[English] 日本語
Yorodumi
- EMDB-61213: Cryo-EM structure of wild type Aquifex aeolicus RseP in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61213
TitleCryo-EM structure of wild type Aquifex aeolicus RseP in complex with Fab
Map data
Sample
  • Complex: RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab
    • Complex: Fab of mouse monoclonal antibody IgG 4A9
      • Protein or peptide: VH-CH1 region of mouse monoclonal antibody IgG 4A9
      • Protein or peptide: L chain of mouse monoclonal antibody IgG 4A9
    • Complex: RseP ortholog wild-type from Aquifex aeolicus
      • Protein or peptide: Putative zinc metalloprotease aq_1964
  • Ligand: ZINC ION
KeywordsProtease / HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964
Similarity search - Component
Biological speciesMus musculus (house mouse) / Aquifex aeolicus (strain VF5) (bacteria) / Aquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsAsahi K / Hirose M / Aruga R / Kato T / Nogi T
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K23825 Japan
Japan Society for the Promotion of Science (JSPS)22H02561 Japan
Japan Society for the Promotion of Science (JSPS)19H03170 Japan
Japan Society for the Promotion of Science (JSPS)26291016 Japan
Japan Society for the Promotion of Science (JSPS)22370039 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Cryo-EM structure of the bacterial intramembrane metalloprotease RseP in the substrate-bound state.
Authors: Kikuko Asahi / Mika Hirose / Rie Aruga / Yosuke Shimizu / Michiko Tajiri / Tsubasa Tanaka / Yuriko Adachi / Yukari Tanaka / Mika K Kaneko / Yukinari Kato / Satoko Akashi / Yoshinori Akiyama ...Authors: Kikuko Asahi / Mika Hirose / Rie Aruga / Yosuke Shimizu / Michiko Tajiri / Tsubasa Tanaka / Yuriko Adachi / Yukari Tanaka / Mika K Kaneko / Yukinari Kato / Satoko Akashi / Yoshinori Akiyama / Yohei Hizukuri / Takayuki Kato / Terukazu Nogi /
Abstract: Site-2 proteases (S2Ps), conserved intramembrane metalloproteases that maintain cellular homeostasis, are associated with chronic infection and persistence leading to multidrug resistance in ...Site-2 proteases (S2Ps), conserved intramembrane metalloproteases that maintain cellular homeostasis, are associated with chronic infection and persistence leading to multidrug resistance in bacterial pathogens. A structural model of how S2Ps discriminate and accommodate substrates could help us develop selective antimicrobial agents. We previously proposed that the S2P RseP unwinds helical substrate segments before cleavage, but the mechanism for accommodating a full-length membrane-spanning substrate remained unclear. Our present cryo-EM analysis of RseP (RseP) revealed that a substrate-like membrane protein fragment from the expression host occupied the active site while spanning a transmembrane cavity that is inaccessible via lateral diffusion. Furthermore, in vivo photocrosslinking supported that this substrate accommodation mode is recapitulated on the cell membrane. Our results suggest that the substrate accommodation by threading through a conserved membrane-associated region stabilizes the substrate-complex and contributes to substrate discrimination on the membrane.
History
DepositionAug 20, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61213.png

Downloads & links

-
Map

FileDownload / File: emd_61213.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.1985594 - 0.48858675
Average (Standard dev.)0.00026100434 (±0.018254424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61213_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61213_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab

EntireName: RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab
Components
  • Complex: RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab
    • Complex: Fab of mouse monoclonal antibody IgG 4A9
      • Protein or peptide: VH-CH1 region of mouse monoclonal antibody IgG 4A9
      • Protein or peptide: L chain of mouse monoclonal antibody IgG 4A9
    • Complex: RseP ortholog wild-type from Aquifex aeolicus
      • Protein or peptide: Putative zinc metalloprotease aq_1964
  • Ligand: ZINC ION

-
Supramolecule #1: RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab

SupramoleculeName: RseP ortholog wild-type from Aquifex aeolicus in complex with 4A9 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 50 KDa

-
Supramolecule #2: Fab of mouse monoclonal antibody IgG 4A9

SupramoleculeName: Fab of mouse monoclonal antibody IgG 4A9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: RseP ortholog wild-type from Aquifex aeolicus

SupramoleculeName: RseP ortholog wild-type from Aquifex aeolicus / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Aquifex aeolicus (strain VF5) (bacteria)

-
Macromolecule #1: Putative zinc metalloprotease aq_1964

MacromoleculeName: Putative zinc metalloprotease aq_1964 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 49.322203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (FME)GLIAFLILI GVLVWVHEFG HFLMAKLFRV KVEIFSIGFG PPIFRRQWGE TVYQIAALPL GGYVKLYGEE ENVHDP RAF STKKPWQKIL IALGGPLFNF LFTILVFALV YTAGVEVPKY LKEPVVVGYV QRDSIAQKIG IKPGDKIIKI (SNN)GY EVRTWE ...String:
(FME)GLIAFLILI GVLVWVHEFG HFLMAKLFRV KVEIFSIGFG PPIFRRQWGE TVYQIAALPL GGYVKLYGEE ENVHDP RAF STKKPWQKIL IALGGPLFNF LFTILVFALV YTAGVEVPKY LKEPVVVGYV QRDSIAQKIG IKPGDKIIKI (SNN)GY EVRTWE DLRDALIRLS LDGVKETTLF LERNGEVLHL TIKVPNVQKG EELGIAPLVK PVVGGVKKGS PADQVGIKPG DLIL EVNGK KINTWYELVE EVRKSQGKAI KLKILRNGKM IEKELIPAKD PKTGTYFIGL FPKTETVVEK KPFGEALASA VNRTW ELTV LTLKTIAGLI TGKVSFQTLG GPIAIAQIAG QAAQSGFIPY LVMMAFISLQ LGIFNLIPLP ILDGGLILLF AIEWLR GRP LPEKFKEYWQ RVGLAIIITL TIFVFINDIL RLLRGRGSHH HHHHHH

UniProtKB: Putative zinc metalloprotease aq_1964

-
Macromolecule #2: VH-CH1 region of mouse monoclonal antibody IgG 4A9

MacromoleculeName: VH-CH1 region of mouse monoclonal antibody IgG 4A9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.564592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSEVKLVESG GGLVQPGGSL RLSCVTSGFT FTDYYMSWVR QPPGKALEWL AFIRNKVNGY TTEYRASVKG RFTISRDSSQ SILYLQVNT LRAEDSATYY CARDRGGNGV YFDYWGQGTT LTVSSAKTTP PSVYPLAPGS AAQTNSMVTL GCLVKGYFPE P VTVTWNSG ...String:
GSEVKLVESG GGLVQPGGSL RLSCVTSGFT FTDYYMSWVR QPPGKALEWL AFIRNKVNGY TTEYRASVKG RFTISRDSSQ SILYLQVNT LRAEDSATYY CARDRGGNGV YFDYWGQGTT LTVSSAKTTP PSVYPLAPGS AAQTNSMVTL GCLVKGYFPE P VTVTWNSG SLSSGVHTFP AVLQSDLYTL SSSVTVPSST WPSETVTCNV AHPASSTKVD KKIVPRDCGG VAMPGAEDDV V

-
Macromolecule #3: L chain of mouse monoclonal antibody IgG 4A9

MacromoleculeName: L chain of mouse monoclonal antibody IgG 4A9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.734125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVG TDVAWYQQKP GQSPKLLIYW ASIRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYSSYPLTFG AGTKLELERA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVG TDVAWYQQKP GQSPKLLIYW ASIRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYSSYPLTFG AGTKLELERA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: CEOS, spherical aberration corrector
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 11400 / Average exposure time: 3.238 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.6470000000000002 µm / Calibrated defocus min: 0.162 µm / Calibrated magnification: 103703 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.019 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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: 1925238
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 88124
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 6 / Avg.num./class: 75707 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainPDB ID
chain_id: A, residue_range: 1-113, source_name: AlphaFold, initial_model_type: in silico model
chain_id: A, residue_range: 114-206, source_name: PDB, initial_model_type: experimental model

6akq

chain_id: A, residue_range: 207-298, source_name: PDB, initial_model_type: experimental model

3wkm

chain_id: A, residue_range: 299-429, source_name: AlphaFold, initial_model_type: in silico model
chain_id: H, source_name: PDB, initial_model_type: experimental model

8zay

chain_id: L, source_name: PDB, initial_model_type: experimental model

8zay

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9j82:
Cryo-EM structure of wild type Aquifex aeolicus RseP in complex with Fab

+
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