[English] 日本語
Yorodumi
- EMDB-0851: cryo-EM structure of cyanobacteria NDH-1LdelV complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0851
Titlecryo-EM structure of cyanobacteria NDH-1LdelV complex
Map data
Sample
  • Complex: NDH-1LDelV
    • Protein or peptide: NDH-1LDelV
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsZhang C / Shuai J / Wu J / Lei M
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into NDH-1 mediated cyclic electron transfer.
Authors: Chunli Zhang / Jin Shuai / Zhaoxing Ran / Jiaohong Zhao / Zhenfang Wu / Rijing Liao / Jian Wu / Weimin Ma / Ming Lei /
Abstract: NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution ...NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment.
History
DepositionNov 2, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateFeb 26, 2020-
Current statusFeb 26, 2020Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0851.png

Downloads & links

-
Map

FileDownload / File: emd_0851.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0126 / Movie #1: 0.0126
Minimum - Maximum-0.03478884 - 0.108126074
Average (Standard dev.)0.0002556506 (±0.0019047185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 396.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0350.1080.000

-
Supplemental data

-
Sample components

-
Entire : NDH-1LDelV

EntireName: NDH-1LDelV
Components
  • Complex: NDH-1LDelV
    • Protein or peptide: NDH-1LDelV

-
Supramolecule #1: NDH-1LDelV

SupramoleculeName: NDH-1LDelV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)

-
Macromolecule #1: NDH-1LDelV

MacromoleculeName: NDH-1LDelV / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
SequenceString: MGRDRIAMES GIDLQGQFIS ALQSLGLSHD LAKLLWLPLP MLMMLIVATV GVLVAVWLER KISAAVQQR IGPEYIGPLG ILAPLADGLK LIFKEDVLPA NSDRWLFTLG PAVVVIPVFL S YIIVPFGQ NLLISNLAMG VFLWIALSSI APIGLLMAGY ASNNKYSLLG ...String:
MGRDRIAMES GIDLQGQFIS ALQSLGLSHD LAKLLWLPLP MLMMLIVATV GVLVAVWLER KISAAVQQR IGPEYIGPLG ILAPLADGLK LIFKEDVLPA NSDRWLFTLG PAVVVIPVFL S YIIVPFGQ NLLISNLAMG VFLWIALSSI APIGLLMAGY ASNNKYSLLG GLRAAAQSIS YE IPLALAV LAVAMMSNGL GTVEIVEQQS QYGILSWNVW RQPIGFLVFW IAALAECERL PFD LPEAEE ELVAGYQTEY AGMKFALFYL GAYVNLVLSA LLVSVLYFGG WSFPIPLETI ANLL GVSET NPFLQIAFAV LGITMTLIKA YFFVFLAILL RWTVPRVRID QLLDLGWKFL LPVGL VNLL LTAGLKLAFP VAFGG MDLV TLAGQLNAGT ILPETILIVT LLVVLLADLI QGRQADRWTP YFAIVGLGGA IATMIP LWT QPATISFFGS FISDHLSLFF RGLIALSALG TILMSIRYVE QTGSSLGEFM TILLTAT VG GMFIAGAQEL VFIFVALETL SIASYLLTGY TKRDSRSNEA ALKYLLIGAA SSAIFLYG S SLLYGLSGGH TQLPAIAQAL SSESLGLVVA LVFVIAGISF KISAVPFHQW TPDVYEGAP TPVVAFLSVG SKAAGFALAI RFLTLAFPSV TDQWQLIFTV LAILSMILGN VVALAQTSMK RMLAYSSIG QAGFVMIGFV VGTEAGYASM LFYLLVYLFM NLGAFTCVIL FSLRTGTDQI S EYAGLYQK DPLLTLGLSL CLLSLGGIPP LAGFFGKIYL FWAGWQAGAY GLVLLGLLTS VI SIYYYIR VVKMMVVKEP QEMSEAVRNY PEVSWSSFGL RPLQVGLVMT VIATSLAGIL ANP LFNLVN TAVWDVPQLA NQPTVMEVAY QALSPAGKS MVAIPRLRDT ATVFVLSGYE YFLGFLIICS LVPVLALAAS ALLRPKSGRM IRLTTYESGM EPIGGAWIQ FNVRYYMFAL VFVIFDVETV FLYPWAVAFH QLGLLAFIEA LIFIAILVVA L VYAWRKRA LEWS MSTFP WLTTIILFPI VAALAIPFIP DPTGKGRPIR WYALAVGLID FALIVYAFTN FYDLN TPGM QLWESYDWIP EIGLRWSVGA DGLSMPLILL TGFITTLAIL AAWPVTLKPR LFYFLM LAM YGGQIAVFAV QDMLVFFLAW ELELIPVYLL LAIWGGHKRQ YAATKFILYT AGSSLFI LV AGLAMAFYGD TVSFDMQTLA AKDYALGFQL LVYAGFLVAY GVKLPIVPLH TWLPDAHG E ATAPVHMLLA GILLKMGGYA LIRMNVDMLP AAHAKFAPVL VILGVVNIIY AALTSYAQR NLKRKIAYSS ISHIGFVLIG IASFTNLGMS GAVLQMVSHG LIGASLFFLV GATYDRTHTL ILEEMGGVG QKMKKIFAMF TACSLASLAL PGMSGFVAEL MVFIGFATSD AYSLPFRVIV V FLAAVGVI LTPIYLLSML REIFYGPENK ELVEHEALVD AEPREVFIIA CLLVPIIGIG LY PKLLTQI YDATTGQVIA RAREVLPTLA QQTEQPLGIL PMVAPQLKAN AQ MQLTYVL ILAALLFCIG IYGLVTSRNA VRVLMSIELL LNAVNLNLIG FANYLDGQQI KGQ VFAVFV ITVAAAEAAV GLAIILAIYR NRDTVDMEKF NLLKW MEPL YQYAWLIPVL PLLGALIVGF GLIAFSETTS KLRRPSAIFI MALMAIAMGH SLTLFW SQV QGHLPYTQMI EWAAAGNLHI AMGYVIDPLA ALMLVIVTTV AFLVMLYSDG YMAHDPG YV RFFAYLSLFG SSMLGLVVSP NLVQVYIFWE LVGMCSYLLI GFWYDRKSAA EAAQKAFV T NRVGDFGLLL GMVGLFWATG TFDFAGMGDR LTELVNTGLL SPSLAAILAI LVFLGPVAK SAQFPLHVWL PDAMEGPTPI SALIHAATMV AAGVFLIARM FPVFEQLPQV MTTIAWTGAF TAFMGATIA ITQNDIKKSL AYSTISQLGY MVMGMGVGAY SAGLFHLMTH AYFKAMLFLG S GSVIHSME GVVGHNPDLA QDMRYMGGLR KYMPITGATF LVGCLAISGV PPFAGFWSKD EI LGAVFHA NPAMWLLTWL TAGLTAFYMF RMYFMTFEGK FRNVPPERQE HHDHHSHHAA VPH ESPWTM TLPLVVLAIP STLIGFVGTP FNNLFEVFIH APGEEKVAEH AVDLTEFLIL GGSS VGIGL MGITVAYLMY LKGTPSPQAI AKAIQPLYQF SLHKWYFDEL YEAVFIKGCR RLARQ VLEV DYNVVDGVVN LTGFVTMVTG EGLKYLQNGR AQFYALIVLL AVLGFVIFSV QT MDLATLT QTITFFALAA AVIIAALGVV LLDNVVYSAF LLGGVFLSIA GLYILMNADF VSA AQILIY VGAVNVLILF AIMLVNKRET YTPVPGRWLR QGGAAVVSLG VFALLTKMIL QTPW QLSSV PPTPDSITTI GQHFFSDFLL PFELASVLLL MALIGAVVLA RRELVLEPEP ILGEE VVPP LELPERPREP VALSEK MPK IETRTEPMVI NMGPHHPSMH GVLRLMVTLD GEDVIDCEPV IGYLHRGMEK IAENRTN IM FIPYVSRWDY AAGMFNEAVT VNAPEKLAGI PVPKRASYIR VIMLELNRIA NHLLWLGP F LADVGAQTPF FYIFREREYI YDLFEAATGM RFINNNYFRI GGVAADLTYG WVTKCRDFC DYFLPKVDEY ERLITNNPIF VRRLQGVGKI SREEAINWGL SGPMLRASGV KWDLRKVDHY ECYDDFDWD VPVATEGDCL ARYIVRIQEM RESVKIIRQA LDGLPGGPYE NLEAKRMLEG A KSEWNGFD YQYIGKKLSP TFKIPKGEHY VRVESGKGEL GIYLIGDDNV FPWRWKIRPP DF NNLQVLP QLLKGMKVAD IVAILGSIDV IMGSVDR MK FLNQITNYAK EAVQSAKYIG QGLSVTFDHM RRRPITVQYP YEKLIPSERF RGRIHFEF D KCIACEVCVR VCPINLPVVD WVFNKELKKK ELKHYSIDFG VCIFCANCVE YCPTNCLSV TEEYELATYD RHELNYDSVA MGRIPYKVTQ DPMVTPIREF AYLPAGVMSG HDLPAGAQRA GERPEAIAN TAKSSEN MS DTPEAPIVEA GPVGRLLQSQ NLSVESLGRD ASGVEMIKVD RDRLLAVCQT LYADGFNY L RCQAAYDSGP GQDLVSTYHL IKLSDNADRP PEVRIKVFVP RDDPRVPSVY WIWKTADWQ ERESYDMFGI VYEGHPNLKR ILMPEDWVGW PLRKDYITPD FYELQEAY M TNTTSPAILN PIARPEVPQE LAENIILTSL NDVYDWARLS SLWPLMYGTA CCFIEFAAM IGSRFDFDRF GLVPRNSPRQ ADLIITSGTI TMKMAPALVR LYEQMPSPKY VIAMGACTIT GGMFSSDSY SAVRGVDKLI PVDVYLPGCP PRPEAIMDAI VKLRKKIANE HINERGNLAQ T HRLFTAKH KMKPVPPILT GQYLNAPSRQ APPPALAAAM GIAVPALGEA VSETTSVAE MAVSTELLVL GVYGALAGLY LLVVPAIVYA YLNARWYVAS SFERAFMYFL VTFFFPGLLL LAPFINFRP QPRSLNS ML LKSTTRHVHI YAGHVVDGEV HPDTETLTLN VDPDNELEWN EAALAKVEAK FRELVANA A GEDLTEYNLR RIGSDLEHFI RSLLMQGEIG YNLNSRVRNY SLGIPRVNHS MGLLAGYQF VKDLESAGAL ALFVPPEGGF EGRYQRRLRS KGYTTLPMSA PGLGDLAAYL T QEHGIRPA HTGKEDIRVY FQPPLVTYHL ENLPPNAKGL VLWLIDGKRL SKQEFAYLAQ LT QTLPKFK VVVEVGGDRV VRWEPLADWV AAA MAIKKG DLVKVVAEKL ANSLEALASD HRYPPYLFEG RGEVVDIRGD YAQIKFPVPT PTVW LRLDQ LEVAQ MDAV ISVKPILLAM TPVFILLCLF FGTRNGFYDT DQYHGNGSAH MATDFNRGI MKFDGADSPA MIAISAVLIL GFIAGLIWWA LHTAYA MIR PIADTYPLLP LSKAQMGQRQ EIINSHKRLW DKTMATDLIM TILPGMTVKV TNPNDTY YQ FQGIVQRITD GKVAVLFEGG NWDKLVTFQA SELEPVVVTP KEKAKAKK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109984

+
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