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- EMDB-3518: cryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-3518
Titlecryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3 Angstrom resolution
Map dataNone
Sample
  • Complex: F420 reducing hydrogenase Frh
    • Protein or peptide: F420-reducing hydrogenase, subunit alpha
    • Protein or peptide: F420-reducing hydrogenase, subunit beta
    • Protein or peptide: F420-reducing hydrogenase, subunit gamma
Biological speciesMethanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (archaea) / Methanothermobacter marburgensis str. Marburg (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBaerland N / Mills DJ / Vonck J
CitationJournal: To Be Published
Title: cryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3 Angstrom resolution
Authors: Baerland N / Mills DJ / Vonck J
History
DepositionNov 29, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseDec 7, 2016-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3518.png

Downloads & links

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Map

FileDownload / File: emd_3518.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 261.6 Å		1.09 Å/pix.
x 240 pix.
= 261.6 Å		1.09 Å/pix.
x 240 pix.
= 261.6 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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.27017736 - 0.41748783
Average (Standard dev.)0.00011792962 (±0.023981089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.600261.600261.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2700.4170.000

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Supplemental data

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Half map: dodecameric F420-reducing hydrogenase, half map 2

Fileemd_3518_half_map_1.map
Annotationdodecameric F420-reducing hydrogenase, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: dodecameric F420-reducing hydrogenase, half map 1

Fileemd_3518_half_map_2.map
Annotationdodecameric F420-reducing hydrogenase, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F420 reducing hydrogenase Frh

EntireName: F420 reducing hydrogenase Frh
Components
  • Complex: F420 reducing hydrogenase Frh
    • Protein or peptide: F420-reducing hydrogenase, subunit alpha
    • Protein or peptide: F420-reducing hydrogenase, subunit beta
    • Protein or peptide: F420-reducing hydrogenase, subunit gamma

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Supramolecule #1: F420 reducing hydrogenase Frh

SupramoleculeName: F420 reducing hydrogenase Frh / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (archaea)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: F420-reducing hydrogenase, subunit alpha

MacromoleculeName: F420-reducing hydrogenase, subunit alpha / type: protein_or_peptide / ID: 1 / Details: contains a [NiFe] cluster / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase
Source (natural)Organism: Methanothermobacter marburgensis str. Marburg (archaea)
SequenceString: MSERIVISPT SRQEGHAELV MEVDDEGIVT KGRYFSITPV RGLEKMVTGK APETAPVMVQ RICGVCPIP HTLASVEAID DSLDIEVPKA GRLLRELTLA AHHVNSHAIH HFLIAPDFVP E NLMADAIN SVSEIRKNAQ YVVDMVAGEG IHPSDVRIGG MADNITELAR ...String:
MSERIVISPT SRQEGHAELV MEVDDEGIVT KGRYFSITPV RGLEKMVTGK APETAPVMVQ RICGVCPIP HTLASVEAID DSLDIEVPKA GRLLRELTLA AHHVNSHAIH HFLIAPDFVP E NLMADAIN SVSEIRKNAQ YVVDMVAGEG IHPSDVRIGG MADNITELAR KRLYARLKQL KP KVNEHVE LMIGLIEDKG LPEGLGVHNQ PTLASHQIYG DRTKFDLDRF TEIMPESWYD DPE IAKRAC STIPLYDGRN VEVGPRARMV EFQGFKERGV VAQHVARALE MKTALSRAIE ILDE LDTSA PVRADFDERG TGKLGIGAIE APRGLDVHMA KVENGKIQFY SALVPTTWNI PTMGP ATEG FHHEYGPHVI RAYDPCLSCA THVMVVDDED KSVIKNEMVK I

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Macromolecule #2: F420-reducing hydrogenase, subunit beta

MacromoleculeName: F420-reducing hydrogenase, subunit beta / type: protein_or_peptide / ID: 2 / Details: FrhB contains a [4Fe4S] cluster and an FAD. / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase
Source (natural)Organism: Methanothermobacter marburgensis str. Marburg (archaea)
SequenceString: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELK AAAGTKYTFS PNVMMLKKAV RQYGIEKLGT VAIPCQTMGI RKMQTYPFGV R FLADKIKL LVGIYCMENF PYTSLQTFIC EKLGVSMELV EKMDIGKGKF ...String:
MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELK AAAGTKYTFS PNVMMLKKAV RQYGIEKLGT VAIPCQTMGI RKMQTYPFGV R FLADKIKL LVGIYCMENF PYTSLQTFIC EKLGVSMELV EKMDIGKGKF WVYTQDDVLT LP LKETHGY EQAGCKICKD YVAELADVST GSVGSPDGWS TVITRTDAGD SIFKQAVEAG LFE TKPIEE VKPGLGLLEK LAAQKKEKAE KNIAARKEMG LPTPF

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Macromolecule #3: F420-reducing hydrogenase, subunit gamma

MacromoleculeName: F420-reducing hydrogenase, subunit gamma / type: protein_or_peptide / ID: 3 / Details: FrhG contains three [4Fe4S] clusters / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase
Source (natural)Organism: Methanothermobacter marburgensis str. Marburg (archaea)
SequenceString: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELKA AAGTKYTFSP NVMMLKKAVR QYGIEKLGTV AIPCQTMGIR KMQTYPFGVR FLADKIKLLV GIYCMENFPY TSLQTFICEK LGVSMELVEK MDIGKGKFWV ...String:
MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELKA AAGTKYTFSP NVMMLKKAVR QYGIEKLGTV AIPCQTMGIR KMQTYPFGVR FLADKIKLLV GIYCMENFPY TSLQTFICEK LGVSMELVEK MDIGKGKFWV YTQDDVLTLP LKETHGYEQA GCKICKDYVA ELADVSTGSV GSPDGWSTVI TRTDAGDSIF KQAVEAGLFE TKPIEEVKPG LGLLEKLAAQ KKEKAEKNIA ARKEMGLPTP F

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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

Concentration0.7 mg/mL
BufferpH: 7.6 / Component:
ConcentrationName
50.0 mMTris
0.025 mMFAD
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 20 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-10 / Average exposure time: 8.0 sec. / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45871 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 47560
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

2513

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 36700
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4) / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4) / Details: relion
FSC plot (resolution estimation)

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