[English] 日本語
Yorodumi
- EMDB-29659: CryoEM structure of nuclear GAPDH under 8h Oxidative Stress -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29659
TitleCryoEM structure of nuclear GAPDH under 8h Oxidative Stress
Map dataGAPDH,Nuclear Oxidation 8h,D2
Sample
  • Complex: GAPDHGlyceraldehyde 3-phosphate dehydrogenase
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsGAPDH / energy / cytosolic protein / TRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex ...Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / microtubule cytoskeleton organization / cellular response to type II interferon / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / killing of cells of another organism / vesicle / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo (humans) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsChoi WY / Wu H / Cheng YF / Manglik A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM.
Authors: Wooyoung Choi / Hao Wu / Klaus Yserentant / Bo Huang / Yifan Cheng /
Abstract: CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor ...CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
History
DepositionFeb 1, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29659.png

Downloads & links

-
Map

FileDownload / File: emd_29659.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGAPDH,Nuclear Oxidation 8h,D2
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.0091
Minimum - Maximum-0.008813469 - 0.038337857
Average (Standard dev.)0.000070306756 (±0.0019736248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 200.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: GAPDH,Nuclear Oxidation 8h,single subunit analysis,inactive

Fileemd_29659_additional_1.map
AnnotationGAPDH,Nuclear Oxidation 8h,single subunit analysis,inactive
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GAPDH,Nuclear Oxidation 8h,single subunit analysis,inactive

Fileemd_29659_additional_2.map
AnnotationGAPDH,Nuclear Oxidation 8h,single subunit analysis,inactive
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined

Fileemd_29659_additional_3.map
AnnotationGAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined

Fileemd_29659_additional_4.map
AnnotationGAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined

Fileemd_29659_additional_5.map
AnnotationGAPDH,Nuclear Oxidation 8h,single subunit analysis,non defined
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GAPDH,Nuclear Oxidation 8h,D2,halfmap1

Fileemd_29659_half_map_1.map
AnnotationGAPDH,Nuclear Oxidation 8h,D2,halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GAPDH,Nuclear Oxidation 8h,D2,halfmap2

Fileemd_29659_half_map_2.map
AnnotationGAPDH,Nuclear Oxidation 8h,D2,halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GAPDH

EntireName: GAPDHGlyceraldehyde 3-phosphate dehydrogenase
Components
  • Complex: GAPDHGlyceraldehyde 3-phosphate dehydrogenase
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase

-
Supramolecule #1: GAPDH

SupramoleculeName: GAPDH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo (humans)

-
Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.983969 KDa
Recombinant expressionOrganism: Homo (humans)
SequenceString: GKVKVGVNGF GRIGRLVTRA AFNSGKVDIV AINDPFIDLN YMVYMFQYDS THGKFHGTVK AENGKLVING NPITIFQERD PSKIKWGDA GAEYVVESTG VFTTMEKAGA HLQGGAKRVI ISAPSADAPM FVMGVNHEKY DNSLKIISNA S(CSO)TTNCL AP LAKVIHDNFG ...String:
GKVKVGVNGF GRIGRLVTRA AFNSGKVDIV AINDPFIDLN YMVYMFQYDS THGKFHGTVK AENGKLVING NPITIFQERD PSKIKWGDA GAEYVVESTG VFTTMEKAGA HLQGGAKRVI ISAPSADAPM FVMGVNHEKY DNSLKIISNA S(CSO)TTNCL AP LAKVIHDNFG IVEGLMTTVH AITATQKTVD GPSGKLWRDG RGALQNIIPA STGAAKAVGK VIPELNGKLT GMAFRVPT A NVSVVDLTCR LEKPAKYDDI KKVVKQASEG PLKGILGYTE HQVVSSDFNS DTHSSTFDAG AGIALNDHFV KLISWYDNE FGYSNRVVDL MAHMASKE

UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: OTHER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 764164

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more