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- PDB-3w1y: Crystal structure of T brucei ATG8.2 in complex with E coli S10 -

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Basic information

Entry
Database: PDB / ID: 3w1y
TitleCrystal structure of T brucei ATG8.2 in complex with E coli S10
Components
  • 30S ribosomal protein S10
  • Microtubule-associated protein 1A/1B, light chain 3
KeywordsTRANSPORT PROTEIN/RIBOSOMAL PROTEIN / Autophage protein 8 / Autophage protein 12 / ubiquitin fold / TRANSPORT PROTEIN-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


cellular response to nitrogen starvation / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / autophagy / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding ...cellular response to nitrogen starvation / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / autophagy / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / structural constituent of ribosome / cytoplasm / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ribosomal protein S10 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain ...Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ribosomal protein S10 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ubiquitin-like domain superfamily / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS10 / Autophagy-related protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuan, Y.A. / Wang, C.
CitationJournal: To be Published
Title: Crystal structure of T brucei ATG8.2
Authors: Yuan, Y.A. / Wang, C.
History
DepositionNov 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein 1A/1B, light chain 3
B: Microtubule-associated protein 1A/1B, light chain 3
C: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Microtubule-associated protein 1A/1B, light chain 3

B: Microtubule-associated protein 1A/1B, light chain 3

C: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area3550 Å2
ΔGint-17 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.012, 61.197, 67.636
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microtubule-associated protein 1A/1B, light chain 3


Mass: 15633.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.7.3320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57WE7
#2: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, MPD, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.329 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h9d

3h9d


Resolution: 2.3→44.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.219 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25649 836 5.1 %RANDOM
Rwork0.20251 ---
all0.214 15654 --
obs0.20521 15654 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.48 Å2
2--1 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 0 81 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222588
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9813495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26522.578128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94915457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5361530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021961
X-RAY DIFFRACTIONr_nbd_refined0.2220.2980
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.212
X-RAY DIFFRACTIONr_mcbond_it0.8631.51615
X-RAY DIFFRACTIONr_mcangle_it1.47622537
X-RAY DIFFRACTIONr_scbond_it2.21631085
X-RAY DIFFRACTIONr_scangle_it3.4834.5958
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 50 -
Rwork0.214 1146 -
obs--97.31 %
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)
11.4235-0.55960.36331.2060.36981.07610.0272-0.0282-0.06750.0790.02290.04190.0710.0012-0.0501-0.076-0.01720.0102-0.11840.0096-0.10446.1861-3.369827.4151
24.5060.1274-2.8060.5568-0.02953.50290.1141-0.31330.117-0.1112-0.0439-0.0049-0.02330.2631-0.0701-0.14220.0011-0.0026-0.07660.0203-0.152115.4135-3.0486-3.1702
33.8751-0.665-2.25841.02630.38572.72610.03690.15490.15410.1985-0.07470.15690.05940.00420.0379-0.1315-0.0017-0.001-0.13660.0401-0.06655.5234-27.892116.6729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 132
2X-RAY DIFFRACTION2B5 - 131
3X-RAY DIFFRACTION3C5 - 103

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