[English] 日本語
Yorodumi
- EMDB-11861: Helical reconstruction of nitrite oxidoreductase from anammox bacteria -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11861
TitleHelical reconstruction of nitrite oxidoreductase from anammox bacteria
Map data
Sample
  • Complex: Nitrite oxidoreductase
    • Protein or peptide: Nitrite oxidoreductase subunit A
    • Protein or peptide: Nitrite oxidoreductase subunit B
    • Protein or peptide: Nitrite oxidoreductase subunit C
    • Protein or peptide: Conserved hypothetical (Monoheme) protein
Function / homology
Function and homology information


nitrate reductase / anammoxosome / nitrate reductase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / heme binding / metal ion binding
Similarity search - Function
DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / 4Fe-4S dicluster domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. ...DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / 4Fe-4S dicluster domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Nitrite oxidoreductase subunit C / Nitrite oxidoreductase subunit B / Nitrite oxidoreductase subunit A
Similarity search - Component
Biological speciesCandidatus Kuenenia stuttgartiensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsParey K
CitationJournal: Nat Microbiol / Year: 2021
Title: Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex.
Authors: Tadeo Moreno Chicano / Lea Dietrich / Naomi M de Almeida / Mohd Akram / Elisabeth Hartmann / Franziska Leidreiter / Daniel Leopoldus / Melanie Mueller / Ricardo Sánchez / Guylaine H L ...Authors: Tadeo Moreno Chicano / Lea Dietrich / Naomi M de Almeida / Mohd Akram / Elisabeth Hartmann / Franziska Leidreiter / Daniel Leopoldus / Melanie Mueller / Ricardo Sánchez / Guylaine H L Nuijten / Joachim Reimann / Kerstin-Anikó Seifert / Ilme Schlichting / Laura van Niftrik / Mike S M Jetten / Andreas Dietl / Boran Kartal / Kristian Parey / Thomas R M Barends /
Abstract: Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) ...Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein's electron transport chain, and elucidate the electron transfer pathways within the complex.
History
DepositionOct 20, 2020-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.037
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.037
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11861.png

Downloads & links

-
Map

FileDownload / File: emd_11861.map.gz / Format: CCP4 / Size: 81.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.037
Minimum - Maximum-0.18947661 - 0.34682587
Average (Standard dev.)-2.3824283e-13 (±0.027077423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin1310133
Dimensions226424223
Spacing223226424
CellA: 186.651 Å / B: 189.162 Å / C: 354.888 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z223226424
origin x/y/z0.0000.0000.000
length x/y/z186.651189.162354.888
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S321
start NC/NR/NS0131133
NC/NR/NS424226223
D min/max/mean-0.1890.347-0.000

-
Supplemental data

-
Mask #1

Fileemd_11861_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_11861_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11861_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11861_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nitrite oxidoreductase

EntireName: Nitrite oxidoreductase
Components
  • Complex: Nitrite oxidoreductase
    • Protein or peptide: Nitrite oxidoreductase subunit A
    • Protein or peptide: Nitrite oxidoreductase subunit B
    • Protein or peptide: Nitrite oxidoreductase subunit C
    • Protein or peptide: Conserved hypothetical (Monoheme) protein

-
Supramolecule #1: Nitrite oxidoreductase

SupramoleculeName: Nitrite oxidoreductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
Molecular weightTheoretical: 230 kDa/nm

-
Macromolecule #1: Nitrite oxidoreductase subunit A

MacromoleculeName: Nitrite oxidoreductase subunit A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: nitrate reductase
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
SequenceString: MKLTRRAFLQ VAGATGATLT LAKNAMAFRL LKPAVVVDNP LDTYPDRRWE SVYRDQYQYD RTFTYCCSP NDTHACRIRA FVRNNVMMRV EQNYDHQNYS DLYGNKATRN WNPRMCLKGY T FHRRVYGP YRLRYPLIRK GWKRWADDGF PELTPENKTK YMFDNRGNDE ...String:
MKLTRRAFLQ VAGATGATLT LAKNAMAFRL LKPAVVVDNP LDTYPDRRWE SVYRDQYQYD RTFTYCCSP NDTHACRIRA FVRNNVMMRV EQNYDHQNYS DLYGNKATRN WNPRMCLKGY T FHRRVYGP YRLRYPLIRK GWKRWADDGF PELTPENKTK YMFDNRGNDE LLRASWDEAF TY ASKGIIH ITKKYSGPEG AQKLIDQGYP KEMVDRMQGA GTRTFKGRGG MGLLGVIGKY GMY RFNNCL AIVDAHNRGV GPDQALGGRN WSNYTWHGDQ APGHPFSHGL QTSDVDMNDV RFSK LLIQT GKNLIENKMP EAHWVTEVME RGGKIVVITP EYSPSAQKAD YWIPIRNNTD TALFL GITK ILIDNKWYDA DYVKKFTDFP LLIRTDTLKR VSPKDIIPNY KLQDISDGPS YHIQGL KDE QREIIGDFVV WDAKSKGPKA ITRDDVGETL VKKGIDPVLE GSFKLKTIDG KEIEVMT LL EMYKIHLRDY DIDSVVSMTN SPKDLIERLA KDIATIKPVA IHYGEGVNHY FHATLMNR S YYLPVMLTGN VGYFGSGSHT WAGNYKAGNF QASKWSGPGF YGWVAEDVFK PNLDPYASA KDLNIKGRAL DEEVAYWNHS ERPLIVNTPK YGRKVFTGKT HMPSPTKVLW FTNVNLINNA KHVYQMLKN VNPNIEQIMS TDIEITGSIE YADFAFPANS WVEFQEFEIT NSCSNPFIQI W GKTGITPV YESKDDVKIL AGMASKLGEL LRDKRFEDNW KFAIEGRASV YINRLLDGST TM KGYTCED ILNGKYGEPG VAMLLFRTYP RHPFWEQVHE SLPFYTPTGR LQAYNDEPEI IEY GENFIV HREGPEATPY LPNAIVSTNP YIRPDDYGIP ENAEYWEDRT VRNIKKSWEE TKKT KNFLW EKGYHFYCVT PKSRHTVHSQ WAVTDWNFIW NNNFGDPYRM DKRMPGVGEH QIHIH PQAA RDLGIEDGDY VYVDANPADR PYEGWKPNDS FYKVSRLMLR AKYNPAYPYN CTMMKH SAW ISSDKTVQAH ETRPDGRALS PSGYQSSFRY GSQQSITRDW SMPMHQLDSL FHKAKIG MK FIFGFEADNH CINTVPKETL VKITKAENGG MGGKGVWDPV KTGYTAGNEN DFMKKFLN G ELIKVDA

-
Macromolecule #2: Nitrite oxidoreductase subunit B

MacromoleculeName: Nitrite oxidoreductase subunit B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: nitrate reductase
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
SequenceString: MTLVHNWHLG RRMEYPYFES RPKHQFAAVF NINRCIACQT CTMACKSTWT FNKGQEFMWW NNVETKPYG GFPQSWDVKT LKLIDSPDNI WYTDDKDKET SQYGTGAPYG TYEGDTIFEV A KKKNINQW AVGYIPEDKE WRSPNFGEDT AKSSNQPGEY STLPEHSRWF ...String:
MTLVHNWHLG RRMEYPYFES RPKHQFAAVF NINRCIACQT CTMACKSTWT FNKGQEFMWW NNVETKPYG GFPQSWDVKT LKLIDSPDNI WYTDDKDKET SQYGTGAPYG TYEGDTIFEV A KKKNINQW AVGYIPEDKE WRSPNFGEDT AKSSNQPGEY STLPEHSRWF FYLQRICNHC TY PGCLAAC PRKAIYKRKE DGIVLIDQKR CRGYRKCVEQ CPYKKPMYRG LTRVSEKCIA CYP RIEGRD SLTDGRPMET RCMSACVGQI RLQGFLDDNP KNPITWLIRH QKIALPLYPQ FGTE PNIYY IPPRWAPRAY LRQMFGPGVD EAIEKFMVPS RELLAVMSLF RMTQTIVYEY KIEEG PKVF ETEIHGKKFT MYNDTVIGFG EDGKEVVRTT VEEPIHIRPD KHYNSI

-
Macromolecule #3: Nitrite oxidoreductase subunit C

MacromoleculeName: Nitrite oxidoreductase subunit C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: nitrate reductase
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
SequenceString: MKKFYRLLGS SSVALLGCLF LSVALCIAEE AEGVKGVAEE ELTPAKEVLN VKYMQIDVPA HITVGALEG AFKNAEGVQV KLQKQDKAFP NGGGSVNSAE IKAIHDGITI YFQVIWDDAT D NKQAIATQ EFRDGAALMF PLGKITISPE EPFSPRMGDR QKPVNLWHWK ...String:
MKKFYRLLGS SSVALLGCLF LSVALCIAEE AEGVKGVAEE ELTPAKEVLN VKYMQIDVPA HITVGALEG AFKNAEGVQV KLQKQDKAFP NGGGSVNSAE IKAIHDGITI YFQVIWDDAT D NKQAIATQ EFRDGAALMF PLGKITISPE EPFSPRMGDR QKPVNLWHWK ADWEADLLAT GG IEECPAR YPNMHDDFST NPHSVNYHKG VIQSAAELSG GYAAHNLLSL PRGRAVEDLN AEG FGTLTS QDHQDVDGCS KFENKKWTVV FCRSLNTGDP LDVQFVPGES TYFNMAVWNG DRED RNGQK NISIQWHPLS LERIAWQ

-
Macromolecule #4: Conserved hypothetical (Monoheme) protein

MacromoleculeName: Conserved hypothetical (Monoheme) protein / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
SequenceString:
MGMIKMKYVV FGVLALIMLG IGNSMFTHKA MGSSGKAAEH EGVIEPTQEL MKDIEKRLTN MLSGILENN LKYVANEAGA VVDQSYKISE FFFPFDPKKN EWFERAGIDP KDAGKITKLR E EFALFQSG IVYKALNVRK MAMEGSQEET LKAFADLIEK TCFACHKKNR DWLFDQPGSH GP GR

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES/NaOH
250.0 mMNaClSodium chloridesodium cloride
10.0 mMEGTA/NaOH
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -2.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 1753 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 9275
CTF correctionSoftware - Name: CTFFIND
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 108.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 121 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5379
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