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- PDB-8onx: High resolution structure of Chaetomium thermophilum MAP2 -

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Basic information

Entry
Database: PDB / ID: 8onx
TitleHigh resolution structure of Chaetomium thermophilum MAP2
ComponentsMethionine aminopeptidase 2
KeywordsMETAL BINDING PROTEIN / Ribosome Associated Factor / Protease / Tunnel exit / Protein Maturation / Proteostasis / NME / p67 / MAP / MetAP / MAP2 / MetAP2 / ES27L / PTE
Function / homology
Function and homology information


initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKlein, M.A. / Wild, K. / Kisonaite, M. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586-6 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.
Authors: Marius A Klein / Klemens Wild / Miglė Kišonaitė / Irmgard Sinning /
Abstract: Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine ...Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8063
Polymers41,6961
Non-polymers1102
Water9,224512
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-13 kcal/mol
Surface area16090 Å2
Unit cell
Length a, b, c (Å)59.938, 73.806, 82.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methionine aminopeptidase 2


Mass: 41695.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0063100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SEA9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9737 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 4, 1021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.3→56.53 Å / Num. obs: 90066 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rpim(I) all: 0.015 / Net I/σ(I): 23
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 4362 / CC1/2: 0.879 / Rpim(I) all: 0.288

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41.02 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 4507 4.97 %
Rwork0.1611 --
obs0.1619 89942 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 2 512 3425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073067
X-RAY DIFFRACTIONf_angle_d0.9544169
X-RAY DIFFRACTIONf_dihedral_angle_d13.111159
X-RAY DIFFRACTIONf_chiral_restr0.075451
X-RAY DIFFRACTIONf_plane_restr0.012560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.27571480.26842794X-RAY DIFFRACTION98
1.31-1.330.261300.24492862X-RAY DIFFRACTION99
1.33-1.340.24291710.22672796X-RAY DIFFRACTION100
1.34-1.360.26571400.21782858X-RAY DIFFRACTION100
1.36-1.380.24111400.23852844X-RAY DIFFRACTION100
1.38-1.40.26171580.24072868X-RAY DIFFRACTION100
1.4-1.420.21631280.22562832X-RAY DIFFRACTION100
1.42-1.440.23651560.2162820X-RAY DIFFRACTION100
1.44-1.460.23591520.20662846X-RAY DIFFRACTION100
1.46-1.480.20741390.19922861X-RAY DIFFRACTION100
1.48-1.510.19931420.19182866X-RAY DIFFRACTION100
1.51-1.540.18251330.18762879X-RAY DIFFRACTION100
1.54-1.570.19651450.17382845X-RAY DIFFRACTION100
1.57-1.60.19131560.18012825X-RAY DIFFRACTION100
1.6-1.630.17641630.17252848X-RAY DIFFRACTION100
1.63-1.670.1981730.17232851X-RAY DIFFRACTION100
1.67-1.710.2021580.16822862X-RAY DIFFRACTION100
1.71-1.760.20341500.17422864X-RAY DIFFRACTION100
1.76-1.810.20591440.17272855X-RAY DIFFRACTION100
1.81-1.870.19761390.17032897X-RAY DIFFRACTION100
1.87-1.940.17671450.16762886X-RAY DIFFRACTION100
1.94-2.010.17381700.15662844X-RAY DIFFRACTION100
2.01-2.110.16771360.1462898X-RAY DIFFRACTION100
2.11-2.220.16021630.152882X-RAY DIFFRACTION100
2.22-2.360.15091470.14042887X-RAY DIFFRACTION100
2.36-2.540.16051650.14342888X-RAY DIFFRACTION100
2.54-2.790.15461420.15212932X-RAY DIFFRACTION100
2.79-3.20.16481430.15162955X-RAY DIFFRACTION100
3.2-4.030.16811610.14572952X-RAY DIFFRACTION100
4.03-41.020.17461700.1613084X-RAY DIFFRACTION99

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