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- EMDB-26425: Structure of G6PD-WT dimer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26425
TitleStructure of G6PD-WT dimer
Map data
Sample
  • Complex: G6PD protein
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase
Keywordsapo protein / OXIDOREDUCTASE
Function / homology
Function and homology information


negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / lipid metabolic process / response to organic cyclic compound / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWei X / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of G6PD-WT dimer
Authors: Wei X / Marmorstein R
History
DepositionMar 12, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26425.png

Downloads & links

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Map

FileDownload / File: emd_26425.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-3.287453 - 3.820141
Average (Standard dev.)0.00019032795 (±0.14413567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 149.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26425_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26425_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : G6PD protein

EntireName: G6PD protein
Components
  • Complex: G6PD protein
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase

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Supramolecule #1: G6PD protein

SupramoleculeName: G6PD protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Glucose-6-phosphate 1-dehydrogenase

MacromoleculeName: Glucose-6-phosphate 1-dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glucose-6-phosphate dehydrogenase (NADP+)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.403754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEQVALSRT QVCGILREEL FQGDAFHQSD THIFIIMGAS GDLAKKKIYP TIWWLFRDGL LPENTFIVGY ARSRLTVADI RKQSEPFFK ATPEEKLKLE DFFARNSYVA GQYDDAASYQ RLNSHMNALH LGSQANRLFY LALPPTVYEA VTKNIHESCM S QIGWNRII ...String:
MAEQVALSRT QVCGILREEL FQGDAFHQSD THIFIIMGAS GDLAKKKIYP TIWWLFRDGL LPENTFIVGY ARSRLTVADI RKQSEPFFK ATPEEKLKLE DFFARNSYVA GQYDDAASYQ RLNSHMNALH LGSQANRLFY LALPPTVYEA VTKNIHESCM S QIGWNRII VEKPFGRDLQ SSDRLSNHIS SLFREDQIYR IDHYLGKEMV QNLMVLRFAN RIFGPIWNRD NIACVILTFK EP FGTEGRG GYFDEFGIIR DVMQNHLLQM LCLVAMEKPA STNSDDVRDE KVKVLKCISE VQANNVVLGQ YVGNPDGEGE ATK GYLDDP TVPRGSTTAT FAAVVLYVEN ERWDGVPFIL RCGKALNERK AEVRLQFHDV AGDIFHQQCK RNELVIRVQP NEAV YTKMM TKKPGMFFNP EESELDLTYG NRYKNVKLPD AYERLILDVF CGSQMHFVRS DELREAWRIF TPLLHQIELE KPKPI PYIY GSRGPTEADE LMKRVGFQYE GTYKWVNPHK LLEHHHHHH

UniProtKB: Glucose-6-phosphate 1-dehydrogenase

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 570405
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2bh9

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76546
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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