[English] 日本語
Yorodumi
- PDB-8v1y: Composite map of AMPylated GlnA bound to hinT -

+
Open data


ID or keywords:

Loading...

-
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 / cytoplasm / cytosol
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. / HIT domain ...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. / HIT domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Histidine triad, conserved site / Glutamine synthetase, catalytic domain / HIT domain signature. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more