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- EMDB-0207: Cryo-EM structure of the hydrazine dehydrogenase from Kuenia stut... -

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Basic information

Entry
Database: EMDB / ID: EMD-0207
TitleCryo-EM structure of the hydrazine dehydrogenase from Kuenia stuttgartiensis in the decameric state
Map data
Sample
  • Complex: Hydrazine dehydrogenase
    • Protein or peptide: Hydrazine dehydrogenase
Biological speciesCandidatus Kuenenia stuttgartiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsParey K / Barends TRM / Prinz S / Mohd A / Dietl A
CitationJournal: Sci Adv / Year: 2019
Title: A 192-heme electron transfer network in the hydrazine dehydrogenase complex.
Authors: M Akram / A Dietl / U Mersdorf / S Prinz / W Maalcke / J Keltjens / C Ferousi / N M de Almeida / J Reimann / B Kartal / M S M Jetten / K Parey / T R M Barends /
Abstract: Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive ...Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
History
DepositionAug 19, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseApr 10, 2019-
UpdateMay 1, 2019-
Current statusMay 1, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0207.png

Downloads & links

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Map

FileDownload / File: emd_0207.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 350 pix.
= 381.5 Å		1.09 Å/pix.
x 350 pix.
= 381.5 Å		1.09 Å/pix.
x 350 pix.
= 381.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.03850354 - 0.19968663
Average (Standard dev.)0.0018866669 (±0.009233065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 381.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z381.500381.500381.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0390.2000.002

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Supplemental data

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Sample components

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Entire : Hydrazine dehydrogenase

EntireName: Hydrazine dehydrogenase
Components
  • Complex: Hydrazine dehydrogenase
    • Protein or peptide: Hydrazine dehydrogenase

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Supramolecule #1: Hydrazine dehydrogenase

SupramoleculeName: Hydrazine dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
Molecular weightTheoretical: 2.0 MDa

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Macromolecule #1: Hydrazine dehydrogenase

MacromoleculeName: Hydrazine dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: hydrazine dehydrogenase
Source (natural)Organism: Candidatus Kuenenia stuttgartiensis (bacteria)
SequenceString: MRKFLKVTLA SALIGCGVIG TVSSLMVKEA KAVEIITHWV PHEVYGMPGE PDNSGKVFFS GLKAKYMGY PKDAQRSPYP GKYSKFWKTL PAYRYYIPDY MYNRDEVRPS NPIKGTFKLE Q CVACHSVM TPGIVRDYNK SAHSKAEPAP TGCDTCHGNN HQKLTMPSSK ...String:
MRKFLKVTLA SALIGCGVIG TVSSLMVKEA KAVEIITHWV PHEVYGMPGE PDNSGKVFFS GLKAKYMGY PKDAQRSPYP GKYSKFWKTL PAYRYYIPDY MYNRDEVRPS NPIKGTFKLE Q CVACHSVM TPGIVRDYNK SAHSKAEPAP TGCDTCHGNN HQKLTMPSSK ACGTAECHET QY NEQGQGG IGSHASCSSF AQVECAWSIE RPPGDTAGCT FCHTSPEERC STCHQRHQFD PAV ARRSEQ CKTCHWGKDH RDWEAYDIGL HGTVYQVNKW DTEQFDFSKK LSDADYVGPT CQYC HMRGG HHNVQRASIV YTSMGMSMAD RGAPLWKEKR DRWVSICDDC HSPRFARENL QAMDE SVKD ASLKYRETFK VAEDLLIDGV LDPMPKDLCP DWSGQHIWSL KIGAYHDGEA YGGTTG ESG EFRMSNCTDV ERLCFESVGY FQTYIYKGMA HGSWNDATYS DGSFGMDRWL VNVKQNA SR ARRLAALEKK VGISWQPEQF WKTGEWLDQL TGPYIVKNHP GKTIFDLCPD PGWLDTHH A PAEEVEYIER KLKELGITAG SHSAHHHESG HDPAARSMKE H

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 25.0 mM / Component - Formula: HEPES / Details: 25 mM HEPES/KOH, pH 7.5, 25 mM KCl
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsGlutaraldehyde cross-linked particles

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 452 / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45872 / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: -2.75 µm / Nominal defocus min: -0.75 µm / Nominal magnification: 200000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10332
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 2071
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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