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- PDB-8ry8: CryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8,... -

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Basic information

Entry
Database: PDB / ID: 8ry8
TitleCryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8, 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: 2.96 Å
AuthorsDolezal, M. / Kouba, T. / Svachova, H. / 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 C
d_2ens_1chain A
d_1ens_2chain B
d_2ens_2chain D
d_1ens_3chain G
d_2ens_3chain E
d_1ens_4chain H
d_2ens_4chain F
d_1ens_5chain H
d_2ens_5chain B
d_3ens_5chain C
d_4ens_5chain D
d_5ens_5chain E
d_6ens_5chain F
d_7ens_5chain G
d_8ens_5chain A

NCS domain segments:

Component-ID: 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-IDEns-IDAuth asym-IDLabel asym-ID
d_1ens_1CC
d_2ens_1AA
d_1ens_2BB
d_2ens_2DD
d_1ens_3GG
d_2ens_3EE
d_1ens_4HH
d_2ens_4FF
d_1ens_5HH
d_2ens_5BB
d_3ens_5CC
d_4ens_5DD
d_5ens_5EE
d_6ens_5FF
d_7ens_5GG
d_8ens_5AA

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.999986916794, 0.00187157332122, 0.00476061484891), (-0.00187278573516, -0.999998215027, -0.000250230828386), (0.004760138026, -0.000259143166144, 0.999988636901)468.776978965, 470.620182629, -0.917289052013
2given(-0.999999592686, 8.23324330158E-5, -0.000898804015591), (-8.14226118716E-5, -0.999999484363, -0.00101224720772), (-0.00089888689291, -0.00101217361245, 0.999999083753)470.307671002, 470.392024982, 0.419795524684
3given(-0.999998652913, 0.00129238367424, -0.00101188722307), (-0.00129095290042, -0.999998167947, -0.00141334440001), (-0.00101371195246, -0.00141203619737, 0.99999848927)470.123603442, 470.882622925, 0.581915753548
4given(-0.99999887932, 0.000856700124793, 0.00122777174427), (-0.000857808552007, -0.99999922478, -0.000902553769624), (0.00122699757455, -0.000903605951252, 0.999998838986)469.591574891, 470.613759759, -0.0348336281392
5given(0.980480731264, 0.196603792712, -0.00211761914031), (0.196600420309, -0.980482220922, -0.00169976200336), (-0.00241046757433, 0.00125025907899, -0.999996313242)-41.0180567761, 419.842797116, 471.629412777
6given(0.197059664096, -0.980387833569, -0.00268040613811), (-0.980385415883, -0.197067335294, 0.00298356903973), (-0.00345327528231, 0.00203988997367, -0.999991956837)419.956232494, 511.021820792, 471.673787733
7given(-0.980461978772, -0.196685561858, 0.00301627903211), (-0.196677712248, 0.980464441783, 0.00271217702664), (-0.00349080039983, 0.00206595159478, -0.999991773044)510.93637534, 50.0753785933, 471.660692964
8given(-0.000457171477143, -0.999998167909, -0.00185880955066), (0.999997038722, -0.000452726265273, -0.00239114733027), (0.00239030141756, -0.00185989721057, 0.99999541361)470.774579332, 0.79827286454, -0.0814158214123
9given(-0.99999887932, 0.000856700124793, 0.00122777174427), (-0.000857808552007, -0.99999922478, -0.000902553769624), (0.00122699757455, -0.000903605951252, 0.999998838986)469.591574891, 470.613759759, -0.0348336281392
10given(-0.000836201293371, 0.999999290673, 0.00084818660208), (-0.999999172708, -0.000837029628444, 0.000976710933221), (0.00097742019773, -0.000847369173436, 0.999999163307)-0.0434458303655, 470.0852668, 0.000401796661663
11given(-0.198908388806, 0.98001589212, -0.00207462151758), (0.980015479514, 0.198902529419, -0.00272831508643), (-0.00226114467598, -0.00257584595936, -0.999994126104)52.0281128821, -41.30524136, 472.617760828

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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 7.8 / 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: 7.8
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 7.8, 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 / 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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191909 / 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: 92.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001827752
ELECTRON MICROSCOPYf_angle_d0.445337776
ELECTRON MICROSCOPYf_chiral_restr0.0414496
ELECTRON MICROSCOPYf_plane_restr0.00355000
ELECTRON MICROSCOPYf_dihedral_angle_d3.06934064
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints7.95277560281E-13
ens_2d_2BBELECTRON MICROSCOPYNCS constraints4.8733442593E-11
ens_3d_2GGELECTRON MICROSCOPYNCS constraints8.00357726514E-13
ens_4d_2HHELECTRON MICROSCOPYNCS constraints8.39583496316E-13
ens_5d_2HHELECTRON MICROSCOPYNCS constraints7.83546951776E-13
ens_5d_3HHELECTRON MICROSCOPYNCS constraints1.91331556106E-11
ens_5d_4HHELECTRON MICROSCOPYNCS constraints2.17203560146E-11
ens_5d_5HHELECTRON MICROSCOPYNCS constraints5.88600819661E-13
ens_5d_6HHELECTRON MICROSCOPYNCS constraints8.39583496316E-13
ens_5d_7HHELECTRON MICROSCOPYNCS constraints7.44313142145E-13
ens_5d_8HHELECTRON MICROSCOPYNCS constraints4.20117696293E-10

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