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- PDB-4eje: Structure Of The Tsg101 UEV Domain In Complex With an Ebola PTAP ... -

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Basic information

Entry
Database: PDB / ID: 4eje
TitleStructure Of The Tsg101 UEV Domain In Complex With an Ebola PTAP late Domain Peptide
Components
  • Matrix protein VP40
  • Tumor susceptibility gene 101 protein
KeywordsPROTEIN TRANSPORT / alpha and beta protein / UEV domain
Function / homology
Function and homology information


positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / intracellular transport of virus / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / intracellular transport of virus / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / regulation of MAP kinase activity / exosomal secretion / host cell late endosome membrane / 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 / endosome to lysosome transport / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / viral release from host cell / host cell membrane / autophagosome maturation / keratinocyte differentiation / multivesicular body / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / protein modification process / calcium-dependent protein binding / transcription corepressor activity / late endosome membrane / late endosome / host cell / early endosome membrane / structural constituent of virion / early endosome / regulation of cell cycle / endosome / endosome membrane / membrane raft / ribonucleoprotein complex / negative regulation of cell population proliferation / cell division / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / RNA binding / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : ...EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / 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
Matrix protein VP40 / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Ebola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsCamara-Artigas, A.
CitationJournal: To be Published
Title: To be published
Authors: Camara-Artigas, A. / Palencia, A. / Andujar-Sanchez, M. / Iglesias-Bexiga, M. / Luque, I. / Martinez, J.C.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: Matrix protein VP40
D: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5795
Polymers38,4834
Non-polymers961
Water1,42379
1
A: Tumor susceptibility gene 101 protein
C: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3373
Polymers19,2412
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-18 kcal/mol
Surface area8680 Å2
MethodPISA
2
B: Tumor susceptibility gene 101 protein
D: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)19,2412
Polymers19,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.544, 105.544, 75.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASP2AA5 - 4019 - 54
21GLUGLUASPASP2BB5 - 4019 - 54
12LEULEUPROPRO4AA55 - 14069 - 154
22LEULEUPROPRO4BB55 - 14069 - 154

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Components

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


Mass: 18241.164 Da / Num. of mol.: 2 / Fragment: UEV domain (UNP Residues 1-145)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99816
#2: Protein/peptide Matrix protein VP40 / Membrane-associated protein VP40


Mass: 1000.144 Da / Num. of mol.: 2 / Fragment: Ebola virus PTAP Late domain (UNP Residues 5-13) / Source method: obtained synthetically
Details: 9 residues peptide of the PTAP Late domain of the Ebola virus
Source: (synth.) Ebola virus / References: UniProt: Q05128
#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.: 79 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M of ammonium sulphate, 25% PEG 4K, 25% 0.1 M Hepes, pH 7.0, vapor diffusion, hanging drop, temperature 278K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 8.2 % / Av σ(I) over netI: 7.6 / Number: 171665 / Rsym value: 0.059 / D res high: 2.199 Å / D res low: 74.631 Å / Num. obs: 21003 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.962090.310.0350.0356.1
4.926.9610010.0440.0448.1
4.024.9210010.0450.0458.5
3.484.0210010.0510.0518.9
3.113.4810010.0640.0649
2.843.1110010.0810.0819
2.632.8410010.130.139
2.462.6310010.1930.1938.8
2.322.4610010.2770.2777.3
2.22.3210010.4040.4046.4
ReflectionResolution: 2.199→74.631 Å / Num. all: 21003 / Num. obs: 21003 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.199-2.326.40.4041.70.4041100
2.32-2.467.30.2772.50.2771100
2.46-2.638.80.1933.50.1931100
2.63-2.8490.135.10.131100
2.84-3.1190.0817.60.0811100
3.11-3.4890.0648.70.0641100
3.48-4.028.90.05110.70.0511100
4.02-4.928.50.04513.10.0451100
4.92-6.968.10.04412.90.0441100
6.96-19.9976.10.035180.035190.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å14.93 Å
Translation2.49 Å14.93 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F0R

2f0r


Resolution: 2.2→14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 7.816 / SU ML: 0.193 / SU R Cruickshank DPI: 0.2627 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27443 2142 10.2 %RANDOM
Rwork0.21072 ---
obs0.21729 18878 99.7 %-
all-20999 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.128 Å2
Baniso -1Baniso -2Baniso -3
1--3.18 Å2-0 Å2-0 Å2
2---3.18 Å2-0 Å2
3---6.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 5 79 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9953442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2775299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4123.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.3151510
X-RAY DIFFRACTIONr_chiral_restr0.1270.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221870
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.51528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15422529
X-RAY DIFFRACTIONr_scbond_it3.4183992
X-RAY DIFFRACTIONr_scangle_it5.1414.5913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
144TIGHT POSITIONAL0.20.05
845MEDIUM POSITIONAL0.380.5
144TIGHT THERMAL1.180.5
845MEDIUM THERMAL1.522
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 156 -
Rwork0.308 1313 -
obs--99.86 %

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