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- PDB-8ry5: CryoEM structure of M. smegmatis GMP reductase in complex with GM... -

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Basic information

Entry
Database: PDB / ID: 8ry5
TitleCryoEM structure of M. smegmatis GMP reductase in complex with GMP and ATP at pH 6.6, compressed conformation.
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
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,22324
Polymers414,2598
Non-polymers6,96316
Water3,855214
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 C
d_2ens_1chain A
d_1ens_2chain B
d_2ens_2chain D
d_1ens_3chain G
d_2ens_3chain E
d_1ens_4chain F
d_2ens_4chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALALAALACC2 - 4812 - 481
d_12ens_15GP5GP5GP5GPCM501
d_13ens_1ATPATPATPATPCN502
d_21ens_1VALVALALAALAAA2 - 4812 - 481
d_22ens_15GP5GP5GP5GPAI501
d_23ens_1ATPATPATPATPAJ502
d_11ens_2VALVALALAALABB2 - 4812 - 481
d_12ens_25GP5GP5GP5GPBK501
d_13ens_2ATPATPATPATPBL502
d_21ens_2VALVALALAALADD2 - 4812 - 481
d_22ens_25GP5GP5GP5GPDO501
d_23ens_2ATPATPATPATPDP502
d_11ens_3VALVALALAALAGG2 - 4812 - 481
d_12ens_35GP5GP5GP5GPGU501
d_13ens_3ATPATPATPATPGV502
d_21ens_3VALVALALAALAEE2 - 4812 - 481
d_22ens_35GP5GP5GP5GPEQ501
d_23ens_3ATPATPATPATPER502
d_11ens_4VALVALALAALAFF2 - 4812 - 481
d_12ens_45GP5GP5GP5GPFS501
d_13ens_4ATPATPATPATPFT502
d_21ens_4VALVALALAALAHH2 - 4812 - 481
d_22ens_45GP5GP5GP5GPHW501
d_23ens_4ATPATPATPATPHX502

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.999999072018, 0.000315172795719, 0.00132537885071), (-0.000315451194104, -0.999999928227, -0.000209848129806), (0.00132531261716, -0.000210266027412, 0.999999099667)366.522061377, 366.856727352, -0.169087877179
2given(-0.999999540918, -0.000121693697247, -0.000950449875392), (0.000122083485232, -0.999999908473, -0.000410061684377), (-0.000950399886477, -0.000410177530358, 0.999999464247)366.946658829, 366.821145093, 0.260492839025
3given(-0.99999974872, -0.000350946340503, -0.000615952101443), (0.000351371048884, -0.999999700535, -0.000689542553066), (-0.000615709924551, -0.000689758807534, 0.999999572567)366.983386319, 366.864984586, 0.24299579012
4given(-0.999999890708, 0.000439549440756, 0.000159314379808), (-0.000439581164168, -0.999999883555, -0.0001991443111), (0.000159226827486, -0.000199214320935, 0.99999996748)366.671265014, 366.904577021, 0.0107463425065

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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
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Msm GMPR with GMP and ATP at pH 6.6 / Type: COMPLEX / Entity ID: #1 / 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 with 2 mM GMP and 5 mM ATP 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 / Cs: 2.7 mm / 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
14PHENIX1.21rc1_4985model refinement
15Coot0.9.8.1 ELmodel refinement
16ISOLDE1.5model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107511 / 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: 38.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001428840
ELECTRON MICROSCOPYf_angle_d0.412539424
ELECTRON MICROSCOPYf_chiral_restr0.04014632
ELECTRON MICROSCOPYf_plane_restr0.00345208
ELECTRON MICROSCOPYf_dihedral_angle_d12.56810488
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints2.40376923566E-12
ens_2d_2BBELECTRON MICROSCOPYNCS constraints1.47171855315E-10
ens_3d_2GGELECTRON MICROSCOPYNCS constraints1.05534989812E-12
ens_4d_2FFELECTRON MICROSCOPYNCS constraints2.4625340412E-12

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