[English] 日本語
Yorodumi
- EMDB-33410: Deterget-solubilized E. coli RseP(L358C) mutant in complex with Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33410
TitleDeterget-solubilized E. coli RseP(L358C) mutant in complex with Fab
Map data
Sample
  • Complex: Binary complex of E. coli RseP(L358C) mutant with Fab
    • Complex: RseP
      • Protein or peptide: E. coli RseP(L358C) mutant
    • Complex: FabFragment antigen-binding
      • Protein or peptide: Heavy chain of Fab
      • Protein or peptide: Light chain of Fab
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 14.0 Å
AuthorsAruga R / Hirose M / Hirose T / Katagiri S / Iwasaki K / Kato T / Nogi T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Adv / Year: 2022
Title: Mechanistic insights into intramembrane proteolysis by site-2 protease homolog RseP.
Authors: Yuki Imaizumi / Kazunori Takanuki / Takuya Miyake / Mizuki Takemoto / Kunio Hirata / Mika Hirose / Rika Oi / Tatsuya Kobayashi / Kenichi Miyoshi / Rie Aruga / Tatsuhiko Yokoyama / Shizuka ...Authors: Yuki Imaizumi / Kazunori Takanuki / Takuya Miyake / Mizuki Takemoto / Kunio Hirata / Mika Hirose / Rika Oi / Tatsuya Kobayashi / Kenichi Miyoshi / Rie Aruga / Tatsuhiko Yokoyama / Shizuka Katagiri / Hiroaki Matsuura / Kenji Iwasaki / Takayuki Kato / Mika K Kaneko / Yukinari Kato / Michiko Tajiri / Satoko Akashi / Osamu Nureki / Yohei Hizukuri / Yoshinori Akiyama / Terukazu Nogi /
Abstract: Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal ...Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments.
History
DepositionMay 9, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateSep 7, 2022-
Current statusSep 7, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33410.png

Downloads & links

-
Map

FileDownload / File: emd_33410.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.07837174 - 0.07731751
Average (Standard dev.)-3.895599e-05 (±0.0030235336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_33410_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_33410_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #3

Fileemd_33410_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #4

Fileemd_33410_additional_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33410_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33410_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Binary complex of E. coli RseP(L358C) mutant with Fab

EntireName: Binary complex of E. coli RseP(L358C) mutant with Fab
Components
  • Complex: Binary complex of E. coli RseP(L358C) mutant with Fab
    • Complex: RseP
      • Protein or peptide: E. coli RseP(L358C) mutant
    • Complex: FabFragment antigen-binding
      • Protein or peptide: Heavy chain of Fab
      • Protein or peptide: Light chain of Fab

-
Supramolecule #1: Binary complex of E. coli RseP(L358C) mutant with Fab

SupramoleculeName: Binary complex of E. coli RseP(L358C) mutant with Fab / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: RseP

SupramoleculeName: RseP / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: Fab

SupramoleculeName: Fab / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: E. coli RseP(L358C) mutant

MacromoleculeName: E. coli RseP(L358C) mutant / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLSFLWDLAS FIVALGVLIT VHGFGHFWV ARRCGVRVER F SIGFGKAL WRRTDKLGTE YV IALIPLG GYVKMLDERA EPV VPELRH HAFNNKSVGQ RAAI IAAGP VANFIFAIFA YWLVF IIGV PGVRPVVGEI AANSIA AEA QIAPGTELKA VDGIETP DW ...String:
MLSFLWDLAS FIVALGVLIT VHGFGHFWV ARRCGVRVER F SIGFGKAL WRRTDKLGTE YV IALIPLG GYVKMLDERA EPV VPELRH HAFNNKSVGQ RAAI IAAGP VANFIFAIFA YWLVF IIGV PGVRPVVGEI AANSIA AEA QIAPGTELKA VDGIETP DW DAVRLQLVDK IGDESTTI T VAPFGSDQRR DVKLDLRHW AFEPDKEDPV SSLGIRPRGP QIEPVLENV QPNSAASKAG L QAGDRIVK VDGQPLTQWV TF VMLVRDN PGKSLALEIE RQG SPLSLT LIPESKPGNG KAIG FVGIE PKVIPLPDEY KVVRQ YGPF NAIVEATDKT WQLMKL TVS MLGKLITGDV KLNNCSG PI SIAKGAGMTA ELGVVYYL P FLALISVNLG IINLFPLPV LDGGHLLFLA IEKIKGGPVS ERVQDFCYR IGSILLVLLM G LALFNDFS RLGTENLYFQ

-
Macromolecule #2: Heavy chain of Fab

MacromoleculeName: Heavy chain of Fab / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: QVQLQQSRAE LARPGASVKM SCKASGYTFT TYTMQWVKQR P GQALEWIG YINPGSGYAK NNQKFKDKAT LTADKSSSTA YMQLSSLTSD DSAVYYCARS GS FFDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGS LSSGVH ...String:
QVQLQQSRAE LARPGASVKM SCKASGYTFT TYTMQWVKQR P GQALEWIG YINPGSGYAK NNQKFKDKAT LTADKSSSTA YMQLSSLTSD DSAVYYCARS GS FFDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGS LSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSETVT CNVAHPASST KVDKKIVPRD C

-
Macromolecule #3: Light chain of Fab

MacromoleculeName: Light chain of Fab / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: DIVLTQSPAI LSVTPGDSVS LSCRASQSVS SNLHWYQQRS HESPRLLIT YAFQSISGIP SRFSGNGSGT DFTLNINSVE TEDFGMYFCQ QSNSWPYTFG G GTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG VL NSWTDQD ...String:
DIVLTQSPAI LSVTPGDSVS LSCRASQSVS SNLHWYQQRS HESPRLLIT YAFQSISGIP SRFSGNGSGT DFTLNINSVE TEDFGMYFCQ QSNSWPYTFG G GTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG VL NSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
StainingType: NEGATIVE / Material: Uranium accetate
GridMaterial: COPPER

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3279209
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 73152 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 5 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 71271

+
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