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- PDB-3iv1: Coiled-coil domain of tumor susceptibility gene 101 -

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Basic information

Entry
Database: PDB / ID: 3iv1
TitleCoiled-coil domain of tumor susceptibility gene 101
ComponentsTumor susceptibility gene 101 protein
KeywordsHYDROLASE / COILED_COIL / TUMORIGENESIS / CELL_CYCLE REGULATION / Alternative splicing / Cell cycle / Cell division / Coiled coil / Cytoplasm / Endosome / Growth regulation / Host-virus interaction / Membrane / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport / Ubl conjugation / Structural Genomics / Structural Genomics Consortium / SGC
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 / regulation of extracellular exosome assembly / negative regulation of epidermal growth factor-activated receptor activity / 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 / regulation of extracellular exosome assembly / negative regulation of epidermal growth factor-activated receptor activity / 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 / viral release from host cell / autophagosome maturation / 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 / Budding and maturation of HIV virion / protein modification process / transcription corepressor activity / calcium-dependent protein binding / late endosome / late endosome membrane / early endosome membrane / early endosome / regulation of cell cycle / endosome membrane / endosome / 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 / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin-conjugating enzyme/RWD-like / Helix non-globular / Special
Similarity search - Domain/homology
Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNeculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Neculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Coiled-Coil Domain of Human Tsg101
Authors: Neculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Tumor susceptibility gene 101 protein
D: Tumor susceptibility gene 101 protein
E: Tumor susceptibility gene 101 protein
F: Tumor susceptibility gene 101 protein
G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,07020
Polymers73,5848
Non-polymers48612
Water1,56787
1
A: Tumor susceptibility gene 101 protein
B: Tumor susceptibility gene 101 protein
C: Tumor susceptibility gene 101 protein
D: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,10111
Polymers36,7924
Non-polymers3097
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-127 kcal/mol
Surface area20550 Å2
MethodPISA
2
E: Tumor susceptibility gene 101 protein
F: Tumor susceptibility gene 101 protein
hetero molecules

E: Tumor susceptibility gene 101 protein
F: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,00510
Polymers36,7924
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11230 Å2
ΔGint-128 kcal/mol
Surface area20770 Å2
MethodPISA
3
G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
hetero molecules

G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9348
Polymers36,7924
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466y-1,x+1,-z+11
Buried area11450 Å2
ΔGint-125 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 56.290, 341.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 9198.006 Da / Num. of mol.: 8 / Fragment: COILED-COIL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99816
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, 1 mM DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25250 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.77 % / Biso Wilson estimate: 40.91 Å2 / Rsym value: 0.071 / Net I/σ(I): 14.87
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.66 % / Mean I/σ(I) obs: 7.78 / Rsym value: 0.16 / % possible all: 92.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXDphasing
SHELXEmodel building
RESOLVEmodel building
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.75 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1286 5.09 %RANDOM
Rwork0.2278 ---
obs-22979 --
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1--4.9259 Å20 Å20 Å2
2---4.9259 Å20 Å2
3---9.8518 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 16 87 5199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.13
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2683 151 5.46 %
Rwork0.209 2615 -

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