[English] 日本語
Yorodumi
- EMDB-22092: Vigna radiata complex I* membrane arm. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22092
TitleVigna radiata complex I* membrane arm.
Map dataVigna radiata complex I* membrane arm.
Sample
  • Complex: Vigna radiata complex I* membrane arm
    • Protein or peptide: Vigna radiata complex I* membrane arm
Biological speciesVigna radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22092.png

Downloads & links

-
Map

FileDownload / File: emd_22092.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVigna radiata complex I* membrane arm.
Voxel sizeX=Y=Z: 0.8332 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.040416285 - 0.11007248
Average (Standard dev.)0.00000485411 (±0.0019669107)
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-0.0400.1100.000

-
Supplemental data

-
Mask #1

Fileemd_22092_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map for Vigna radiata complex I* membrane arm.

Fileemd_22092_half_map_1.map
AnnotationHalf-map for Vigna radiata complex I* membrane arm.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map for Vigna radiata complex I* membrane arm.

Fileemd_22092_half_map_2.map
AnnotationHalf-map for Vigna radiata complex I* membrane arm.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vigna radiata complex I* membrane arm

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

-
Supramolecule #1: Vigna radiata complex I* membrane arm

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

-
Macromolecule #1: Vigna radiata complex I* membrane arm

MacromoleculeName: Vigna radiata complex I* membrane arm / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
SequenceString: MYIAVPAEI LGIILPLLLG VAFLVLAERK VMAFVQRRKG PDVVGSFGLL QPLADGLKLI L KEPISPSS ANFSLFRMAP VATFMLSLVA RAVVPFDYGM VLSDSNIGLL YLFAISSLGV YG IITAGWS SNSKYAFLGA LRSAAQMVSY EVSIGLILIT VLICVGPRNS ...String:
MYIAVPAEI LGIILPLLLG VAFLVLAERK VMAFVQRRKG PDVVGSFGLL QPLADGLKLI L KEPISPSS ANFSLFRMAP VATFMLSLVA RAVVPFDYGM VLSDSNIGLL YLFAISSLGV YG IITAGWS SNSKYAFLGA LRSAAQMVSY EVSIGLILIT VLICVGPRNS SEIVMAQKQI WSG IPLFPV LVMFFISRLA ETNRAPFDLP EAEAESVAGY NVEYSSMGSA LFFLGEYANM ILMS GPCTS LSPGGWPPIL DLPIFKRIPG SIWFSIKVIL FLFLYIWVRA AFPRYRYDQL MGLGR KVFL PLSLARVVAV SGVSVTFPWL P MFNLFLAV YPEIFIINAT SILLIHGVVF STSKKYDYPP LVSNVGWLGL LSVLITLLLL AA GAPLLTI AHLFRNNLFR RDNFTYFCQI LLLLSTAGTI SMCFDSSEQE RFDAFEFIVL IPL PTRSML FMISAHDSIA MYLAIEPQSL CFYVMAASKR KSEFSTEAGS KYLILGAFSS GILL FGCSM IYGSTGATHF DQLAKILTGY EITGARSSGI FMGILSIAVG SLFKITAVPF HMWAP DIYE GSPTPVTAFL SIAPKISIFA NISRVSIYGS YGATLQQIFC FCSIASMILG ALAAMA QTK VKRPLAHSSI GHVGYIRTGF SCGTIEGIQS LLIGIFIYAL MTIDAFAIVL ALRQTRV KY IADLGALAKT NPISAITFSI TMFSYVGIPP LAGFCSKFYL FFAALGCGAY FLAPVGVV T SVIGCFYYIR LAKRMFFDTP RTWILYEPMD RDKSLLLAMT SSFITSSFPY PSPLFSVTH QMALSSYL M SEFAPICIYL VISLLVSLIL LGLPFPFASN SSTYPEKLSA YECGFDPFGD ARSRFDIRF YLVSILFIIP DPEVTFSFPW AVPPNKIDPF GSWSMMAFLL ILTIGSLYEW KRGASDRE M DPIKYFTFSM IISILGIRGI LLNRRNIPIM SMPIESMLLA VNSNFLVFSV SSDDMMGQS FASLVSTVAA AESAIGLAIF VITFRVRGTI AVEFINSIQG MILSVLSSP ALVSGLMVAR AKNPVHSVLF PIPVFRDTSG LLLLLGLDFS AMIFPVVHIG A IAVSFLFV VMMFHIQIAE IHEEVLRYLP VSGIIGLILW WEMFFILDNE TIPLLPTQIN TT SLIYTVY AGKVRSWTNL ETLGNLLYTY YFVWFLVPSL ILLVAMIGAI VLTMHRTTKV KRQ DVFRRN AIDFRRTIMR RTTDPLTID MGTLGRAFYA VGFWIRETGQ AIDRLGSRLQ GNYLFQEQLS RHRPLMNLFD KYPSVHKDAF VAPSASLLG DVHVGPASSI WYGCVLRGDV NGIVIGSGTN IQDNSLVHVA KSNLTGKVLP T IIGDNVTV GHSAVLQGCT VEDEAFIGMG ATLLDGVYVE KHAMVAAGAL VRQNTRIPYG EV WGGNPAK FLRKLTEDEM AFFSQSALNY SNLAQAHAAE NAKELEETEF VKVLHKKFAP RGE EYDSIL DGGQETPAKL NLQDNVLLDK APKA MGTLG RAIYSVGFWI RETGQAIDRL GSRLQGGYFF QEQLSRHRTL MNIFDKAPVV DKDVF VAPS ASVIGDVQVG RGSSIWYGCV LRGDVNSIRV GSGTNIQDNS LVHVAKSNLS GKVLPT VIG DNVTVGHSAV LHGCTVEDEA FVGMGAVLLD GVVVEKNAMV AAGALVRQNT RIPSGEV WA GNPAKFLRKL SNEEITFISQ SAINYTNLAQ VHAAENSKSY DEIEFEKVLR KKYARKDE E YDSMLGVVRE IPPELILPDN VLPDKAEKAL QK MANLARF SKRALRSAHS LVRHAQSQVQ PQLFAEERAF STEAAKSITP SPDRVKWDYR GQR KIIPLG QWLPKVAVDA YVAPNVVLAG QVTVWDGASV WPGCVLRGDL NKISIGFCSN VQER SVLHA AWTSPTGLPA DTSIERYVTI GAYSLLRSCT IEPECIIGQH SILMEGSLVE TQSIL EAGS VVPPGRRIPS GELWAGNPAR FVRTLTHEEI LEIPKLAVAI NDLSRDHYSE FLPYST VYL EVEKFKKSLG ISV MNTDIT ASTKPEYPVV DRNPPFTKVV GNFSTLDYLR FVTITGVSVT VGYLSGIKPG IRGP SMVTG GLIGVMGGFM YAYQNSAGRL MGFFPNDDEV ARHNKK MVL SATTIGALLG LGTQMYSNAL RKLPYMRHPW EHVVGMGLGA VFVNQLLKWE AQVEQDL DK MLEKAKAANE RRYIDGDDD MASAVDASGN PIPSSSVLMA SSKHIGIRCH SENLDFLKCK KKDPNPEKCL DKGRDVTRCV LGLLKDLHQ KCTKEMDDYV GCMYYHTNEF DLCRKEQQAF EKKCSLE MT EAYIRNKPGM VSVKDMPVLQ DGPPPGGFAP VRFARRIPNK GPSAVAIFLA AFGTFSWG M YQVGQGNKIR RALKEEKYAA RRSILPVLQA EEDERFVREW HKYLAYEAEV MKDVPGWKV GESVYNSGRW VPPASGELRP DIW MNLRWM EAVLPLGIIA GMLCVMGNAQ YYIHKAAHGR PKHIGNDLWD VAMERRDKKL HEQA ASSSN MASGWGITG NKGRCYDFWM DFSECMSRCR EPKDCGLLRE DYLECLHHSK EFQRRNRIYK E EQRKIRAA AKKAKDDGVV KEHHYLHGNT TDSNPHLSKV KKMSRRSSRT VYVGNLPGDI RE REVEDLF LKYGHITHID LKVPPRPPGY AFVEFEDAQD AEDAIRGRDG YDFDGHRLRV EPA HGGRGH SSSRDRHSSH SNGRAGRGVS RRSEYRVLVT GLPSSASWQD LKDHMRKAGD VCFS QVFHD GRGTTGIVDY TNYDDMKYAI KKLDDSEFRN AFSKGYVRVR EYDSRRDSSR SPSRG PSHS RGRSYSRSRS RSRSYSRDRS QSKSPKGKSS QRSPPAKSPS RSPAARSRSR SRSRSL SGS RSRSRSPLPP RNKSPKRGSA SRSPSRSRSR SKSLSR MAV MEKLKMFVVQ EPVVAASCLI AGFGLFLPAV VRPILDSYQA TKQPPQPALS DVVAGMT GK K MAARVAAR YGSRRLFSSG SGKILSEEEK AAENAYFKKA EQDKLEKLAR KGPQPEASSG GS VIDAKPS GSGHTGASAE RVSTDKHRNY AVVAGTITIL GALGWYLKGT AKKPEVQD

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Pretreatment - Atmosphere: AIR
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.

-
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

-
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 34407
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

+
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