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- PDB-3obq: Crystal Structure of the Tsg101 UEV domain in complex with a huma... -

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Basic information

Entry
Database: PDB / ID: 3obq
TitleCrystal Structure of the Tsg101 UEV domain in complex with a human HRS PSAP peptide
Components
  • Hepatocyte growth factor-regulated tyrosine kinase substrate
  • Tumor susceptibility gene 101 protein
KeywordsPROTEIN TRANSPORT / Protein Transprot / Ubiquitin Binding
Function / homology
Function and homology information


Inhibition of membrane repair / ESCRT-0 complex / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / membrane invagination / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding ...Inhibition of membrane repair / ESCRT-0 complex / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / membrane invagination / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / phagocytic vesicle lumen / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / RHOBTB3 ATPase cycle / positive regulation of exosomal secretion / negative regulation of receptor signaling pathway via JAK-STAT / protein targeting to lysosome / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / endocytic recycling / Flemming body / virion binding / protein localization to membrane / negative regulation of platelet-derived growth factor receptor signaling pathway / endosomal transport / Lysosome Vesicle Biogenesis / negative regulation of vascular endothelial growth factor receptor signaling pathway / endosome to lysosome transport / regulation of protein catabolic process / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / ubiquitin-like protein ligase binding / viral release from host cell / RHOU GTPase cycle / autophagosome maturation / keratinocyte differentiation / multivesicular body / Prevention of phagosomal-lysosomal fusion / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / negative regulation of angiogenesis / HCMV Late Events / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / regulation of cell growth / macroautophagy / EGFR downregulation / Late endosomal microautophagy / Budding and maturation of HIV virion / Negative regulation of MET activity / protein modification process / receptor internalization / calcium-dependent protein binding / transcription corepressor activity / late endosome membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / early endosome / lysosome / regulation of cell cycle / endosome / endosome membrane / Ub-specific processing proteases / protein domain specific binding / negative regulation of cell population proliferation / cell division / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / DNA binding / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. ...Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / 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 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / ENTH/VHS / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor-regulated tyrosine kinase substrate / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.2May 27, 2015Group: Source and taxonomy
Revision 1.3Sep 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

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Assembly

Deposited unit
A: Tumor susceptibility gene 101 protein
B: Hepatocyte growth factor-regulated tyrosine kinase substrate


Theoretical massNumber of molelcules
Total (without water)17,3792
Polymers17,3792
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.654, 45.126, 87.734
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: pGST-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q99816
#2: Protein/peptide Hepatocyte growth factor-regulated tyrosine kinase substrate / Protein pp110 / Hrs


Mass: 878.022 Da / Num. of mol.: 1 / Fragment: PSAP sequence (nonapeptide) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14964
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.92 Å3/Da / Density % sol: 35.82 %
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: 1.4→50 Å / Num. all: 26634 / Num. obs: 25924 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1265 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F0R

2f0r


Resolution: 1.4→31.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 815094.89 / 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
Rfree0.224 1289 5 %RANDOM
Rwork0.207 ---
all0.21 27186 --
obs0.207 25897 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5815 Å2 / ksol: 0.34091 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.4→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 198 1393
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_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
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: 1.4→1.49 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 218 5.2 %
Rwork0.242 3965 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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