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- EMDB-28232: Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional ... -

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Basic information

Entry
Database: EMDB / ID: EMD-28232
TitleCryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein
Map dataCryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein
Sample
  • Complex: H6PD
    • Protein or peptide: GDH/6PGL endoplasmic bifunctional protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH6PD / OXIDOREDUCTASE / HYDROLASE
Function / homology
Function and homology information


regulation of cortisol biosynthetic process / glucose-6-phosphate dehydrogenase [NAD(P)+] / 6-phosphogluconolactonase / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / 6-phosphogluconolactonase activity / glucose 1-dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / response to alcohol ...regulation of cortisol biosynthetic process / glucose-6-phosphate dehydrogenase [NAD(P)+] / 6-phosphogluconolactonase / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / 6-phosphogluconolactonase activity / glucose 1-dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / response to alcohol / sarcoplasmic reticulum / response to nutrient levels / glucose metabolic process / NADP binding / carbohydrate binding / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / 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 ...6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / 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 / NagB/RpiA transferase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
GDH/6PGL endoplasmic bifunctional protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsSu CC / Lyu M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2023
Title: High-resolution structural-omics of human liver enzymes.
Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu /
Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
History
DepositionSep 26, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28232.png

Downloads & links

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Map

FileDownload / File: emd_28232.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.1890504 - 1.5642397
Average (Standard dev.)-0.0002662865 (±0.026425334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_28232_additional_1.map
Annotationunsharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional...

Fileemd_28232_half_map_1.map
AnnotationCryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional...

Fileemd_28232_half_map_2.map
AnnotationCryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H6PD

EntireName: H6PD
Components
  • Complex: H6PD
    • Protein or peptide: GDH/6PGL endoplasmic bifunctional protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H6PD

SupramoleculeName: H6PD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GDH/6PGL endoplasmic bifunctional protein

MacromoleculeName: GDH/6PGL endoplasmic bifunctional protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glucose 1-dehydrogenase [NAD(P)+]
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.001578 KDa
SequenceString: MWNMLIVAMC LALLGCLQAQ ELQGHVSIIL LGATGDLAKK YLWQGLFQLY LDEAGRGHSF SFHGAALTAP KQGQELMAKA LESLSCPKD MAPSHCAEHK DQFLQLSQYR QLKTAEDYQA LNKDIEAQLQ HAGLREAGRI FYFSVPPFAY EDIARNINSS C RPGPGAWL ...String:
MWNMLIVAMC LALLGCLQAQ ELQGHVSIIL LGATGDLAKK YLWQGLFQLY LDEAGRGHSF SFHGAALTAP KQGQELMAKA LESLSCPKD MAPSHCAEHK DQFLQLSQYR QLKTAEDYQA LNKDIEAQLQ HAGLREAGRI FYFSVPPFAY EDIARNINSS C RPGPGAWL RVVLEKPFGH DHFSAQQLAT ELGTFFQEEE MYRVDHYLGK QAVAQILPFR DQNRKALDGL WNRHHVERVE II MKETVDA EGRTSFYEEY GVIRDVLQNH LTEVLTLVAM ELPHNVSSAE AVLRHKLQVF QALRGLQRGS AVVGQYQSYS EQV RRELQK PDSFHSLTPT FAAVLVHIDN LRWEGVPFIL MSGKALDERV GYARILFKNQ ACCVQSEKHW AAAQSQCLPR QLVF HIGHG DLGSPAVLVS RNLFRPSLPS SWKEMEGPPG LRLFGSPLSD YYAYSPVRER DAHSVLLSHI FHGRKNFFIT TENLL ASWN FWTPLLESLA HKAPRLYPGG AENGRLLDFE FSSGRLFFSQ QQPEQLVPGP GPAPMPSDFQ VLRAKYRESP LVSAWS EEL ISKLANDIEA TAVRAVRRFG QFHLALSGGS SPVALFQQLA TAHYGFPWAH THLWLVDERC VPLSDPESNF QGLQAHL LQ HVRIPYYNIH PMPVHLQQRL CAEEDQGAQI YAREISALVA NSSFDLVLLG MGADGHTASL FPQSPTGLDG EQLVVLTT S PSQPHRRMSL SLPLINRAKK VAVLVMGRMK REITTLVSRV GHEPKKWPIS GVLPHSGQLV WYMDYDAFLG

UniProtKB: GDH/6PGL endoplasmic bifunctional protein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis is from a heterogeneous and impure protein sample.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 29.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab initio reconstruction by cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196757
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8em2:
Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein

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