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- EMDB-12938: Cryo-EM structure of Medicago truncatula HISN5 protein -

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Basic information

Entry
Database: EMDB / ID: EMD-12938
TitleCryo-EM structure of Medicago truncatula HISN5 protein
Map data
Sample
  • Complex: Medicago truncatula HISN5 protein
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: water
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRuszkowski M / Witek W
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/D/NZ1/03630 Poland
CitationJournal: To Be Published
Title: Cryo-EM and crystal structures of a herbicide development target, HISN5
Authors: Witek W / Ruszkowski M
History
DepositionMay 13, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.076
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.076
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oj5
  • Surface level: 0.076
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oj5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12938.png

Downloads & links

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Map

FileDownload / File: emd_12938.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.076 / Movie #1: 0.076
Minimum - Maximum-0.27863917 - 0.49912426
Average (Standard dev.)1.6332258e-05 (±0.016990839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z302.720302.720302.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ560560560
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.2790.4990.000

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Supplemental data

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Sample components

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Entire : Medicago truncatula HISN5 protein

EntireName: Medicago truncatula HISN5 protein
Components
  • Complex: Medicago truncatula HISN5 protein
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: Medicago truncatula HISN5 protein

SupramoleculeName: Medicago truncatula HISN5 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Imidazoleglycerol-phosphate dehydratase
Source (natural)Organism: Medicago truncatula (barrel medic)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Imidazoleglycerol-phosphate dehydratase

MacromoleculeName: Imidazoleglycerol-phosphate dehydratase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: imidazoleglycerol-phosphate dehydratase
Source (natural)Organism: Medicago truncatula (barrel medic)
Molecular weightTheoretical: 22.692453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSTFPIDSGA RIGEMKRVTK ETNVSVKINL DGTGVADNSS GIPFLDHMLD QLASHGLFDV HVKATGDTHI DDHHTNEDVA LAIGTALLQ ALGDRKGINR FGNFSAPLDE ALVHVSLDLS GRPHLGYDLN IPTQRVGKYD TQLVEHFFQS LVNTSGMTLH I RQFSGTNS ...String:
MSTFPIDSGA RIGEMKRVTK ETNVSVKINL DGTGVADNSS GIPFLDHMLD QLASHGLFDV HVKATGDTHI DDHHTNEDVA LAIGTALLQ ALGDRKGINR FGNFSAPLDE ALVHVSLDLS GRPHLGYDLN IPTQRVGKYD TQLVEHFFQS LVNTSGMTLH I RQFSGTNS HHIIEATFKA FARALRQATE YDTRRRGTIP SSKGVLSRS

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 48 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 931 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 1008 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229366
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ezj

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7oj5:
Cryo-EM structure of Medicago truncatula HISN5 protein

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