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- PDB-7nlc: Crystallographic structure of human Tsg101 UEV domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7nlc
TitleCrystallographic structure of human Tsg101 UEV domain in complex with a HEV ORF3 peptide
Components
  • Protein ORF3
  • Tsg101 UEV domain
KeywordsPROTEIN TRANSPORT / HEV / proline-rich / ESCRT-I complex
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 / host cell cytoplasm / membrane => GO:0016020 / early endosome / endosome membrane / regulation of cell cycle / endosome / cell cycle / negative regulation of cell population proliferation / cell division / 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 / cytoplasm / cytosol
Similarity search - Function
Hepatitis E virus Orf2, capsid / Hepatitis E virus ORF-2 (Putative capsid protein) / 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 E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
AMMONIUM ION / Protein ORF3 / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis E virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsMoschidi, D. / Dupre, E. / Villeret, V. / Hanoulle, X.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ101316 France
CitationJournal: To Be Published
Title: Crystallographic structure of human Tsg101 UEV domain in complex with a HEV ORF3 peptide
Authors: Moschidi, D. / Dupre, E. / Villeret, V. / Hanoulle, X.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tsg101 UEV domain
B: Protein ORF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,79355
Polymers17,7252
Non-polymers1,06953
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-0 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.570, 42.570, 188.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Tsg101 UEV domain / ESCRT-I complex subunit TSG101 / Tumor susceptibility gene 101 protein


Mass: 16761.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99816
#2: Protein/peptide Protein ORF3


Mass: 963.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis E virus / References: UniProt: E9N3C1

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Non-polymers , 4 types, 142 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M Citric Acid, 2M Ammonium sulfate pH 3.5, 13.34% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980108 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980108 Å / Relative weight: 1
ReflectionResolution: 1.398→47.084 Å / Num. obs: 35532 / % possible obs: 100 % / Redundancy: 4.6 % / CC1/2: 1 / Net I/σ(I): 23.7
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 5587 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OBQ

3obq


Resolution: 1.398→47.084 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.334 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.239 1777 5.001 %
Rwork0.2199 33754 -
all0.221 --
obs-35531 99.952 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.312 Å2
Baniso -1Baniso -2Baniso -3
1-0.244 Å2-0 Å20 Å2
2--0.244 Å20 Å2
3----0.489 Å2
Refinement stepCycle: LAST / Resolution: 1.398→47.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 57 89 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131314
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171251
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6581815
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5712909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86422.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.385155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_nbd_refined0.230.2261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21115
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2620
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3190.211
X-RAY DIFFRACTIONr_nbd_other0.2270.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.28
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.398-1.4340.4641280.4642439X-RAY DIFFRACTION99.4191
1.434-1.4740.4411250.3922375X-RAY DIFFRACTION100
1.474-1.5160.3041220.3042318X-RAY DIFFRACTION100
1.516-1.5630.3361180.2922230X-RAY DIFFRACTION100
1.563-1.6140.2651150.2652189X-RAY DIFFRACTION100
1.614-1.6710.2611120.2612127X-RAY DIFFRACTION100
1.671-1.7340.2471070.2472036X-RAY DIFFRACTION100
1.734-1.8050.2761040.2471977X-RAY DIFFRACTION100
1.805-1.8850.2531010.2371909X-RAY DIFFRACTION100
1.885-1.9770.237950.2231821X-RAY DIFFRACTION100
1.977-2.0840.278920.2341742X-RAY DIFFRACTION100
2.084-2.2110.241870.221660X-RAY DIFFRACTION100
2.211-2.3630.221830.211573X-RAY DIFFRACTION100
2.363-2.5520.218760.2051447X-RAY DIFFRACTION100
2.552-2.7960.227720.1951366X-RAY DIFFRACTION100
2.796-3.1260.229650.21232X-RAY DIFFRACTION100
3.126-3.6090.205590.21110X-RAY DIFFRACTION100
3.609-4.420.162500.151956X-RAY DIFFRACTION100
4.42-6.2490.286410.214775X-RAY DIFFRACTION100
6.249-100.252250.252472X-RAY DIFFRACTION99.5992

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