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- EMDB-17966: Structure of human apo ALDH1A1 determined by cryoEM at 100 keV -

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Basic information

Entry
Database: EMDB / ID: EMD-17966
TitleStructure of human apo ALDH1A1 determined by cryoEM at 100 keV
Map data
Sample
  • Complex: Human apo ALDH1A1
    • Protein or peptide: Aldehyde dehydrogenase 1A1
  • Ligand: CHLORIDE ION
KeywordsOxidoreductase Aldehyde dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / Fructose catabolism / aldehyde metabolic process / Ethanol oxidation / RA biosynthesis pathway / aldehyde dehydrogenase (NAD+) / androgen binding / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase (NAD+) activity / retinol metabolic process / negative regulation of cold-induced thermogenesis / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMcMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y ...McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y / Hutchings KA / Gittins O / Sobhy M / Wells T / El-Gomati MM / Dalby J / Meffert M / Schulze-Briese C / Henderson R / Russo CJ
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Medical Research Council (MRC, United Kingdom)MC U105184322 United Kingdom
Wellcome Trust220526/B/20/Z United Kingdom
Engineering and Physical Sciences Research CouncilR122522 United Kingdom
Innovate UK103806 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure determination by cryoEM at 100 keV.
Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo /
Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
History
DepositionJul 17, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17966.png

Downloads & links

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Map

FileDownload / File: emd_17966.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.28 Å		0.84 Å/pix.
x 320 pix.
= 269.28 Å		0.84 Å/pix.
x 320 pix.
= 269.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8415 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.15267889 - 0.24959537
Average (Standard dev.)0.000060494087 (±0.005385387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17966_msk_1.map
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Half map: #1

Fileemd_17966_half_map_1.map
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Half map: #2

Fileemd_17966_half_map_2.map
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Sample components

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Entire : Human apo ALDH1A1

EntireName: Human apo ALDH1A1
Components
  • Complex: Human apo ALDH1A1
    • Protein or peptide: Aldehyde dehydrogenase 1A1
  • Ligand: CHLORIDE ION

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Supramolecule #1: Human apo ALDH1A1

SupramoleculeName: Human apo ALDH1A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aldehyde dehydrogenase 1A1

MacromoleculeName: Aldehyde dehydrogenase 1A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: aminobutyraldehyde dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.99298 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYYHHHHHH LESTSLYKKA GSAAAPFTSS SGTPDLPVLL TDLKIQYTKI FINNEWHDSV SGKKFPVFNP ATEEELCQVE EGDKEDVDK AVKAARQAFQ IGSPWRTMDA SERGRLLYKL ADLIERDRLL LATMESMNGG KLYSNAYLND LAGCIKTLRY C AGWADKIQ ...String:
MSYYHHHHHH LESTSLYKKA GSAAAPFTSS SGTPDLPVLL TDLKIQYTKI FINNEWHDSV SGKKFPVFNP ATEEELCQVE EGDKEDVDK AVKAARQAFQ IGSPWRTMDA SERGRLLYKL ADLIERDRLL LATMESMNGG KLYSNAYLND LAGCIKTLRY C AGWADKIQ GRTIPIDGNF FTYTRHEPIG VCGQIIPWNF PLVMLIWKIG PALSCGNTVV VKPAEQTPLT ALHVASLIKE AG FPPGVVN IVPGYGPTAG AAISSHMDID KVAFTGSTEV GKLIKEAAGK SNLKRVTLEL GGKSPCIVLA DADLDNAVEF AHH GVFYHQ GQCCIAASRI FVEESIYDEF VRRSVERAKK YILGNPLTPG VTQGPQIDKE QYDKILDLIE SGKKEGAKLE CGGG PWGNK GYFVQPTVFS NVTDEMRIAK EEIFGPVQQI MKFKSLDDVI KRANNTFYGL SAGVFTKDID KAITISSALQ AGTVW VNCY GVVSAQCPFG GFKMSGNGRE LGEYGFHEYT EVKTVTVKIS QKNS

UniProtKB: Aldehyde dehydrogenase 1A1

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

BufferpH: 7.4
GridModel: UltrAuFoil R0./1 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1400/HR + YPS FEG
Image recordingFilm or detector model: DECTRIS SINGLA (1k x 1k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

13256

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32968
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4wj9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-8pvh:
Structure of human apo ALDH1A1 determined by cryoEM at 100 keV

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