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- PDB-6j9r: Coiled-coil Domain of Drosophila TRIM Protein Brat -

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Basic information

Entry
Database: PDB / ID: 6j9r
TitleCoiled-coil Domain of Drosophila TRIM Protein Brat
ComponentsBrain tumor protein
KeywordsTRANSLATION / Coiled-coil Domain / TRIM / BRAT / Translational repressor
Function / homology
Function and homology information


asymmetric neuroblast division resulting in ganglion mother cell formation / ganglion mother cell fate determination / neuroblast development / regulation of synaptic assembly at neuromuscular junction / neuroblast fate determination / segmentation / asymmetric cell division / basal cortex / ventral cord development / regulation of neuroblast proliferation ...asymmetric neuroblast division resulting in ganglion mother cell formation / ganglion mother cell fate determination / neuroblast development / regulation of synaptic assembly at neuromuscular junction / neuroblast fate determination / segmentation / asymmetric cell division / basal cortex / ventral cord development / regulation of neuroblast proliferation / neuroblast differentiation / Neutrophil degranulation / apical cortex / regulation of synaptic vesicle endocytosis / negative regulation of neuroblast proliferation / oogenesis / rRNA transcription / regulation of neurogenesis / neuroblast proliferation / translation regulator activity / translation repressor activity / mRNA 3'-UTR binding / neuron differentiation / brain development / regulation of translation / negative regulation of translation / negative regulation of cell population proliferation / negative regulation of gene expression / neuronal cell body / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
NHL repeat profile. / NHL repeat / NHL repeat / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster American nodavirus SW-2009a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsShan, Z. / Wang, W.
CitationJournal: Proteins / Year: 2019
Title: Crystal structure of the coiled-coil domain of Drosophila TRIM protein Brat.
Authors: Liu, C. / Shan, Z. / Diao, J. / Wen, W. / Wang, W.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brain tumor protein
B: Brain tumor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7503
Polymers30,6582
Non-polymers921
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-56 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.612, 61.100, 128.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA7 - 131
211chain BB5 - 132

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Components

#1: Protein Brain tumor protein / Protein Brat


Mass: 15328.776 Da / Num. of mol.: 2 / Fragment: Coiled-coil Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster American nodavirus (ANV) SW-2009a
Production host: Escherichia coli (E. coli) / References: UniProt: Q8MQJ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 5.5 / Details: 0.2M NaCl,0.1M Na2(CH3COO).3H2O,30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14770 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 30.21 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Χ2: 0.916 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.5-2.5413.30.3737120.990.1060.3890.924
2.54-2.5913.20.3437290.9920.0980.3570.942
2.59-2.6413.20.3077080.9890.0890.320.922
2.64-2.6912.80.2567180.9920.0750.2670.921
2.69-2.7512.10.2447430.9890.0730.2550.949
2.75-2.82120.1937070.9970.0580.2010.945
2.82-2.8912.30.187450.9960.0530.1880.949
2.89-2.9613.40.1677210.9950.0470.1740.959
2.96-3.0513.70.1587290.9960.0440.1651
3.05-3.1513.70.1497170.9970.0420.1551.01
3.15-3.2613.50.1347330.9960.0380.1391.042
3.26-3.3913.50.127340.9960.0340.1241.02
3.39-3.5513.20.1057340.9960.030.111.024
3.55-3.73130.0937410.9970.0270.0970.981
3.73-3.9711.90.0847370.9980.0250.0870.949
3.97-4.2711.70.0757410.9970.0230.0780.835
4.27-4.713.20.0747600.9970.0220.0770.821
4.7-5.3813.20.077440.9960.0210.0730.741
5.38-6.7812.30.0647840.9970.0190.0670.638
6.78-5011.30.0678330.9980.020.070.743

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.186 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2686 719 5.06 %
Rwork0.2237 --
obs0.2259 14219 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.47 Å2 / Biso mean: 46.69 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 2.5→40.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 6 24 1846
Biso mean--71.95 42.57 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081862
X-RAY DIFFRACTIONf_angle_d1.0922525
X-RAY DIFFRACTIONf_chiral_restr0.051304
X-RAY DIFFRACTIONf_plane_restr0.006326
X-RAY DIFFRACTIONf_dihedral_angle_d14.517664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A902X-RAY DIFFRACTION10.8TORSIONAL
12B902X-RAY DIFFRACTION10.8TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.6930.28311180.24262365248387
2.693-2.9640.27091500.233827062856100
2.964-3.39270.29241610.226527332894100
3.3927-4.27360.21621480.196227772925100
4.2736-40.19130.30031420.235929193061100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.37994.07673.44723.96233.45453.174-0.44820.02520.4534-0.494-0.37960.3937-0.9428-0.40020.91830.35030.0299-0.10280.3116-0.07870.35714.0129-18.80485.7561
20.6948-0.13941.62930.0841-1.19073.62150.08540.04720.1005-0.1863-0.1178-0.02140.7535-0.243-0.05210.53190.21450.00410.3960.02520.38120.9995-18.544217.2269
32.0171-0.55090.81722.7806-1.23728.6064-0.1210.1246-0.0110.3588-0.1949-0.2583-0.41681.80820.23230.1754-0.0433-0.05040.39370.1030.3753-3.9158-1.5424-23.6359
46.2183-1.61573.03953.30420.5712.1304-0.5159-0.83130.15960.0093-0.0659-0.2358-0.09051.24360.55050.28930.06750.03361.18990.20870.68534.6581-2.9462-24.3989
50.2551-0.1231-0.0341-0.06760.08152.6453-0.01790.12610.07250.0002-0.0847-0.07050.2070.41520.12730.4493-0.0202-0.04210.22910.03840.349113.561-24.526744.0281
66.96931.18541.94865.85960.8352.245-0.1882-0.09630.2082-0.07680.0448-0.4836-0.60360.56480.14610.3341-0.04720.02660.2656-0.00970.306523.1514-19.478285.3555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 29 )A7 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 103 )A30 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 131 )A104 - 131
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 29 )B5 - 29
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 103 )B30 - 103
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 132 )B104 - 132

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