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- PDB-4zny: Structure of the human TSG101-UEV Domain in complex with the PTAP... -

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Entry
Database: PDB / ID: 4zny
TitleStructure of the human TSG101-UEV Domain in complex with the PTAP motif of the p19 gag protein of the Human T-cell Leukemia type I virus
Components
  • T-cell leukemia virus type I, partial gag gene; HTLV1 (human T-lymphotropic virus type I)
  • Tumor susceptibility gene 101 protein
KeywordsPROTEIN TRANSPORT / ESCRT-I COMPLEX SUBUNIT TSG101
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 / telomerase activity ...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 / telomerase activity / 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 / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / DNA integration / protein modification process / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / calcium-dependent protein binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / late endosome membrane / transcription corepressor activity / late endosome / viral nucleocapsid / early endosome membrane / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / early endosome / regulation of cell cycle / endosome / endosome membrane / symbiont-mediated suppression of host gene expression / viral translational frameshifting / negative regulation of cell population proliferation / cell division / ubiquitin protein ligase binding / centrosome / symbiont entry into host cell / protein-containing complex binding / nucleolus / structural molecule activity / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / proteolysis / DNA binding / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / 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 ...Delta-retroviral matrix protein / Major core protein p19 / 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 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / gag protein p24 N-terminal domain / Ubiquitin-conjugating enzyme/RWD-like / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Gag-Pro-Pol polyprotein / Delta-retroviral matrix protein domain-containing protein / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsCamara-Artigas, A. / Bacarizo, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOBIO2012-39922-C02-02 Spain
CitationJournal: to be published
Title: Structure of the human TSG101-UEV Domain in complex with the PTAP motif of the p19 gag protein of the Human T-cell Leukemia type I virus
Authors: Camara-Artigas, A. / Bacarizo, J.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: T-cell leukemia virus type I, partial gag gene; HTLV1 (human T-lymphotropic virus type I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5443
Polymers17,4482
Non-polymers961
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-20 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.622, 119.743, 41.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16331.946 Da / Num. of mol.: 1 / Fragment: UEV domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pRSETa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99816
#2: Protein/peptide T-cell leukemia virus type I, partial gag gene; HTLV1 (human T-lymphotropic virus type I)


Mass: 1116.262 Da / Num. of mol.: 1 / Fragment: L-domain, UNP residues 105-114 / Source method: obtained synthetically / Source: (synth.) Human T-lymphotropic virus 1 / References: UniProt: Q85594, UniProt: P14078*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG4k, 0.1 ammonium sulfate, 0.1 MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationMonochromator: Si(111) channel-cut crystal monochromator and a pair of KB mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Number: 37420 / Rmerge(I) obs: 0.032 / D res high: 2.4 Å / D res low: 19.96 Å / Num. obs: 8020 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.42.4910.2795.3
8.9819.9610.023.8
ReflectionResolution: 2.4→19.96 Å / Num. obs: 8020 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 54.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.017 / Net I/σ(I): 34.6 / Num. measured all: 37420
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.495.30.2799.743768300.9770.134100
8.98-19.963.80.0262.66351660.9990.01291.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJE

4eje


Resolution: 2.4→19.957 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 35.62 / Stereochemistry target values: ML
Details: The statistics of the data collection are those of the non-anomalous data, while the structure was refined with the anomalous data.
RfactorNum. reflection% reflection
Rfree0.2431 750 5.23 %
Rwork0.2299 13590 -
obs0.2306 14340 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.03 Å2 / Biso mean: 76.975 Å2 / Biso min: 49.18 Å2
Refinement stepCycle: final / Resolution: 2.4→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 5 5 1168
Biso mean--67 57.56 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031197
X-RAY DIFFRACTIONf_angle_d0.8421651
X-RAY DIFFRACTIONf_chiral_restr0.03196
X-RAY DIFFRACTIONf_plane_restr0.004206
X-RAY DIFFRACTIONf_dihedral_angle_d9.253415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.5850.38511530.37422568272191
2.585-2.84440.43741460.372663280995
2.8444-3.25450.35821470.30422750289798
3.2545-4.09450.29581430.22662796293999
4.0945-19.95780.14881610.170928132974100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13350.010.03470.0074-0.01560.01931.16641.0734-1.064-1.11880.00610.125-0.1468-0.4125-0.00391.24830.026-0.17181.1402-0.1450.950818.31615.2283-15.9105
20.00840.01370.02160.02380.03810.046-0.36320.609-0.1591-0.70450.4087-0.50231.1062-0.30240.00121.40110.18390.27470.8855-0.03650.778229.60677.697-17.0403
31.23930.27020.0390.04360.03430.5385-0.1327-0.2985-1.5232-0.4621-0.9583-0.70820.8944-0.1463-0.00160.92750.01320.19340.72080.01220.986923.53383.0368-7.741
40.2581-0.39070.27730.5111-0.40540.2452-0.1142-0.0214-0.1292-1.2693-0.5706-0.07910.1874-0.4233-0.0020.97060.1382-0.01180.9049-0.06890.673620.557515.3984-8.3409
50.44610.1535-0.17650.178-0.04430.07230.6968-1.2219-0.0343-0.08770.3807-0.3055-0.19391.52290.00740.97620.20660.46110.97780.21241.217134.742924.9438-15.8106
62.66171.7029-0.25293.1610.15730.0974-0.0177-0.0751-0.2331-0.5132-0.2167-0.03460.0603-0.4953-0.00080.65960.14730.03620.70950.03650.61920.039117.14631.154
72.89340.7246-1.65681.6888-0.23833.3712-0.3237-0.4570.0163-0.3824-0.011-0.40470.5090.35170.00010.66840.17850.06990.65560.09060.679830.326717.2594-0.9291
81.14110.4714-0.88090.4586-0.45091.3057-0.3126-0.6670.07810.4370.1662-0.30180.50380.377-0.00010.58840.22190.02750.86140.10370.687423.278518.06967.8206
90.05590.301-0.21650.4508-0.53290.5929-0.1714-0.5344-0.1234-0.572-0.45010.509-0.3406-0.3261-0.00730.59510.1141-0.01970.8524-0.01330.69312.429823.21077.7855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 11 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 17 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 31 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 43 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 48 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 49 through 75 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 123 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 124 through 145 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 130 )B0

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