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- PDB-9e7c: TRK-fused Gene (TFG) PB1 Domain D60A/D62R Variant -

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Basic information

Entry
Database: PDB / ID: 9e7c
TitleTRK-fused Gene (TFG) PB1 Domain D60A/D62R Variant
ComponentsProtein TFG
KeywordsPROTEIN TRANSPORT / Type I/II PB1 domain / octamer / ubiquitin like beta-grasp fold / globular
Function / homology
Function and homology information


COPII vesicle coating / COPII-mediated vesicle transport / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / Signaling by ALK fusions and activated point mutants / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Protein TFG / TFG, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.906 Å
AuthorsSchuh, A.L. / Bhattacharyya, B. / Keck, J.L. / Audhya, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134865 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS124165 United States
CitationJournal: Biorxiv / Year: 2024
Title: Multiple roles for TFG ring complexes in neuronal cargo trafficking.
Authors: Zhang, Z. / Lettman, M.M. / Schuh, A.L. / Bhattacharyya, B. / Randolph, P. / Nandakumar, T. / Kulkarni, I. / Roach, A. / Alvin, J.R. / Gengler, D. / Stagg, S.M. / Keck, J.L. / Audhya, A.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TFG


Theoretical massNumber of molelcules
Total (without water)11,4041
Polymers11,4041
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.018, 32.488, 29.246
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein TFG / TRK-fused gene protein


Mass: 11404.229 Da / Num. of mol.: 1 / Mutation: D60A, D62R
Source method: isolated from a genetically manipulated source
Details: The first 9 N-terminal amino acids of TFG as well as the GST protein purification tag were not well resolved in the diffraction data and therefore not included in the final structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: TFG / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92734
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 203 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.906→51.73 Å / Num. obs: 7690 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.1 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Rsym value: 0.071 / Χ2: 0.873 / Net I/av σ(I): 26.9 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.91-1.946.10.5363420.890.970.2240.5820.5494
1.94-1.985.90.4113680.9480.9870.1770.4490.56996.1
1.98-2.026.60.3513790.9560.9890.1440.3810.56298.4
2.02-2.066.90.3413680.9630.990.1380.3690.61199.2
2.06-2.17.10.2734020.9790.9950.110.2940.5899.8
2.1-2.157.30.2423710.9850.9960.0950.260.609100
2.15-2.27.50.2093900.9830.9960.0820.2250.684100
2.2-2.267.40.1713860.9890.9970.0670.1840.66100
2.26-2.337.60.1553830.990.9970.060.1660.679100
2.33-2.417.50.1353820.9940.9990.0530.1450.702100
2.41-2.497.50.123870.9960.9990.0470.1290.684100
2.49-2.597.50.1093880.9950.9990.0420.1170.723100
2.59-2.717.50.0943920.9960.9990.0370.1010.761100
2.71-2.857.50.0773740.9980.9990.030.0830.838100
2.85-3.037.50.0783870.9960.9990.030.0841.038100
3.03-3.277.50.0683960.9980.9990.0270.0731.438100
3.27-3.597.50.0693930.9970.9990.0270.0741.9100
3.59-4.117.50.0593870.9980.9990.0230.0641.59100
4.11-5.187.40.0384020.99910.0150.0410.993100
5.18-5070.0314130.99910.0130.0330.96599.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data scaling
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.906→51.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.496 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25406 352 4.6 %RANDOM
Rwork0.21369 ---
obs0.21555 7337 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.708 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å2-0.67 Å2
2--2.64 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.906→51.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 0 51 758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019723
X-RAY DIFFRACTIONr_bond_other_d0.0010.02735
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.996974
X-RAY DIFFRACTIONr_angle_other_deg0.74931690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.918588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04423.63633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90215145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.96157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8763.144352
X-RAY DIFFRACTIONr_mcbond_other2.8663.136351
X-RAY DIFFRACTIONr_mcangle_it5.0194.687440
X-RAY DIFFRACTIONr_mcangle_other5.0184.695441
X-RAY DIFFRACTIONr_scbond_it2.8963.7371
X-RAY DIFFRACTIONr_scbond_other2.8893.698371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0395.355534
X-RAY DIFFRACTIONr_long_range_B_refined8.60625.074796
X-RAY DIFFRACTIONr_long_range_B_other8.50524.878777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 19 -
Rwork0.244 492 -
obs--91.74 %

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