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- PDB-24bx: Crystal structure of nuclease MYG1(H50A) bound to Mn2+ and AMP -

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Basic information

Entry
Database: PDB / ID: 24bx
TitleCrystal structure of nuclease MYG1(H50A) bound to Mn2+ and AMP
ComponentsMYG1 exonuclease
KeywordsHYDROLASE / MYG1 / nuclease / Mn2+ / DHH family
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
ADENOSINE MONOPHOSPHATE / : / MYG1 exonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6144
Polymers36,8641
Non-polymers7493
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-11 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.234, 97.155, 116.842
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: 36864.457 Da / Num. of mol.: 1 / Mutation: H50A
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: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#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.: 360 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.5, 16% w/v PEG 8000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.01→56.92 Å / Num. obs: 27166 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 25.12 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.3
Reflection shellResolution: 2.01→2.08 Å / Num. unique obs: 3890 / CC1/2: 0.85

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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: 2.01→56.92 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 2000 7.37 %
Rwork0.1796 25129 -
obs0.1818 27129 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.66 Å2
Refinement stepCycle: LAST / Resolution: 2.01→56.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 47 360 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662648
X-RAY DIFFRACTIONf_angle_d0.86593607
X-RAY DIFFRACTIONf_chiral_restr0.0511388
X-RAY DIFFRACTIONf_plane_restr0.0084466
X-RAY DIFFRACTIONf_dihedral_angle_d15.4762956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.28531390.23511748X-RAY DIFFRACTION99.95
2.06-2.110.22311420.21551779X-RAY DIFFRACTION99.95
2.11-2.170.22431400.1911761X-RAY DIFFRACTION99.89
2.17-2.240.23841390.19211759X-RAY DIFFRACTION99.95
2.24-2.320.22171440.19461794X-RAY DIFFRACTION99.95
2.32-2.420.27341420.18871782X-RAY DIFFRACTION99.9
2.42-2.530.23081410.19541774X-RAY DIFFRACTION99.9
2.53-2.660.24431410.19391771X-RAY DIFFRACTION99.95
2.66-2.830.2381430.18871800X-RAY DIFFRACTION100
2.83-3.040.22621450.18491814X-RAY DIFFRACTION100
3.04-3.350.22381430.18321796X-RAY DIFFRACTION100
3.35-3.840.19411430.16271801X-RAY DIFFRACTION100
3.84-4.830.15851450.14561837X-RAY DIFFRACTION100
4.83-56.920.18131530.17921913X-RAY DIFFRACTION99.76

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