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- PDB-7ug2: Crystal structure of the coiled-coil domain of TRIM75 -

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Basic information

Entry
Database: PDB / ID: 7ug2
TitleCrystal structure of the coiled-coil domain of TRIM75
ComponentsTripartite motif-containing protein 75
KeywordsLIGASE / TRIM75 / tetramerization / E3 ubiquitin ligase / Ubiquitination / coiled-coil
Function / homology
Function and homology information


female meiosis I / spindle / ubiquitin protein ligase activity / regulation of gene expression / protein ubiquitination / innate immune response / zinc ion binding / cytoplasm
Similarity search - Function
TRIM75, PRY/SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain ...TRIM75, PRY/SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ACETYL GROUP / ISOPROPYL ALCOHOL / Tripartite motif-containing protein 75
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 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)R56 AI148215 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Structural studies of the coiled-coil domain of TRIM75 reveal a tetramer architecture facilitating its E3 ligase complex.
Authors: Lou, X. / Ma, B. / Zhuang, Y. / Xiao, X. / Minze, L.J. / Xing, J. / Zhang, Z. / Li, X.C.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9664
Polymers6,8181
Non-polymers1483
Water54030
1
A: Tripartite motif-containing protein 75
hetero molecules

A: Tripartite motif-containing protein 75
hetero molecules

A: Tripartite motif-containing protein 75
hetero molecules

A: Tripartite motif-containing protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,86316
Polymers27,2714
Non-polymers59312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area9800 Å2
ΔGint-40 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.070, 43.070, 134.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-302-

ACE

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Components

#1: Protein Tripartite motif-containing protein 75


Mass: 6817.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim75, Gm794 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3UWZ0
#2: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.6
Details: 0.1 M Acetate pH 4.6 20% Isopropanol 0.2 M Calcium chloride

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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: 2.05→8 Å / Num. obs: 4039 / % possible obs: 96.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 2.05→2.16 Å / Rmerge(I) obs: 0.248 / Num. unique obs: 594 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SI8

7si8
PDB Unreleased entry


Resolution: 2.052→7.985 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.22 / Average fsc free: 0.9037 / Average fsc work: 0.929 / Cross valid method: FREE R-VALUE / ESU R: 0.243 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 317 7.85 %Random selectoin
Rwork0.2114 3721 --
all0.215 ---
obs-4038 94.5 %-
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: 53.022 Å2
Baniso -1Baniso -2Baniso -3
1-1.407 Å20 Å20 Å2
2--1.407 Å20 Å2
3----2.814 Å2
Refinement stepCycle: LAST / Resolution: 2.052→7.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms410 0 0 30 440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012471
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.647631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61922.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7811596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.087156
X-RAY DIFFRACTIONr_chiral_restr0.1020.258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02373
X-RAY DIFFRACTIONr_nbd_refined0.260.2203
X-RAY DIFFRACTIONr_nbtor_refined0.280.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3280.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.27
X-RAY DIFFRACTIONr_mcbond_it5.3644.887227
X-RAY DIFFRACTIONr_mcangle_it7.0637.237287
X-RAY DIFFRACTIONr_scbond_it7.6835.59243
X-RAY DIFFRACTIONr_scangle_it11.0218.083340
X-RAY DIFFRACTIONr_lrange_it14.92891.2072027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.052-2.1020.224310.243245X-RAY DIFFRACTION98.9247
2.102-2.1550.357210.23257X-RAY DIFFRACTION99.2857
2.155-2.2130.2240.216242X-RAY DIFFRACTION99.2537
2.213-2.2760.306200.219247X-RAY DIFFRACTION98.524
2.276-2.3440.14140.239240X-RAY DIFFRACTION99.2188
2.344-2.4190.289160.218230X-RAY DIFFRACTION97.2332
2.419-2.5010.423170.237211X-RAY DIFFRACTION95.3975
2.501-2.5930.389170.228205X-RAY DIFFRACTION94.0678
2.593-2.6960.314240.231206X-RAY DIFFRACTION99.1379
2.696-2.8110.359130.219203X-RAY DIFFRACTION98.1818
2.811-2.9430.306220.225189X-RAY DIFFRACTION98.5981
2.943-3.0960.365110.228191X-RAY DIFFRACTION97.5845
3.096-3.2750.294200.241163X-RAY DIFFRACTION96.8254
3.275-3.4890.233140.211163X-RAY DIFFRACTION95.6757
3.489-3.7510.22290.164144X-RAY DIFFRACTION90.5325
3.751-4.0830.16390.161146X-RAY DIFFRACTION93.3735
4.083-4.5220.157120.147127X-RAY DIFFRACTION93.2886
4.522-5.1430.20970.173125X-RAY DIFFRACTION94.2857
5.143-6.1180.18980.259108X-RAY DIFFRACTION93.5484
6.118-7.9850.43780.42179X-RAY DIFFRACTION87

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