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- EMDB-22093: Vigna radiata complex I* peripheral arm -

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Basic information

Entry
Database: EMDB / ID: EMD-22093
TitleVigna radiata complex I* peripheral arm
Map dataVigna radiata complex I* peripheral arm.
Sample
  • Complex: Vigna radiata complex I* peripheral arm
    • Protein or peptide: Vigna radiata complex I* peripheral arm
Biological speciesVigna radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLetts JA / Maldonado M / Padavannil A / Long Z / Guo F
CitationJournal: Elife / Year: 2020
Title: Atomic structure of a mitochondrial complex I intermediate from vascular plants.
Authors: Maria Maldonado / Abhilash Padavannil / Long Zhou / Fei Guo / James A Letts /
Abstract: Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large ...Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC. For plants, limited availability of mitochondrial material has curbed detailed biochemical and structural studies of their mETC. Here, we present the cryoEM structure of the known CI assembly intermediate CI* from at 3.9 Å resolution. CI* contains CI's NADH-binding and CoQ-binding modules, the proximal-pumping module and the plant-specific γ-carbonic-anhydrase domain (γCA). Our structure reveals significant differences in core and accessory subunits of the plant complex compared to yeast, mammals and bacteria, as well as the details of the γCA domain subunit composition and membrane anchoring. The structure sheds light on differences in CI assembly across lineages and suggests potential physiological roles for CI* beyond assembly.
History
DepositionJun 1, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22093.png

Downloads & links

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Map

FileDownload / File: emd_22093.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVigna radiata complex I* peripheral arm.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04137164 - 0.112137124
Average (Standard dev.)0.0000043258 (±0.0017880722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.5984 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.833199218750.833199218750.83319921875
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z426.598426.598426.598
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0410.1120.000

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Supplemental data

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Mask #1

Fileemd_22093_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Vigna radiata complex I* peripheral arm half-map.

Fileemd_22093_half_map_1.map
AnnotationVigna radiata complex I* peripheral arm half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Vigna radiata complex I* peripheral arm half-map.

Fileemd_22093_half_map_2.map
AnnotationVigna radiata complex I* peripheral arm half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vigna radiata complex I* peripheral arm

EntireName: Vigna radiata complex I* peripheral arm
Components
  • Complex: Vigna radiata complex I* peripheral arm
    • Protein or peptide: Vigna radiata complex I* peripheral arm

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Supramolecule #1: Vigna radiata complex I* peripheral arm

SupramoleculeName: Vigna radiata complex I* peripheral arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Peripheral arm of complex I 800 kDa assembly intermediate (complex I*)
Source (natural)Organism: Vigna radiata (mung bean)

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Macromolecule #1: Vigna radiata complex I* peripheral arm

MacromoleculeName: Vigna radiata complex I* peripheral arm / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
SequenceString: MGFGLLASK ALRPTSRLLL SSQNPTIFLR TIVSKPQLCN PEASAAQPAQ PPPVDLPPRS P LAGARVHF ANPDDAIEVF VDGYPVKIPK GMTVLQACEV AGVDIPRFCY HSRLSIAGNC RM CLVEVEK SPKPVASCAM PALPGMKIKT DTPVAKKARE GVMEFLLMNH ...String:
MGFGLLASK ALRPTSRLLL SSQNPTIFLR TIVSKPQLCN PEASAAQPAQ PPPVDLPPRS P LAGARVHF ANPDDAIEVF VDGYPVKIPK GMTVLQACEV AGVDIPRFCY HSRLSIAGNC RM CLVEVEK SPKPVASCAM PALPGMKIKT DTPVAKKARE GVMEFLLMNH PLDCPICDQG GEC DLQDQS MAFGSDRGRF TEVKRSVVDK NLGPLVKTVM TRCIQCTRCV RFATEVAGVQ DLGM LGRGS GEEIGTYVEK LLTSELSGNV IDICPVGALT SKPFAFKARN WELKGTETID VTDAV GSNI RIDSRGPEVM RIVPRLNEDI NEEWISDKTR FCYDGLKRQR LNDPMIRGPD GRFKAV NWR DALSVIADIA HQVKPEEIVG VAGKLSDAES MIALKDFLNR MGSNDVWGEG IGVNTNA DF RSGYIMNTSI AGLEKADVFL LVGTQPRVEA AMVNARIRKT VRSNQAKVGY IGPATDFN Y DHKHLGTDPQ TLVEIAEGRH PFFKTLSDAK NPVIIVGAGV FERKDQDAIF AAVETIAQK ANVVRPDWNG LNVLLLHAAQ AAALDLGLVP QSEKSLESAK FVYLMGADDV NLDKIPDDAF VVYQGHHGD KSVYRANVIL PTAAFSEKEG TYQNTEGCTQ QTLPAVPTVG DSRDDWKIIR A LSEVAGVR LPYDTIGAVR ARIRNVAPNL VNVDEREPAT LPSSLRPSFT QKVDTTPFGT VI ENFYMTD AITRASKIMA QCSATLLKK MTTRNGQIKN FTSNFGPQHP AAHGVSRSVL EMNGEVVERA EPHIGSLHRG TEKLIEYKTY LQALPYSDR LDYVSTMAQE HAHSSAVERL LNCEVPLRAQ YIRVLFREIT RISNHLLALT T HAMDVGAS TPSLWAFEER EKLLEFYERV SGARMHASFI RPGGVAQDLP LGLCRDIDSF TQ QFASRID ELEEMSTGNR IWKQRLVDIG TVTAQQAKDW GFSGVMLRGP GVCWDSRRAA PYD VHDQSD PDVPVGTRGD RYDRYCIRIE EMRQSMRIIW QCPNKIPSGM IKADDRKLCP PSRC RMKLS MESSIHHFEL YTEGFSVPAP STYTAVEAPK GEFGVFLVSN GSNRPYRRKI RAPGS AHSQ GLDSMSKHHM PADVVTIIGT QDIVSGEVDR MDNQSIFKY SWETLPKKWV KKMERSEHGN RSDTKTDYLF QLLCFLKLHT YTRVQVSIDI C GVDYPSRK RRFEVVYNLL STRYNSRIRV QTSADEVTRI SPVVSLFPSA GRWEREVWDM FG VSSINHP DLRRISTDYG FEGHPLRKDL PLSGYVEVRY DDPEKRVVSE PIEMTQEFRY FDF ASPWEQ RSDG MALLS RASSRIYQVH SYQRALSLHT TLPALNASTS THTPTPYAPP PPPSASSPVG VSKAA EFVI SKVDDLMNWA RRGSIWPMTF GLACCAVEMM HTGAARYDLD RFGIIFRPSP RQSDCM IVA GTLTNKMAPA LRKVYDQMPE PRWVISMGSC ANGGGYYHYS YSVVRGCDRI VPVDIYV PG CPPTAEALLY GLLQLQKKIN RRKDFLHWWT K MAAILARK SLLALRARQL AVSGQGLHSS QSYGLRLSAH SFSTKLEDEQ REQLAKEISK DW SSVFERS INTLFLTEMV RGLMLTLKYF FETKVTINYP FEKGPLSPRF RGEHALRRYP TGE ERCIAC KLCEAICPAQ AITIEAEERE DGSRRTTRYD IDMTKCIYCG FCQEACPVDA IVEG PNFEF ATETHEELLY DKEKLLENGD RWETEIAENL RSESLYR MR GILSLRSALV QHRSEKLGLG LRQFSTQGAS TPTSPQPPPP PASPQPPPPP PPPEKTHF G GLKDEDRIFT NLYGLHDPFL KGAMKRGDWY RTKDLVIKGT DWIVNEMKKS GLRGRGGAG FPSGLKWSFM PKVSDGRPSY LVVNADESEP GTCKDREIMR HDPHKLLEGC LIAGVGMRAT AAYIYIRGE YVNERKNLEK ARQEAYAAGL LGKNACGSGY DFDVHIHFGA GAYICGEETA L LESLEGKQ GKPRLKPPFP ANAGLYGCPT TVTNVETVAV SPTILRRGPE WFAGFGRKNN AG TKLFCVS GHVNKPCTVE EEMSIPLKEL IERHCGGVRG GWDNLLAVIP GGSSVPLLPK SIC DDVLMD YDALKAVQSG LGTAAVIVMD KSTDVVDAIA RLSYFYKHES CGQCTPCREG TGWL WTIME RMKVGNAKLE EIDMLQELTK QIEGHTICAL GDAAAWPVQG LIRHFRPELE RRIRE NAER ELLQATG ML ARLAANRFNE IRHIFRQPSR AFSTALNYHL DSPDNNPNLP WEFTEPNKAK VTEILSHY P SNYKQSAVIP LLDLAQQQHG GWLPVSAMNA VANIIEVPPI RVYEVATFYS MFNRAKVGK YHLLVCGTTP CMIRGSRGIE EALLKHLGVK RNEVTPDGLF SVGEMECMGC CVNAPMITVA DYSNGSEGY TYNYYEDVTP EKVVEIVEKL RKGEKPPHGT QNPLRIRSGP EGGNTTLLGE P KPPPCRDL DAC MAWRGQ LSKNIKELRF LMCQSSSASA SARAFVEKNY KELKTLNPKL PILIRECSGV EPQL WARYD LGVEKAIKLE GLSEAQISKA LEDLAKAGQS SKA MFLRAV ARPLMAKVKA STGIVGLEVV PNAREVLIGL YSKTLKEIQK VPEDEGYRKA VESF TKHRL SVCKEEEDWE AIEKRLGCGQ VEELIEEAQD ELKLISYMIE WDPWGVPDDY ECEVI ENDA PVPKHVPLHR PPPLPTEFHK TLEALSSQSG KDIPGASSTE SPSKT MASA LRNVKVLPNS ASVEEARQRV FDFFRATCRS LPSVMEIYNL YDVTSVAQLR STVASE IRK NIGVSDPKVI DMLLFKGMEE LMNVVNHSKQ RHHIIGQYVV GQQGQVQDSA SKDPAIS PF LKNFYSSNYF MAKSASNSL VQTLKRYIKK PWEITGPCAD PEYRSAVPLA TEYRLQCPAT TKEKPCIPNS L PETVYDIK YFSRDQRRNR PPIRRTVLKK ADVEKLAKEQ TFAVSDFPPV YLNSAVEEDI NA IGGGYQG MQTIARRLG HQSLKSSTSI RAIYPISDHH YVADHQRYVS TIATKGVGHL VRKGTGGRSS V SGIIATVF GATGFLGRYV VQQLAKMGSQ VLVPFRGSED CPRHLKLMGD LGQIVPMKYN PR DESSVKA VMAKANVVIN LIGRDYETRN YSFEEVHYHM AENLAKISRE HGGILRFIQV SCL GASPSS PSRMLRAKAA AEEVVLRELP EATILKPAVM IGTEDRILNP WAHFAKKYGF IPLF GNGST KIQPVYVVDV AAALTTVLKD DGTSMGKTYE LGGPEIFTVH DLAELMYETI REWPR YVKV PFPIAKALAT PREILLNKVP FPLPTPEILN LDKIQALTTD TIVSENALTF NDLGII PHK LKGYPVEFLI SYRKGGPQFG STISERVTPD AWP MASVVK NVLKSIREKG FGTFLRELKD EGYLRCLPDG NLLQTKIHNI GATLVGVDKF GNKY YEKLG DTQYGRHRWV EYAEKSRYNA SQVPPEWHGW LHFITDHTGD ELLLLKPKRY GVEHK ENLS GEGEQYIYHS KGHALNPGQR DWTRYQPWES KA MANTLQR ALRATMARRF STQALVETKP GEIGMVSGIP QEHLRRRVVI YSPARTASQQ GSG KVGRWK INFLSTQKWE NPLMGWTSTG DPYAHVGDSA LTFDSAEAAK AFAEKHGWEY SVKK RHTPL LKVKSYADNF KWKGFPKPAE E MASSVLRN LMRFSSPRNT STRSFSLVTS QISNHTAKWM QDTSKKSPME LINEVPPIKV EG RIVACEG DTNPALGHPI EFICLDLPEP AVCKYCGLRY VQDHHH

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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

Concentration6 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClSodium chloridesodium chloride
0.1 %digitonindigitonin
1.0 mMedtaEthylenediaminetetraacetic acidEDTAEthylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III
Details: Blotted for 9 seconds at 100% humidity, 15 degrees C..
DetailsExtracted from V. radiata mitochondrial membranes with digitonin, exchanged into amphipole A8-35, purified on sucrose gradient.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 190951
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 344007
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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