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- PDB-7ntm: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 ... -

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Basic information

Entry
Database: PDB / ID: 7ntm
TitleCryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
ComponentsAlcohol dehydrogenase 1
KeywordsOXIDOREDUCTASE / ADH1 / tetramer / S.cerevisiae
Function / homology
Function and homology information


methylglyoxal reductase (NADH) / amino acid catabolic process to alcohol via Ehrlich pathway / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / pyruvate fermentation to ethanol / butanol dehydrogenase (NAD+) activity / ethanol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase (NAD+) activity / allyl-alcohol dehydrogenase ...methylglyoxal reductase (NADH) / amino acid catabolic process to alcohol via Ehrlich pathway / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / pyruvate fermentation to ethanol / butanol dehydrogenase (NAD+) activity / ethanol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase (NAD+) activity / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / alcohol dehydrogenase / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsNzigou Mandouckou, J.A. / Carroni, M. / Haeggstrom, J.Z. / Thulasingam, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-02818 Sweden
CitationJournal: To Be Published
Title: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
Authors: Nzigou Mandouckou, J.A. / Carroni, M. / Haeggstrom, J.Z. / Thulasingam, M.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ncs_dom_lim
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase 1
B: Alcohol dehydrogenase 1
D: Alcohol dehydrogenase 1
C: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,56312
Polymers147,0404
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12070 Å2
ΔGint-284 kcal/mol
Surface area53160 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23C
14B
24D
15B
25C
16D
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 347 / Label seq-ID: 1 - 347

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22DC
13AA
23CD
14BB
24DC
15BB
25CD
16DC
26CD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alcohol dehydrogenase 1 / Alcohol dehydrogenase I / YADH-1


Mass: 36759.906 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00330, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
Type: COMPLEX
Details: Stable homotetramer, composed of four monomers labelled as A, B, C and D.
Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.147 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 130 mradians
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14964
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

SoftwareName: REFMAC / Version: 5.8.0257 / Classification: refinement
EM software
IDNameVersionCategory
1Warp40particle selection
2EPU2.7image acquisition
4Warp40CTF correction
7MOLREPmodel fitting
9cryoSPARCv2.15.041initial Euler assignment
10cryoSPARCv2.15.041final Euler assignment
12cryoSPARCv2.15.0413D reconstruction
15MOLREPmolecular replacement
19REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 639189
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222802 / Symmetry type: POINT
Atomic model buildingB value: 123 / Protocol: BACKBONE TRACE / Space: REAL
Details: Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. ...Details: Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. This model was docked into our Cryo-EM map using MolRep (Brown et al, 2014). The resulting starting model was manually adjusted in Coot (Emsley et al, 2010). REFMAC 5 (Brown et al, 2014) used for structure model refinement.
Atomic model buildingPDB-ID: 5ENV

5env


Pdb chain-ID: A / Accession code: 5ENV / Pdb chain residue range: 1-347 / Source name: PDB / Type: experimental model
RefinementResolution: 2.86→242.88 Å / Cor.coef. Fo:Fc: 0.997 / SU B: 0.244 / SU ML: 0.005 / ESU R: 0.012
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.04464 --
obs0.04464 1282621 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 54.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Total: 10336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0910.01210548
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg6.761.62114300
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.09151384
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.56923.67436
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.792151716
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.7921532
ELECTRON MICROSCOPYr_chiral_restr0.5820.21352
ELECTRON MICROSCOPYr_gen_planes_refined0.0320.027976
ELECTRON MICROSCOPYr_gen_planes_other
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_it7.1345.5245548
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it6.5718.216928
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it8.9365.3855000
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined8.79540930
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A195640.11
12B195640.11
21A194980.11
22D194980.11
31A195440.1
32C195440.1
41B196740.1
42D196740.1
51B196220.1
52C196220.1
61D196620.09
62C196620.09
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.075 94631 -
obs--100 %

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