[English] 日本語
Yorodumi
- EMDB-33358: Cryo-EM structure of occupied ring subunit 4 (OR4) of GroEL from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33358
TitleCryo-EM structure of occupied ring subunit 4 (OR4) of GroEL from GroEL-UGT1A double occupied ring complex
Map dataPrimary EM-map of OR(4)-GroEL-UGT1A (unmasked)
Sample
  • Complex: GroEL-UGT1A double occupied ring complex
    • Complex: Occupied Ring subunit 4 (OR4) of GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: UDP-glucuronosyltransferase 1A (UGT1A)
Keywordscryogenic electron microscopy / single-particle analysis / molecular motion / structure-function relationship / focus classification / separating heterogeneity / GroEL / chaperone / unfolded protein
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsStapleton K / Takagi J / Mizohata E
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21am0101075 Japan
Japan Agency for Medical Research and Development (AMED)22ama121025j0001 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101066 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06513 Japan
Japan Science and TechnologyJPMJPR17GB Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05780 Japan
New Energy and Industrial Technology Development Organization (NEDO)JPNP18016 Japan
CitationJournal: To Be Published
Title: Unmasking GroEL: Structure, dynamics, and substrate binding revealed by single-particle cryo-EM
Authors: Stapleton KM / Mizobata T / Miyazaki N / Takatsuji T / Kato T / Iwasaki K / Standley DM / Kawamura T / Nakane T / Takagi J / Mizohata E
History
DepositionMay 1, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33358.png

Downloads & links

-
Map

FileDownload / File: emd_33358.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary EM-map of OR(4)-GroEL-UGT1A (unmasked)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.039217047 - 0.093780935
Average (Standard dev.)-0.00016465981 (±0.0056041484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_33358_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_33358_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional EM-map of a GroEL subunit that was...

Fileemd_33358_additional_1.map
AnnotationAdditional EM-map of a GroEL subunit that was used for modeling the atomic coordinates (subunit OR-4)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map-1 used for processing the Primary EM-map OR(4)-GroEL-UGT1A

Fileemd_33358_half_map_1.map
AnnotationHalf_map-1 used for processing the Primary EM-map OR(4)-GroEL-UGT1A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map-2 used for processing the Primary EM-map OR(4)-GroEL-UGT1A

Fileemd_33358_half_map_2.map
AnnotationHalf_map-2 used for processing the Primary EM-map OR(4)-GroEL-UGT1A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GroEL-UGT1A double occupied ring complex

EntireName: GroEL-UGT1A double occupied ring complex
Components
  • Complex: GroEL-UGT1A double occupied ring complex
    • Complex: Occupied Ring subunit 4 (OR4) of GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: UDP-glucuronosyltransferase 1A (UGT1A)

-
Supramolecule #1: GroEL-UGT1A double occupied ring complex

SupramoleculeName: GroEL-UGT1A double occupied ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #2: Occupied Ring subunit 4 (OR4) of GroEL

SupramoleculeName: Occupied Ring subunit 4 (OR4) of GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: The model was built in the additional EM-map of OR4-GroEL-UGT1A (masked)
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: UDP-glucuronosyltransferase 1A (UGT1A)

SupramoleculeName: UDP-glucuronosyltransferase 1A (UGT1A) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: all / Details: Model is not built
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 57.260504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV ...String:
AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV GKEGVITVED GTGLQDELDV VEGMQFDRGY LSPYFINKPE TGAVELESPF ILLADKKISN IREMLPVLEA VA KAGKPLL IIAEDVEGEA LATLVVNTMR GIVKVAAVKA PGFGDRRKAM LQDIATLTGG TVISEEIGME LEKATLEDLG QAK RVVINK DTTTIIDGVG EEAAIQGRVA QIRQQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGVVAGGG VALIRVASKL ADLRGQNEDQ NVGIKVALRA MEAPLRQIVL NCGEEPSVVA NTVKGGDGNY GYNAA TEEY GNMIDMGILD PTKVTRSALQ YAASVAGLMI TTECMVTDLP KNDAADLGAA GGMGGMGGMG GMM

UniProtKB: Chaperonin GroEL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration33 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Cloride
20.0 mMTris-HClTris Hydrochloride Acid

Details: Sample containing GorEL-UGT1A was made fresh and used without undergoing any freeze-thaw cycles to avoid degradation in the solution. The sample was in a buffer solution of 150mM NaCl, 20mM Tris-HCl at pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3 ul of 33 mg/ml GroEL-UGT1A was placed on Holey carbon Quanitifoil copper grids (300 mesh size R1.2/1.3) and blotted for 3 seconds (blot force =1).

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2951 / Average electron dose: 40.0 e/Å2
Details: Using a Titan KRIOS TEM operated at 300 kV, 2,951 movies were collected using the Falcon III DED in Counting mode at a magnification of 75000x corresponding to a pixel size of 0.87 Pixel/A ...Details: Using a Titan KRIOS TEM operated at 300 kV, 2,951 movies were collected using the Falcon III DED in Counting mode at a magnification of 75000x corresponding to a pixel size of 0.87 Pixel/A at the specimen level. All 2,951 movies were imported into the RELION pipeline and prepared for single-particle analysis
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1289236
Details: Parameters for auto picking (LoG) single particles from motion-corrected micrographs with estimated CTF parameters resulted in 1,289,236 particles picked (an average of 437 particles per ...Details: Parameters for auto picking (LoG) single particles from motion-corrected micrographs with estimated CTF parameters resulted in 1,289,236 particles picked (an average of 437 particles per micrograph). All particle images were then extracted with a box size of 300 pixels and a spherical mask diameter of 240 A for 2D classification.
Startup modelType of model: INSILICO MODEL
Details: The initial model was from a previously derived map generated from screening data of the same sample and grid
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 86029
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7xos:
Cryo-EM structure of occupied ring subunit 4 (OR4) of GroEL from GroEL-UGT1A double occupied ring complex

+
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