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- PDB-5ons: Crystal structure of the minimal DENR-MCTS1 complex -

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Basic information

Entry
Database: PDB / ID: 5ons
TitleCrystal structure of the minimal DENR-MCTS1 complex
Components
  • Density-regulated protein
  • Malignant T-cell-amplified sequence 1
KeywordsTRANSLATION / translation initiation / Ribosome
Function / homology
Function and homology information


translation reinitiation / IRES-dependent viral translational initiation / formation of translation preinitiation complex / ribosome disassembly / translation initiation factor activity / cell cycle / mRNA binding / DNA damage response / positive regulation of cell population proliferation / RNA binding / cytoplasm
Similarity search - Function
Sulfate adenylyltransferase - #20 / DENR family, eukaryotes / DENR, C-terminal domain / : / DENR, N-terminal / MCT-1/Tma20 / Pre-PUA domain / Pre-PUA-like domain / Sulfate adenylyltransferase / Uncharacterised domain CHP00451 ...Sulfate adenylyltransferase - #20 / DENR family, eukaryotes / DENR, C-terminal domain / : / DENR, N-terminal / MCT-1/Tma20 / Pre-PUA domain / Pre-PUA-like domain / Sulfate adenylyltransferase / Uncharacterised domain CHP00451 / PUA domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Density-regulated protein / Malignant T-cell-amplified sequence 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsAhmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: PLoS Biol. / Year: 2018
Title: DENR-MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation.
Authors: Ahmed, Y.L. / Schleich, S. / Bohlen, J. / Mandel, N. / Simon, B. / Sinning, I. / Teleman, A.A.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malignant T-cell-amplified sequence 1
B: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0756
Polymers24,7332
Non-polymers3424
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-36 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.030, 49.030, 207.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein Malignant T-cell-amplified sequence 1 / MCT-1 / Multiple copies T-cell malignancies


Mass: 20585.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCTS1, MCT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ULC4
#2: Protein/peptide Density-regulated protein / DRP / Protein DRP1 / Smooth muscle cell-associated protein 3 / SMAP-3


Mass: 4147.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DENR, DRP1, H14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43583
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.53 Å3/Da / Density % sol: 51.32 % / Description: rod shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M Ammonium sulphate 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.28226 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28226 Å / Relative weight: 1
ReflectionResolution: 2.14→44.35 Å / Num. obs: 14846 / % possible obs: 99.5 % / Redundancy: 12.4 % / Biso Wilson estimate: 50.52 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.61
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.839 / Mean I/σ(I) obs: 1.19 / Num. measured obs: 17005 / Num. unique all: 1430 / CC1/2: 0.65 / % possible all: 98.96

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.14→44.348 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 30.08
RfactorNum. reflection% reflection
Rfree0.2501 784 5.28 %
Rwork0.2002 --
obs0.2028 14842 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.21 Å2 / Biso mean: 70.4816 Å2 / Biso min: 30.22 Å2
Refinement stepCycle: final / Resolution: 2.14→44.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 19 33 1688
Biso mean--88.09 63.58 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091691
X-RAY DIFFRACTIONf_angle_d1.0422280
X-RAY DIFFRACTIONf_chiral_restr0.061249
X-RAY DIFFRACTIONf_plane_restr0.007287
X-RAY DIFFRACTIONf_dihedral_angle_d7.1461026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.27410.3521020.28322258236099
2.2741-2.44970.25791420.24822271241399
2.4497-2.69620.37611190.243722962415100
2.6962-3.08620.31641300.236823352465100
3.0862-3.8880.26171470.193723512498100
3.888-44.35740.21261440.17625472691100
Refinement TLS params.Method: refined / Origin x: -0.8607 Å / Origin y: 25.8357 Å / Origin z: 15.3027 Å
111213212223313233
T0.3632 Å2-0.0048 Å20.0155 Å2-0.35 Å2-0.012 Å2--0.3725 Å2
L3.2643 °20.7698 °2-0.9906 °2-1.6109 °20.119 °2--5.0311 °2
S-0.0921 Å °-0.1769 Å °-0.0072 Å °0.1693 Å °0.0669 Å °-0.0255 Å °0.2482 Å °-0.2858 Å °-0.0017 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 181
2X-RAY DIFFRACTION1allB25 - 48
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allW1 - 33

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