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- PDB-4bl7: Crystal structure of the AIMP3-MRS N-terminal domain complex in d... -

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Basic information

Entry
Database: PDB / ID: 4bl7
TitleCrystal structure of the AIMP3-MRS N-terminal domain complex in different space group
Components
  • EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
  • METHIONINE--TRNA LIGASE, CYTOPLASMIC
KeywordsTRANSLATION / LIGASE
Function / homology
Function and homology information


Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / rRNA transcription ...Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / rRNA transcription / cellular response to platelet-derived growth factor stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / positive regulation of cellular senescence / tRNA binding / positive regulation of apoptotic process / translation / negative regulation of cell population proliferation / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Glutaredoxin / Glutaredoxin / S15/NS1, RNA-binding / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation elongation factor 1 epsilon-1 / Methionine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsCho, H.Y. / Seo, W.W. / Cho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of the Aimp3-Mrs N-Terminal Domain Complex in Different Space Group
Authors: Cho, H.Y. / Seo, W.W. / Cho, H.J. / Kang, B.S.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHIONINE--TRNA LIGASE, CYTOPLASMIC
B: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1


Theoretical massNumber of molelcules
Total (without water)47,1122
Polymers47,1122
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-7.5 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.685, 72.029, 123.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2054-

HOH

21A-2055-

HOH

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Components

#1: Protein METHIONINE--TRNA LIGASE, CYTOPLASMIC / METHIONYL-TRNA SYNTHETASE / METRS


Mass: 25886.238 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-224
Source method: isolated from a genetically manipulated source
Details: M1 TO E224 OF MRS N-TERMINUS DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P56192, methionine-tRNA ligase
#2: Protein EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1 / AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 3 / ELONGATION FACTOR P18 / ...AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 3 / ELONGATION FACTOR P18 / MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P18 / AIMP3


Mass: 21226.016 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M1 TO H174 OF AIMP3 WITH ADDITIONAL S SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43324
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.32 Å3/Da / Density % sol: 46.97 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 100 MM BIS-TRIS, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29322 / % possible obs: 92 % / Observed criterion σ(I): -2 / Redundancy: 11.2 % / Biso Wilson estimate: 18.92 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 53
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.14 / % possible all: 60.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BJW

4bjw
PDB Unreleased entry


Resolution: 1.892→37.352 Å / SU ML: 0.2 / σ(F): 0.13 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1949 6.9 %
Rwork0.1804 --
obs0.1837 28425 89.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→37.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 0 153 3116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073031
X-RAY DIFFRACTIONf_angle_d1.1094125
X-RAY DIFFRACTIONf_dihedral_angle_d14.2761104
X-RAY DIFFRACTIONf_chiral_restr0.075469
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8924-1.93970.2835760.24271004X-RAY DIFFRACTION48
1.9397-1.99210.286980.22381296X-RAY DIFFRACTION62
1.9921-2.05070.26871160.20631549X-RAY DIFFRACTION75
2.0507-2.11690.22961260.18691729X-RAY DIFFRACTION83
2.1169-2.19260.21781390.18041894X-RAY DIFFRACTION90
2.1926-2.28040.2411490.17422006X-RAY DIFFRACTION96
2.2804-2.38410.24741470.18282044X-RAY DIFFRACTION98
2.3841-2.50980.24681520.18982084X-RAY DIFFRACTION99
2.5098-2.6670.26831540.18942100X-RAY DIFFRACTION99
2.667-2.87290.24661550.19392116X-RAY DIFFRACTION100
2.8729-3.16180.25691550.2042113X-RAY DIFFRACTION99
3.1618-3.6190.22021580.17982137X-RAY DIFFRACTION100
3.619-4.55830.18381590.14872156X-RAY DIFFRACTION99
4.5583-37.35940.20951650.16652248X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -18.4083 Å / Origin y: 18.919 Å / Origin z: -19.7389 Å
111213212223313233
T0.0975 Å2-0.0358 Å20.0017 Å2-0.0472 Å20.0058 Å2--0.0687 Å2
L0.457 °20.0899 °2-0.1894 °2-1.2283 °2-0.1684 °2--0.5308 °2
S0.0466 Å °0.0369 Å °-0.062 Å °0.3205 Å °-0.0735 Å °-0.0004 Å °-0.0693 Å °0.0994 Å °0.0177 Å °
Refinement TLS groupSelection details: ALL

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