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- EMDB-28217: Cryo-EM structure of the human PRDX4-ErP46 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28217
TitleCryo-EM structure of the human PRDX4-ErP46 complex
Map data
Sample
  • Complex: H6PD
    • Protein or peptide: Peroxiredoxin-4
    • Protein or peptide: Thioredoxin domain-containing protein 5
KeywordsPeroxiredoxin-4 / OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / I-kappaB phosphorylation / protein disulfide-isomerase / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / I-kappaB phosphorylation / protein disulfide-isomerase / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / molecular sequestering activity / extracellular matrix organization / lysosomal lumen / cell redox homeostasis / protein maturation / hydrogen peroxide catabolic process / male gonad development / azurophil granule lumen / protein folding / response to oxidative stress / secretory granule lumen / spermatogenesis / molecular adaptor activity / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol
Similarity search - Function
: / Disulphide isomerase / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site ...: / Disulphide isomerase / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Peroxiredoxin-4 / Thioredoxin domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 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 22, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28217.png

Downloads & links

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Map

FileDownload / File: emd_28217.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.55984354 - 1.0265205
Average (Standard dev.)-0.00007237072 (±0.03274565)
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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Mask #1

Fileemd_28217_msk_1.map
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Additional map: Unsharpened map

Fileemd_28217_additional_1.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_28217_half_map_1.map
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Half map: #1

Fileemd_28217_half_map_2.map
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Sample components

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Entire : H6PD

EntireName: H6PD
Components
  • Complex: H6PD
    • Protein or peptide: Peroxiredoxin-4
    • Protein or peptide: Thioredoxin domain-containing protein 5

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Supramolecule #1: H6PD

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

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Macromolecule #1: Peroxiredoxin-4

MacromoleculeName: Peroxiredoxin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: thioredoxin-dependent peroxiredoxin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.578873 KDa
SequenceString: MEALPLLAAT TPDHGRHRRL LLLPLLLFLL PAGAVQGWET EERPRTREEE CHFYAGGQVY PGEASRVSVA DHSLHLSKAK ISKPAPYWE GTAVIDGEFK ELKLTDYRGK YLVFFFYPLD FTFVCPTEII AFGDRLEEFR SINTEVVACS VDSQFTHLAW I NTPRRQGG ...String:
MEALPLLAAT TPDHGRHRRL LLLPLLLFLL PAGAVQGWET EERPRTREEE CHFYAGGQVY PGEASRVSVA DHSLHLSKAK ISKPAPYWE GTAVIDGEFK ELKLTDYRGK YLVFFFYPLD FTFVCPTEII AFGDRLEEFR SINTEVVACS VDSQFTHLAW I NTPRRQGG LGPIRIPLLS DLTHQISKDY GVYLEDSGHT LRGLFIIDDK GILRQITLND LPVGRSVDET LRLVQAFQYT DK HGEVCPA GWKPGSETII PDPAGKLKYF DKLN

UniProtKB: Peroxiredoxin-4

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Macromolecule #2: Thioredoxin domain-containing protein 5

MacromoleculeName: Thioredoxin domain-containing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.687727 KDa
SequenceString: MPARPGRLLP LLARPAALTA LLLLLLGHGG GGRWGARAQE AAAAAADGPP AADGEDGQDP HSKHLYTADM FTHGIQSAAH FVMFFAPWC GHCQRLQPTW NDLGDKYNSM EDAKVYVAKV DCTAHSDVCS AQGVRGYPTL KLFKPGQEAV KYQGPRDFQT L ENWMLQTL ...String:
MPARPGRLLP LLARPAALTA LLLLLLGHGG GGRWGARAQE AAAAAADGPP AADGEDGQDP HSKHLYTADM FTHGIQSAAH FVMFFAPWC GHCQRLQPTW NDLGDKYNSM EDAKVYVAKV DCTAHSDVCS AQGVRGYPTL KLFKPGQEAV KYQGPRDFQT L ENWMLQTL NEEPVTPEPE VEPPSAPELK QGLYELSASN FELHVAQGDH FIKFFAPWCG HCKALAPTWE QLALGLEHSE TV KIGKVDC TQHYELCSGN QVRGYPTLLW FRDGKKVDQY KGKRDLESLR EYVESQLQRT ETGATETVTP SEAPVLAAEP EAD KGTVLA LTENNFDDTI AEGITFIKFY APWCGHCKTL APTWEELSKK EFPGLAGVKI AEVDCTAERN ICSKYSVRGY PTLL LFRGG KKVSEHSGGR DLDSLHRFVL SQAKDEL

UniProtKB: Thioredoxin domain-containing protein 5

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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: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22035
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-8eky:
Cryo-EM structure of the human PRDX4-ErP46 complex

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