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- PDB-8ry6: CryoEM structure of M. smegmatis GMP reductase apoform at pH 6.6,... -

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Basic information

Entry
Database: PDB / ID: 8ry6
TitleCryoEM structure of M. smegmatis GMP reductase apoform at pH 6.6, extended conformation I.
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis
Function / homology
Function and homology information


GMP reductase / GMP reductase activity / IMP salvage / IMP dehydrogenase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
GMP reductase-like / : / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsDolezal, M. / Kouba, T. / Pichova, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.
Authors: Dolezal, M. / Knejzlik, Z. / Kouba, T. / Filimonenko, A. / Svachova, H. / Klima, M. / Pichova, I.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP reductase
B: GMP reductase
C: GMP reductase
D: GMP reductase
E: GMP reductase
F: GMP reductase
G: GMP reductase
H: GMP reductase


Theoretical massNumber of molelcules
Total (without water)414,2598
Polymers414,2598
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain D
d_2ens_1chain B
d_3ens_1chain C
d_4ens_1chain A
d_5ens_1chain E
d_6ens_1chain F
d_7ens_1chain G
d_8ens_1chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 2 - 470 / Label seq-ID: 2 - 470

Dom-IDAuth asym-IDLabel asym-ID
d_1DD
d_2BB
d_3CC
d_4AA
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(-0.999999999926, 1.20051582047E-5, -1.89425838106E-6), (-1.20052606659E-5, -0.999999998465, 5.4099690745E-5), (-1.89360890281E-6, 5.4099713482E-5, 0.999999998535)366.782232756, 366.773127992, -0.00712098502726
2given(-0.00130818321078, 0.999998369421, 0.00124491449172), (-0.999998446148, -0.00130671019583, -0.00118330450652), (-0.00118167583459, -0.0012464605364, 0.999998524988)-0.157410757393, 366.905281227, 0.402900781648
3given(0.00117349687811, -0.999998465525, -0.00130071212687), (0.999998839736, 0.00117223194238, 0.000972830881155), (-0.000971304652068, -0.00130185223171, 0.999998680873)366.976264433, -0.0564451507962, 0.369451527704
4given(-0.99946089892, -0.0327444230428, 0.00239045806969), (-0.0327473908883, 0.99946292413, -0.00121312783586), (-0.00234945104128, -0.00129075510215, -0.999996407009)372.128234849, 6.37396444082, 366.805034169
5given(-0.0326074117209, 0.999468221036, 0.000178439395419), (0.999460186229, 0.0326064319606, 0.00401954453086), (0.00401158874963, 0.000309410014824, -0.999991905678)5.85934752254, -6.45863408431, 365.416581329
6given(0.999461922064, 0.0327076983189, -0.0024643082411), (0.0327106833499, -0.99946416479, 0.0011808873454), (-0.00242436367093, -0.00126086114253, -0.999996266338)-5.32299475781, 360.423516398, 366.814600861
7given(0.0325876043076, -0.999468867029, -0.000178563992611), (-0.999460955623, -0.0325866337456, -0.00398866974683), (0.00398073243339, 0.000308448930118, -0.999992029283)360.927624118, 373.232094674, 365.422583663

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Components

#1: Protein
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


Mass: 51782.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Guanosine 5'-monophosphate reductase / Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Msm GMPR apoform at pH 6.6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTriex
Buffer solutionpH: 6.6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2100 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 20 mg/ml Msm GMPR in the storage buffer (50 mM Tris, pH 8.0, 2.5 mM TCEP) was diluted with the cryoEM buffer (50 mM HEPES, pH 6.6, 100 mM KCl, 2 mM MgCl2).
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / C2 aperture diameter: 30 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7MOLREP11.9.02model fitting
8UCSF ChimeraX1.5model fitting
11RELION4final Euler assignment
14Coot0.9.8.1model refinement
15PHENIX1.21rc1_4985model refinement
16ISOLDE1.5model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107713 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and ...Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and Isolde, and automatic refinement in phenix.real_space_refine.
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002627752
ELECTRON MICROSCOPYf_angle_d0.481237776
ELECTRON MICROSCOPYf_chiral_restr0.0424496
ELECTRON MICROSCOPYf_plane_restr0.00365000
ELECTRON MICROSCOPYf_dihedral_angle_d3.01274064
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints6.06683382492E-13
ens_1d_3DDELECTRON MICROSCOPYNCS constraints8.8857472006E-13
ens_1d_4DDELECTRON MICROSCOPYNCS constraints9.95028573841E-13
ens_1d_5DDELECTRON MICROSCOPYNCS constraints8.30956142676E-13
ens_1d_6DDELECTRON MICROSCOPYNCS constraints6.20290170779E-13
ens_1d_7DDELECTRON MICROSCOPYNCS constraints1.69016840482E-10
ens_1d_8DDELECTRON MICROSCOPYNCS constraints9.65379377062E-13

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