[English] 日本語
Yorodumi
- EMDB-53160: NorQD complex state 1 from Jhaorihella thermophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53160
TitleNorQD complex state 1 from Jhaorihella thermophila
Map datamain map
Sample
  • Complex: NorQD complex from J. thermophila
    • Protein or peptide: Nitric oxide reductase NorQ protein
    • Protein or peptide: Nitric oxide reductase NorD protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ Protein / MoxR / VWA domain / Nitric Oxide Reductase / CHAPERONE
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
: / CbbQ/NirQ/NorQ, C-terminal / CbbQ/NirQ/NorQ C-terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A ...: / CbbQ/NirQ/NorQ, C-terminal / CbbQ/NirQ/NorQ C-terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nitric oxide reductase NorQ protein / Nitric oxide reductase NorD protein
Similarity search - Component
Biological speciesJhaorihella thermophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKahle M / Appelgren S / Carroni M / Adelroth P / Wendler P
Funding support Germany, Sweden, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: NorQD - a MoxR like AAA+ complex with a twist
Authors: Kahle M / Appelgren S / Carroni M / Adelroth P / Wendler P
History
DepositionMar 15, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53160.png

Downloads & links

-
Map

FileDownload / File: emd_53160.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 243.648 Å		0.85 Å/pix.
x 288 pix.
= 243.648 Å		0.85 Å/pix.
x 288 pix.
= 243.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.20288873 - 0.42996424
Average (Standard dev.)0.0010071003 (±0.017749723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 243.64801 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53160_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened map

Fileemd_53160_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_53160_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_53160_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NorQD complex from J. thermophila

EntireName: NorQD complex from J. thermophila
Components
  • Complex: NorQD complex from J. thermophila
    • Protein or peptide: Nitric oxide reductase NorQ protein
    • Protein or peptide: Nitric oxide reductase NorD protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: NorQD complex from J. thermophila

SupramoleculeName: NorQD complex from J. thermophila / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Jhaorihella thermophila (bacteria)
Molecular weightTheoretical: 258 KDa

-
Macromolecule #1: Nitric oxide reductase NorQ protein

MacromoleculeName: Nitric oxide reductase NorQ protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Jhaorihella thermophila (bacteria)
Molecular weightTheoretical: 29.382672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDGSTTFGGA ATAPFYLPQA DECEVFAAAH ENDLPVLLKG PTGCGKTRFV AHMAQRLGRK LYTVACHDDL AAADLIGRYL LKGGETVWV DGPLTRAVRE GAICYLDQVV EARKDVTVVL HPLTDDRRIL PIDRTGEELE AAPGFMLVAS YNPGYQNILK T LKPSTRQR ...String:
MDGSTTFGGA ATAPFYLPQA DECEVFAAAH ENDLPVLLKG PTGCGKTRFV AHMAQRLGRK LYTVACHDDL AAADLIGRYL LKGGETVWV DGPLTRAVRE GAICYLDQVV EARKDVTVVL HPLTDDRRIL PIDRTGEELE AAPGFMLVAS YNPGYQNILK T LKPSTRQR FISIEFDFPH PDLETEVVAQ ESGLPLERCK PLIRLANKLR ALKGQDLEEG VSTRLVVYAA TLIAQGMNTD RA IRAAMIE PLTDDEDVKR GLLDLVTAVF G

UniProtKB: Nitric oxide reductase NorQ protein

-
Macromolecule #2: Nitric oxide reductase NorD protein

MacromoleculeName: Nitric oxide reductase NorD protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Jhaorihella thermophila (bacteria)
Molecular weightTheoretical: 71.726891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDRIEFEPWE PEETVGKLWH KFASRLDAPE AHEGAAVDLS EIGGRLAVLF RGLGGASSVE LRPVSPEISR HRLSWRRRLG AEAEAVPRA SFDGEVLRLP DRLAVFPSRE ANGALYVWLA ACAAHASDRV DQDDPLRADL AALAASRAMV AATLEDAPGL R PLYEGLCA ...String:
MDRIEFEPWE PEETVGKLWH KFASRLDAPE AHEGAAVDLS EIGGRLAVLF RGLGGASSVE LRPVSPEISR HRLSWRRRLG AEAEAVPRA SFDGEVLRLP DRLAVFPSRE ANGALYVWLA ACAAHASDRV DQDDPLRADL AALAASRAMV AATLEDAPGL R PLYEGLCA ALLHQRRVPD LPRDEAAVEA VIRNMLGDPA PLSDRAAAFQ AACAGDPLDP AITAPRKYRP FRPVPLWPEL RP VEFSEAG EVETREIEGT PEEAGEKTHR ARRRKSDQAE RRDSLILHKF EAILSWAEFL NLNRRVDDDD PDNAKKAADD QEE IGLGQI SKAPPTRLKL HLDLAPEDVD RERLSGRITY PEWDTRTGAY LPDHVCVLTS DVEAKPEQEA YAHDPAASRR IRAV RRQFE ALRPGRVTTR GHLDGDDLDI EAAVRAEVDR LASGEGSERI WLRSRPEARD LAVSILLDVS RSTESAVSGR AVIDI EREA LDALAWGLDA CGDDFAIHAF SSLKRHRVHV QRCKGFDEPM GPEVERRIGG LRPGFYTRLG AAIRHVSAEL SQQARK RRL LLVITDGKPN DLDHYEGRHG IEDTAMAVRE ARRAGHSVFG ITVDAKGKAW FSRMFGQGGF AVIPDPEKLI FALPQIY RQ LVGA

UniProtKB: Nitric oxide reductase NorD protein

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 50mM TRIS/HCl,150mM KCl
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.05 kPa / Details: PELCO easiGlow at 20mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 265840
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qhd:
NorQD complex state 1 from Jhaorihella thermophila

+
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