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- PDB-2f0r: Crystallographic structure of human Tsg101 UEV domain -

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Basic information

Entry
Database: PDB / ID: 2f0r
TitleCrystallographic structure of human Tsg101 UEV domain
ComponentsTumor susceptibility gene 101 protein
KeywordsUNKNOWN FUNCTION / 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 / 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 / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsCamara-Artigas, A. / Luque, I. / Palencia, A. / Martinez, J.C. / Mateo, P.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of human TSG101 UEV domain.
Authors: Palencia, A. / Martinez, J.C. / Mateo, P.L. / Luque, I. / Camara-Artigas, A.
History
DepositionNov 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6744
Polymers36,4822
Non-polymers1922
Water4,342241
1
A: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3372
Polymers18,2411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3372
Polymers18,2411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.865, 97.865, 110.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU3AA3 - 3917 - 53
21VALVALLEULEU3BB3 - 3917 - 53
12METMETPROPRO3AA53 - 14567 - 159
22METMETPROPRO3BB53 - 14567 - 159
13ASPASPLEULEU5AA40 - 5254 - 66
23ASPASPLEULEU5BB40 - 5254 - 66

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Tumor susceptibility gene 101 protein / Tsg101(Uev) Domain


Mass: 18241.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99816
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2 M ammonium sulphate, 0.1 M Tris , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER PROTEUM X8 / Detector: CCD / Date: Oct 5, 2005
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→60 Å / Num. obs: 17160 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 41.713 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.04 / Net I/σ(I): 26.3
Reflection shellResolution: 2.255→2.314 Å / % possible all: 91.73

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SAINTdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s1q

1s1q


Resolution: 2.26→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.52 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24271 870 5.1 %RANDOM
Rwork0.18768 ---
all0.19059 17062 --
obs0.19059 16192 91.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.011 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å2-1.81 Å20 Å2
2---3.62 Å20 Å2
3---5.43 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 10 241 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222388
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9933260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.8394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33515410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.4751510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021774
X-RAY DIFFRACTIONr_nbd_refined0.2250.21060
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.215
X-RAY DIFFRACTIONr_mcbond_it0.9291.51480
X-RAY DIFFRACTIONr_mcangle_it1.46222386
X-RAY DIFFRACTIONr_scbond_it2.57331055
X-RAY DIFFRACTIONr_scangle_it3.8554.5874
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1148tight positional0.090.05
2372tight positional0.080.05
352medium positional0.30.5
1159loose positional0.655
2374loose positional0.365
352loose positional0.95
1148tight thermal0.250.5
2372tight thermal0.210.5
352medium thermal0.392
1159loose thermal2.2610
2374loose thermal1.5210
352loose thermal1.3310
LS refinement shellResolution: 2.255→2.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 35 -
Rwork0.228 769 -
obs--59.12 %
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)
14.47640.66960.42561.5230.11970.72110.005-0.09390.0880.08420.03920.0514-0.0573-0.1493-0.0441-0.00690.08350.0392-0.06880.0186-0.284615.084-9.5164.424
217.235219.069713.343626.695517.831814.0655-0.526-0.38761.0994-0.4452-0.46121.6443-0.3483-0.42610.98720.15140.1987-0.0080.089-0.0455-0.003315.303-9.7274.39
32.75660.324-0.16621.2508-0.09490.65640.0002-0.1339-0.2343-0.00520.0283-0.2559-0.0061-0.048-0.0285-0.12890.053-0.0084-0.15-0.0095-0.313924.006-13.6534.606
42.46280.1042-0.0410.95580.13480.7651-0.0245-0.0768-0.10190.0643-0.0125-0.09260.0092-0.01490.037-0.1170.0306-0.024-0.1141-0.0276-0.322725.72-14.3544.649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 40
2X-RAY DIFFRACTION1B3 - 40
3X-RAY DIFFRACTION2A41 - 52
4X-RAY DIFFRACTION2B41 - 52
5X-RAY DIFFRACTION3A53 - 88
6X-RAY DIFFRACTION3B53 - 88
7X-RAY DIFFRACTION4A89 - 143
8X-RAY DIFFRACTION4B89 - 143

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