[English] 日本語
Yorodumi
- EMDB-44489: Cryo-EM Structure of GCN2 HRSL Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44489
TitleCryo-EM Structure of GCN2 HRSL Domain
Map data
Sample
  • Complex: GCN2 HRSL Domain
    • Protein or peptide: non-specific serine/threonine protein kinase
KeywordsKinase / Homodimer / Regulatory Domain / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation in response to stress / DNA damage checkpoint signaling / eukaryotic translation initiation factor 2alpha kinase activity / non-specific serine/threonine protein kinase / ATP binding / nucleus / cytosol
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain profile. / RWD / RWD domain / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / : ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain profile. / RWD / RWD domain / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / : / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSolorio-Kirpichyan KM / Golovenko D / Xiao F / Yan N / Korostelev AA / Korennykh AV
Funding support United States, France, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM110161-01 United States
Burroughs Wellcome FundAWD1004002 United States
The Vallee Foundation Inc.1013579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007388 United States
Human Frontier Science Program (HFSP)LT000754 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of GCN2 HisRS-Like Domain
Authors: Solorio-Kirpichyan KM / Golovenko D / Xiao F / Yan N / Korostelev AA / Korennykh AV
History
DepositionApr 16, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44489.png

Downloads & links

-
Map

FileDownload / File: emd_44489.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.16984165 - 0.45297754
Average (Standard dev.)0.004280999 (±0.017557615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_44489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GCN2 HRSL Domain

EntireName: GCN2 HRSL Domain
Components
  • Complex: GCN2 HRSL Domain
    • Protein or peptide: non-specific serine/threonine protein kinase

-
Supramolecule #1: GCN2 HRSL Domain

SupramoleculeName: GCN2 HRSL Domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 116 KDa

-
Macromolecule #1: non-specific serine/threonine protein kinase

MacromoleculeName: non-specific serine/threonine protein kinase / type: protein_or_peptide / ID: 1 / Details: Sequences for unresolved loops were deleted / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 190.970547 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSMSNLTLEQ YYEIQKLEME AIQSIYMDDF TDLTKRHSSW DKHPQIIFEV RLRSQESKPA ESSLDLHVVL PSTYPHASPQ ITFKHVVNV PDGQLNKVRK DIKEIHQRAK GQEIIYEIII AVQEILEDSQ KRVVTDSLED QRLQRIKDEE ERMKREEEQK L KQREKQKM ...String:
MSMSNLTLEQ YYEIQKLEME AIQSIYMDDF TDLTKRHSSW DKHPQIIFEV RLRSQESKPA ESSLDLHVVL PSTYPHASPQ ITFKHVVNV PDGQLNKVRK DIKEIHQRAK GQEIIYEIII AVQEILEDSQ KRVVTDSLED QRLQRIKDEE ERMKREEEQK L KQREKQKM QEQQYIDELF QKELAKRLDD DVADDNDKEI DLLPPPELTA SGQAFIFPRP ITAKLPNNSH YKFRAVIQPQ PI TLCDDPL SFANQMLVKP YIPAESPLYN VLKSSDKLDS IQYLLSEIIL DNPYFNTSNG KKEIALLEKD LESVLQVTHD NVC SLYAFH VERVGKNSAT FQWKIRLLTE YSQFNSLNDV VTSVGFVNLY TARGWILRLL EGLENLHKHG IAHKLIDMHT VQLT KDTDF GTTLPKFIHP SYGYSILSMI CRYPNKHGVK LEFPESKWTA PELIKFKGSK PQRKTDIWQL AVLFIVIITG VDTTL NYRS PGDFLESVEM DEALYDFLRK MLNPEPKQRL TPLELLPMKF LRTNIDPSWN KLNLYPDTSH SSRLLSNVAS SSGTQV LHS RTTSRASTDG GRRRSFNIGS RFSSLTSTSR SRYATDFEEI AVLGKGAYGQ VVKARNALDS RYYAIKKIRH SEEKLST IL SEVMLLASLN HRYVVRYYAA WLEEENSYTD SNAIDSDDDS STGSDLESDL DSDITRSSDG LSSRNRSLAH LNSNNWDF I SNSFQGSYPE IVFGNSSDED IEDGCDVSAS VDEKAGADST MDETEEKDNV TDMKFNKIKR QNGRFGSQKS SLKSTLFIQ MEYCENRTLY DLIHTESLNN QREEYWRLFR QILEALSYIH SQGIIHRDLK PMNIFIDESR NIKIGDFGLA KNVQKPQESL GRDSFASAG SSGDLTSAIG TALYVASEII TSHGNYNEKV DMYSLGVIFF EMIYPFDTGM ERVDVLKKLR SVDVEFPSDF D EKKLPTEK KIIRLLLDHD PTKRPSASAL LRSGWVPVKN QDELIKEALK NISDPSSPWQ QQVRESLFSQ PYHLSNDILF DL SRTDTTP FLQLLRAQMM DEVTKIFRRH GAIENNEPPM IFPKAPIYST QNVYEVLDRG GSVLQLQYDL TYPMARYLSK NPN TTSKQY RMQYVFRPSE SNHSSTEPRK FGEVDFDIIS NTTTDSAVHD AECLKVVDEI VSAFPVFTKT NVTLVLNHSD ILDG VFDFC NIDKAQRSLV SHMLSQLGFG KTFKDLKADL KTQLNISSTA LNDLELFDFK SDLDTAKKRL EKHLVDSPYL KRVEE ALVY ISKVVDYFKP LGVTRNVVIA PLSNYNNGFY KGGLMFQSVF DSGRSRSLIS AGGRYDNLIS LIARPSGGKL NHIQKA VGF NLAWETMFLI VKNYFKLAGG RSTKKISKGL KLTNSEWKPK RCEVLISSFS NSLLNTIGIE VISKLWKAGI SADIVRD CF SVEDVITAAQ KDGVDWIVLI KQQNYSISNN KRRYKPFKVK NLSSNLDSDM DFEEFLLTYE DSFSKDSTND SMNKEDYF N EYDDRNRWDD NSSQERSQDG ETDNLSSNGP QKVIYIPNPA TRAKGKPSKK DKWVYEESAR NASKQLIHSL SSVPIFAVD AIRDETLEII SITSLAQKDE WLRKVFGSAA NSAPRSFATS IYNNLSKEAA KGGRWAIVHC NKTGKSCVVD LQR

UniProtKB: eIF-2-alpha kinase GCN2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
350.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
2.0 mMMgCl2magnesium chloride
5.0 mMC4H10O2S2DTT
0.1 %Triton-x 100
1.0 %C3H8O3Glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9048 / Average exposure time: 5.9 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1697401
CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 215101
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 185957 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

+
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