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- EMDB-52241: Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-52241
TitleCryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 closed subunits
Map data
Sample
  • Complex: S-adenosyl-L-homocysteine hydrolase
    • Protein or peptide: Adenosylhomocysteinase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ADENOSINE
KeywordsSAM-DEPENDENT METHYLATION / PROTEIN DYNAMICS / CRYOEM / HYDROLASE
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMalecki PH / Wozniak K / Ruszkowski M / Brzezinski K
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 4, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52241.png

Downloads & links

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Map

FileDownload / File: emd_52241.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0017664136 - 2.3198009
Average (Standard dev.)0.0030664194 (±0.039162815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52241_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52241_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52241_half_map_2.map
Projections & Slices
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Sample components

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Entire : S-adenosyl-L-homocysteine hydrolase

EntireName: S-adenosyl-L-homocysteine hydrolase
Components
  • Complex: S-adenosyl-L-homocysteine hydrolase
    • Protein or peptide: Adenosylhomocysteinase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ADENOSINE

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Supramolecule #1: S-adenosyl-L-homocysteine hydrolase

SupramoleculeName: S-adenosyl-L-homocysteine hydrolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Adenosylhomocysteinase

MacromoleculeName: Adenosylhomocysteinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: adenosylhomocysteinase
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 51.735031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSAVMTP AGFTDYKVAD ITLAAWGRRE LIIAESEMPA LMGLRRKYAG QQPLKGAKIL GCIHMTIQTG VLIETLVALG AEVRWSSCN IFSTQDQAAA AIAAAGIPVF AWKGETEEEY EWCIEQTILK DGQPWDANMV LDDGGDLTEI LHKKYPQMLE R IHGITEET ...String:
SNAMSAVMTP AGFTDYKVAD ITLAAWGRRE LIIAESEMPA LMGLRRKYAG QQPLKGAKIL GCIHMTIQTG VLIETLVALG AEVRWSSCN IFSTQDQAAA AIAAAGIPVF AWKGETEEEY EWCIEQTILK DGQPWDANMV LDDGGDLTEI LHKKYPQMLE R IHGITEET TTGVHRLLDM LKNGTLKVPA INVNDSVTKS KNDNKYGCRH SLNDAIKRGT DHLLSGKQAL VIGYGDVGKG SS QSLRQEG MIVKVAEVDP ICAMQACMDG FEVVSPYKNG INDGTEASID AALLGKIDLI VTTTGNVNVC DANMLKALKK RAV VCNIGH FDNEIDTAFM RKNWAWEEVK PQVHKIHRTG KDGFDAHNDD YLILLAEGRL VNLGNATGHP SRIMDGSFAN QVLA QIHLF EQKYADLPAA EKAKRLSVEV LPKKLDEEVA LEMVKGFGGV VTQLTPKQAE YIGVSVEGPF KPDTYRY

UniProtKB: Adenosylhomocysteinase

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #3: ADENOSINE

MacromoleculeName: ADENOSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADN
Molecular weightTheoretical: 267.241 Da
Chemical component information

ChemComp-ADN:
ADENOSINE

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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

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6384 / Average electron dose: 40.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8cfb

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8cfb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9hkz:
Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase with 2 wide open, 1 open and 1 closed subunits

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