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- PDB-3obs: Crystal structure of Tsg101 UEV domain -

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Basic information

Entry
Database: PDB / ID: 3obs
TitleCrystal structure of Tsg101 UEV domain
ComponentsTumor susceptibility gene 101 proteinTSG101
KeywordsPROTEIN TRANSPORT / Protein Transprot / Ubiquitin Binding
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 / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / negative regulation of epidermal growth factor receptor signaling pathway / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / keratinocyte differentiation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / Late endosomal microautophagy / protein modification process / Budding and maturation of HIV virion / transcription corepressor activity / calcium-dependent protein binding / late endosome / late endosome membrane / early endosome membrane / early endosome / endosome membrane / regulation of cell cycle / endosome / cell cycle / cell division / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / 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 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...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 / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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


Theoretical massNumber of molelcules
Total (without water)16,5011
Polymers16,5011
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.571, 45.502, 50.205
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor susceptibility gene 101 protein / TSG101 / 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
Details: to improve the crystallization properies, residues 43-49 in the beta1-beta2 loop were mutated to Gly-Thr-Gly
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101, Tsg101 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q99816
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH (pH 7.5), 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2009 / 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: 1.5→50 Å / Num. all: 22608 / Num. obs: 22570 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 47.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 25.3 / Num. unique all: 1130 / % possible all: 96.2

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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: 1.5→32.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 600106.44 / 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
Rfree0.232 1135 5 %RANDOM
Rwork0.215 ---
all0.22 23649 --
obs0.215 22514 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2413 Å2 / ksol: 0.381544 e/Å3
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.29 Å2
2---0.04 Å20 Å2
3---0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.5→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 0 217 1337
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
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: 1.5→1.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 183 4.9 %
Rwork0.21 3544 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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