[English] 日本語
Yorodumi
- EMDB-37318: DegQ-b-casein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37318
TitleDegQ-b-casein complex
Map data
Sample
  • Complex: DegQ-beta casein complex
    • Protein or peptide: peptidase Do
    • Protein or peptide: Casein fragment
    • Protein or peptide: Casein fragment
KeywordsComplex / HYDROLASE
Function / homology
Function and homology information


peptidase Do / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLee I-G / Jeon H
Funding support1 items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02
CitationJournal: To Be Published
Title: Structure of E. coli Deg-b-casein complex
Authors: Lee I-G / Jeon H
History
DepositionAug 28, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37318.png

Downloads & links

-
Map

FileDownload / File: emd_37318.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.44 Å/pix.
x 720 pix.
= 314.46 Å		0.44 Å/pix.
x 720 pix.
= 314.46 Å		0.44 Å/pix.
x 720 pix.
= 314.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.43675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0248
Minimum - Maximum-0.016317097 - 0.19825412
Average (Standard dev.)0.00061606726 (±0.0031531376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 314.46 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37318_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37318_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DegQ-beta casein complex

EntireName: DegQ-beta casein complex
Components
  • Complex: DegQ-beta casein complex
    • Protein or peptide: peptidase Do
    • Protein or peptide: Casein fragment
    • Protein or peptide: Casein fragment

-
Supramolecule #1: DegQ-beta casein complex

SupramoleculeName: DegQ-beta casein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: peptidase Do

MacromoleculeName: peptidase Do / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.361047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFE GLGSGVIINA SKGYVLTNNH VINQAQKISI QLNDGREFDA KLIGSDDQSD IALLQIQNPS KLTQIAIADS D KLRVGDFA ...String:
MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFE GLGSGVIINA SKGYVLTNNH VINQAQKISI QLNDGREFDA KLIGSDDQSD IALLQIQNPS KLTQIAIADS D KLRVGDFA VAVGNPFGLG QTATSGIVSA LGRSGLNLEG LENFIQTDAS INRGNAGGAL LNLNGELIGI NTAILAPGGG SV GIGFAIP SNMARTLAQQ LIDFGEIKRG LLGIKGTEMS ADIAKAFNLD VQRGAFVSEV LPGSGSAKAG VKAGDIITSL NGK PLNSFA ELRSRIATTE PGTKVKLGLL RNGKPLEVEV TLDTSTSSSA SAEMITPALE GATLSDGQLK DGGKGIKIDE VVKG SPAAQ AGLQKDDVII GVNRDRVNSI AEMRKVLAAK PAIIALQIVR GNESIYLLMR LWHHHHHH

UniProtKB: peptidase Do

-
Macromolecule #2: Casein fragment

MacromoleculeName: Casein fragment / type: protein_or_peptide / ID: 2
Details: We would like to assign these residues as unknown (UNK).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
Macromolecule #3: Casein fragment

MacromoleculeName: Casein fragment / type: protein_or_peptide / ID: 3
Details: We would like to assign these residues as unknown (UNK)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 613.749 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3stj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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