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- PDB-8v1y: Composite map of AMPylated GlnA bound to hinT -

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Basic information

Entry
Database: PDB / ID: 8v1y
TitleComposite map of AMPylated GlnA bound to hinT
Components
  • Glutamine synthetase
  • Purine nucleoside phosphoramidase
KeywordsLIGASE/HYDROLASE / AMPylation / adenyltransferase / nucleotide binding protein / LIGASE-HYDROLASE complex
Function / homology
Function and homology information


ammonia assimilation cycle / D-alanine catabolic process / nitrogen utilization / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / nucleotide binding ...ammonia assimilation cycle / D-alanine catabolic process / nitrogen utilization / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / nucleotide binding / protein homodimerization activity / ATP binding / metal ion binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Histidine triad (HIT) protein / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Histidine triad (HIT) protein / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Glutamine synthetase / Purine nucleoside phosphoramidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHan, Y. / Sreelatha, A. / Gonzalez, A. / Chen, Z.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK123194 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR190106 United States
Welch FoundationI-2046-20200401 United States
Welch FoundationI-2046-20230405 United States
CitationJournal: To Be Published
Title: Composite map of AMPylated GlnA bound to hinT
Authors: Gonzalez, A. / Sreelatha, A.
History
DepositionNov 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Purine nucleoside phosphoramidase
D: Purine nucleoside phosphoramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,1146
Polymers132,4204
Non-polymers6942
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamine synthetase / GS / Glutamate--ammonia ligase / Glutamine synthetase I beta / GSI beta


Mass: 52572.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glnA, b3870, JW3841 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9C5, glutamine synthetase
#2: Protein Purine nucleoside phosphoramidase / Histidine triad nucleotide binding protein HinT / HIT protein


Mass: 13637.674 Da / Num. of mol.: 2 / Mutation: H101N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hinT, ycfF, b1103, JW1089 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ACE7, Hydrolases; Acting on phosphorus-nitrogen bonds
#3: 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
Has ligand of interestY
Has protein modificationY

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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: GlnA dimer binding to hinT dimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.125 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2SerialEM4image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
12RELION4.0.1classification
13RELION4.0.13D reconstruction
14PHENIX1.20.1-4487model refinement
15REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225422 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementResolution: 2.7→2.7 Å / Cor.coef. Fo:Fc: 0.877 / SU B: 16.198 / SU ML: 0.292 / ESU R: 0.305
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31449 --
obs0.31449 121185 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 81.607 Å2
Refinement stepCycle: 1 / Total: 8918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0129116
ELECTRON MICROSCOPYr_bond_other_d00.0168543
ELECTRON MICROSCOPYr_angle_refined_deg1.2221.65512347
ELECTRON MICROSCOPYr_angle_other_deg0.3741.57619693
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.6451125
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.771560
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.867101516
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0620.21358
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0210729
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022055
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it13.0516.5014536
ELECTRON MICROSCOPYr_mcbond_other13.0516.5014536
ELECTRON MICROSCOPYr_mcangle_it19.65111.7585649
ELECTRON MICROSCOPYr_mcangle_other19.65211.7615650
ELECTRON MICROSCOPYr_scbond_it16.7799.0744580
ELECTRON MICROSCOPYr_scbond_other16.7779.0764581
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other27.98215.4126699
ELECTRON MICROSCOPYr_long_range_B_refined34.20787.7736661
ELECTRON MICROSCOPYr_long_range_B_other34.20687.7836662
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.448 8971 -
obs--100 %

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