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- PDB-8sde: Electrostatic-Mediated Tetramerization of the Coiled-Coil Domain ... -

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Basic information

Entry
Database: PDB / ID: 8sde
TitleElectrostatic-Mediated Tetramerization of the Coiled-Coil Domain in TRIM29
ComponentsTripartite motif-containing protein 29
KeywordsLIGASE / E3 ubiquitin ligase / Ubiquitination / coiled-coil
Function / homology
Function and homology information


negative regulation of protein localization to nucleus / p53 binding / lysosome / innate immune response / negative regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile.
Similarity search - Domain/homology
Tripartite motif-containing protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLou, X.H. / Zhuang, Y. / Ma, B.B. / 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: Electrostatic-Mediated Tetramerization of the Coiled-Coil Domain in TRIM29
Authors: Lou, X.H. / Zhuang, Y. / Ma, B.B. / 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 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0663
Polymers10,8821
Non-polymers1842
Water27015
1
A: Tripartite motif-containing protein 29
hetero molecules

A: Tripartite motif-containing protein 29
hetero molecules

A: Tripartite motif-containing protein 29
hetero molecules

A: Tripartite motif-containing protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,26512
Polymers43,5294
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)45.050, 47.630, 107.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Tripartite motif-containing protein 29


Mass: 10882.185 Da / Num. of mol.: 1 / Fragment: coiled coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8R2Q0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.7 / Details: 10% glycerol, 38% MPD, and 0.1M Acetic acid pH4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.27→8 Å / Num. obs: 5400 / % possible obs: 96.9 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.5
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.319 / Num. unique obs: 782 / CC1/2: 0.985 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→7.981 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.274 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.339 / ESU R Free: 0.255 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2751 392 7.267 %
Rwork0.2267 5002 -
all0.23 --
obs-5394 95.757 %
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: 86.024 Å2
Baniso -1Baniso -2Baniso -3
1-5.301 Å2-0 Å2-0 Å2
2--2.596 Å20 Å2
3----7.897 Å2
Refinement stepCycle: LAST / Resolution: 2.27→7.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 12 15 771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012758
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.6521009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.247588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12725.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.31915169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.121155
X-RAY DIFFRACTIONr_chiral_restr0.1080.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02541
X-RAY DIFFRACTIONr_nbd_refined0.230.2294
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1890.27
X-RAY DIFFRACTIONr_mcbond_it6.2616.169355
X-RAY DIFFRACTIONr_mcangle_it7.9539.224442
X-RAY DIFFRACTIONr_scbond_it10.7147.7402
X-RAY DIFFRACTIONr_scangle_it16.00410.99566
X-RAY DIFFRACTIONr_lrange_it17.27384.0371070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.3240.281190.268342X-RAY DIFFRACTION98.6339
2.324-2.3820.286190.245347X-RAY DIFFRACTION98.1233
2.382-2.4450.358260.223318X-RAY DIFFRACTION98.0057
2.445-2.5130.298350.239321X-RAY DIFFRACTION99.4413
2.513-2.5870.299230.203295X-RAY DIFFRACTION98.7578
2.587-2.6680.259230.191306X-RAY DIFFRACTION98.503
2.668-2.7570.155230.208294X-RAY DIFFRACTION98.1424
2.757-2.8550.334280.237279X-RAY DIFFRACTION98.7138
2.855-2.9650.308260.265270X-RAY DIFFRACTION98.9967
2.965-3.0880.218220.221262X-RAY DIFFRACTION98.6111
3.088-3.2290.267170.23251X-RAY DIFFRACTION98.893
3.229-3.390.174180.216247X-RAY DIFFRACTION98.1481
3.39-3.5790.36210.238229X-RAY DIFFRACTION98.0392
3.579-3.8030.211120.208221X-RAY DIFFRACTION98.3122
3.803-4.0750.223160.189211X-RAY DIFFRACTION97.8448
4.075-4.4150.208130.192196X-RAY DIFFRACTION98.5849
4.415-4.8570.214170.2183X-RAY DIFFRACTION98.5222
4.857-5.4660.28120.251158X-RAY DIFFRACTION97.7011
5.466-6.3830.372110.298148X-RAY DIFFRACTION98.7578
6.383-7.9810.996110.3124X-RAY DIFFRACTION98.5401
Refinement TLS params.Method: refined / Origin x: -15.2666 Å / Origin y: -8.1262 Å / Origin z: -23.6626 Å
111213212223313233
T0.105 Å20.0044 Å2-0.0004 Å2-0.1679 Å2-0.0224 Å2--0.1474 Å2
L0.0556 °20.0076 °20.1946 °2-0.5027 °22.411 °2--12.6897 °2
S-0.0696 Å °0.0226 Å °0.0001 Å °0.0446 Å °-0.0943 Å °0.048 Å °0.1093 Å °-0.0762 Å °0.1639 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA258 - 346
2X-RAY DIFFRACTION1ALLA401 - 415
3X-RAY DIFFRACTION1ALLA501

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