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- PDB-8sdi: Hydrophobic Interactions Drive the Tetrameric Assembly of the TRI... -

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Basic information

Entry
Database: PDB / ID: 8sdi
TitleHydrophobic Interactions Drive the Tetrameric Assembly of the TRIM45 Coiled-Coil Domain
ComponentsTripartite motif-containing protein 45
KeywordsLIGASE / E3 ubiquitin ligase / Ubiquitination / coiled-coil
Function / homology
Function and homology information


intercellular bridge / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / bone development / negative regulation of inflammatory response / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
: / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like ...: / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM45
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLou, X.H. / Ma, B.B. / Zhuang, Y. / Li, X.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI155488 United States
CitationJournal: To Be Published
Title: Hydrophobic Interactions Drive the Tetrameric Assembly of the TRIM45 Coiled-Coil Domain
Authors: Lou, X.H. / Ma, B.B. / Zhuang, Y. / Li, X.C.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 45
B: Tripartite motif-containing protein 45
C: Tripartite motif-containing protein 45
D: Tripartite motif-containing protein 45


Theoretical massNumber of molelcules
Total (without water)37,8704
Polymers37,8704
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Tetramer was determined by SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-124 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.850, 55.850, 347.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
Tripartite motif-containing protein 45


Mass: 9467.619 Da / Num. of mol.: 4 / Fragment: coiled coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim45 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PFY8

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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: 3.57 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2M Ammonium dihydrogen phosphate, 35% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→11.985 Å / Num. obs: 14141 / % possible obs: 97.6 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.267 / Num. unique obs: 2100 / CC1/2: 0.978 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→11.985 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.582 / ESU R Free: 0.326 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2707 655 4.634 %
Rwork0.2393 13479 -
all0.241 --
obs-14134 97.321 %
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: 101.729 Å2
Baniso -1Baniso -2Baniso -3
1-8.774 Å20 Å2-0 Å2
2--8.774 Å2-0 Å2
3----17.547 Å2
Refinement stepCycle: LAST / Resolution: 2.7→11.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 0 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122557
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6323441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5323.533167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.27615510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.721524
X-RAY DIFFRACTIONr_chiral_restr0.1390.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021908
X-RAY DIFFRACTIONr_nbd_refined0.2840.21256
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2109
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3050.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.22
X-RAY DIFFRACTIONr_mcbond_it8.8399.5011282
X-RAY DIFFRACTIONr_mcangle_it12.70714.2341597
X-RAY DIFFRACTIONr_scbond_it12.48210.6171275
X-RAY DIFFRACTIONr_scangle_it18.05615.411840
X-RAY DIFFRACTIONr_lrange_it19.825182.65310648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7670.556310.3951007X-RAY DIFFRACTION99.0458
2.767-2.8380.438330.409929X-RAY DIFFRACTION97.8637
2.838-2.9160.465330.387884X-RAY DIFFRACTION93.3809
2.916-30.445360.363873X-RAY DIFFRACTION98.9119
3-3.0920.336420.321889X-RAY DIFFRACTION100
3.092-3.1930.454440.315821X-RAY DIFFRACTION99.7693
3.193-3.3040.281430.316839X-RAY DIFFRACTION99.8867
3.304-3.4280.337440.289751X-RAY DIFFRACTION99.7491
3.428-3.5680.421450.278764X-RAY DIFFRACTION99.2638
3.568-3.7250.27400.229717X-RAY DIFFRACTION99.2136
3.725-3.9060.196470.212672X-RAY DIFFRACTION99.1724
3.906-4.1160.26400.194644X-RAY DIFFRACTION97.8541
4.116-4.3630.209250.228601X-RAY DIFFRACTION95.2816
4.363-4.6620.323210.198609X-RAY DIFFRACTION99.6835
4.662-5.0320.166250.15540X-RAY DIFFRACTION99.8233
5.032-5.5060.27330.212497X-RAY DIFFRACTION99.6241
5.506-6.1460.401240.329454X-RAY DIFFRACTION99.7912
6.146-7.0770.238290.295393X-RAY DIFFRACTION98.1395
7.077-8.6210.193140.179319X-RAY DIFFRACTION94.3343
8.621-11.980.08560.133276X-RAY DIFFRACTION98.6014

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