Authors: Im, Y.J. / Kuo, L. / Ren, X. / Burgos, P.V. / Zhao, X.Z. / Liu, F. / Burke, T.R. / Bonifacino, J.S. / Freed, E.O. / Hurley, J.H.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)17,4672
Polymers17,4672
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-5 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.526, 45.769, 85.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101


Mass: 16501.195 Da / Num. of mol.: 1 / Fragment: N-terminal UEV domain (UNP residues 2 to 145) / Mutation: 43VFNDGS48 -> GTG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: Q99816
#2: Protein/peptide Gag polyprotein


Mass: 965.997 Da / Num. of mol.: 1 / Fragment: HIV-1 Gag PTAP motif (5-13) / Source method: obtained synthetically
Details: This sequence occurs naturally in human immunodeficiency virus type 1.
References: UniProt: Q72497
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED MUTATION 43VFNDGS48 -> GTG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH (pH7.5), 25% PEG 3350, 0.2M Sodium Nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 18250 / Num. obs: 17689 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 30.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 4.1 / Num. unique all: 799 / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F0R

2f0r


Resolution: 1.6→42.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 874513.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 894 5.1 %RANDOM
Rwork0.199 ---
all0.21 18540 --
obs0.199 17646 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.613 Å2 / ksol: 0.358431 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---4.41 Å20 Å2
3---5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 0 156 1363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 139 5.2 %
Rwork0.239 2549 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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