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- PDB-24br: Crystal structure of nuclease MYG1(D57A) bound to Mn2+ and UUUU -

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Basic information

Entry
Database: PDB / ID: 24br
TitleCrystal structure of nuclease MYG1(D57A) bound to Mn2+ and UUUU
Components
  • MYG1 exonuclease
  • RNA (5'-R(P*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / MYG1 / nuclease / Mn2+ / DHH family / HYDROLASE-RNA complex
Function / homology
Function and homology information


mitochondrial RNA metabolic process / locomotory exploration behavior / mRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm ...mitochondrial RNA metabolic process / locomotory exploration behavior / mRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Metal-dependent protein hydrolase / Uncharacterised protein family (UPF0160)
Similarity search - Domain/homology
: / RNA / MYG1 exonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDing, J. / Lan, C. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2026
Title: Biochemical and structural studies reveal the substrate specificity and catalytic mechanism of MYG1 as a two-metal ion-dependent 3'→5' exonuclease.
Authors: Lan, C. / Chen, Z. / Wang, G. / Ding, J.
History
DepositionFeb 27, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYG1 exonuclease
C: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1223
Polymers38,0672
Non-polymers551
Water2,864159
1
A: MYG1 exonuclease
hetero molecules

C: RNA (5'-R(P*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)38,1223
Polymers38,0672
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.510, 97.560, 116.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MYG1 exonuclease


Mass: 36887.516 Da / Num. of mol.: 1 / Mutation: D57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYG1, C12orf10 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HB07, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→33.74 Å / Num. obs: 23523 / % possible obs: 98.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.17 Å / Num. unique obs: 1580 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.20.1_4487data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.74 Å / SU ML: 0.2257 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 1159 4.94 %
Rwork0.1853 22314 -
obs0.1872 23473 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 73 1 159 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692680
X-RAY DIFFRACTIONf_angle_d0.80353655
X-RAY DIFFRACTIONf_chiral_restr0.0503398
X-RAY DIFFRACTIONf_plane_restr0.0078467
X-RAY DIFFRACTIONf_dihedral_angle_d6.7178395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.33521320.24312590X-RAY DIFFRACTION92.37
2.2-2.310.28421440.20682771X-RAY DIFFRACTION98.98
2.31-2.460.28151560.20062737X-RAY DIFFRACTION99.08
2.46-2.650.25861430.20332810X-RAY DIFFRACTION99.29
2.65-2.910.27651420.20272797X-RAY DIFFRACTION99.59
2.91-3.330.25741290.1942844X-RAY DIFFRACTION99.46
3.33-4.20.19621510.16552831X-RAY DIFFRACTION99.83
4.2-33.740.18241620.17462934X-RAY DIFFRACTION99.1

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