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- EMDB-24821: Structure of photosystem I with bound ferredoxin from Synechococc... -

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Basic information

Entry
Database: EMDB / ID: EMD-24821
TitleStructure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light
Map dataSharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335
Sample
  • Complex: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
    • Protein or peptide: x 12 types
  • Ligand: x 13 types
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / : / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / : / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
Photosystem I 16 kDa polypeptide / 2Fe-2S ferredoxin-type domain-containing protein / Photosystem I reaction center subunit PsaK / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / PSI subunit V / Uncharacterized protein / PSI-F / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsGisriel CJ / Flesher DA / Shen G / Wang J / Ho M / Brudvig GW / Bryant DA
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.
Authors: Christopher J Gisriel / David A Flesher / Gaozhong Shen / Jimin Wang / Ming-Yang Ho / Gary W Brudvig / Donald A Bryant /
Abstract: Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes ...Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation.
History
DepositionSep 5, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateDec 29, 2021-
Current statusDec 29, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7s3d
  • Surface level: 0.0302
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7s3d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24821.png

Downloads & links

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Map

FileDownload / File: emd_24821.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.0302 / Movie #1: 0.0302
Minimum - Maximum-0.20111874 - 0.31543994
Average (Standard dev.)0.00018521286 (±0.010041001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2010.3150.000

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Supplemental data

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Additional map: Unsharpened map for Far-red light-acclimated PSI from Synechococcus...

Fileemd_24821_additional_1.map
AnnotationUnsharpened map for Far-red light-acclimated PSI from Synechococcus sp. PCC 7335
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335

EntireName: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
Components
  • Complex: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: PsaC
    • Protein or peptide: Photosystem I 16 kDa polypeptide
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: PSI-F
    • Protein or peptide: PsaI2
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK
    • Protein or peptide: PSI subunit V
    • Protein or peptide: PsaM
    • Protein or peptide: 2Fe-2S ferredoxin-type domain-containing protein
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll F
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CHLORIDE IONChloride
  • Ligand: CALCIUM IONCalcium
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: water

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Supramolecule #1: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335

SupramoleculeName: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 86.411227 KDa
SequenceString: MTASPPKRNQ ASAATEQSPI PTSFERWAKP GHFDRTLARG PKTTTWIWNL HADAHDFDSH TNDLQDISRK IFSAHFGHLA VVFVWLSGM YFHGARFSNF SSWMADPTHI RPSAQVVWPL VGQDILNGDM GGGFRGIQIT SGLFQMWRGE GFTNEFQLYC T AIGALVMA ...String:
MTASPPKRNQ ASAATEQSPI PTSFERWAKP GHFDRTLARG PKTTTWIWNL HADAHDFDSH TNDLQDISRK IFSAHFGHLA VVFVWLSGM YFHGARFSNF SSWMADPTHI RPSAQVVWPL VGQDILNGDM GGGFRGIQIT SGLFQMWRGE GFTNEFQLYC T AIGALVMA GLMIFAGWFH YHVRSPKLEW FQNVQSMLNH HLAGLLGLGS LGWAGHLIHV ALPTNKLLDA GVAPQDIPLP HE FVLDKAL MAELYPSFAQ GIRPFFTLNW ATYSDFLTFN GGLNPVTGGL WMTDIAHHHV AIAVLFIFAG HMYRTNWGIG HSI RTMLED ARHPKMLPFL SFIGPVGHRG LFEVLTTSWH AQLSINLAMM GSLSIIVAQH MYSMPPYPYL ATDYGTVTSL FTHH MWIGG FLIVGAAAHA GIFMVRDYDP AENVNNVLDR VLRHRDAIIS HLVWVCQFLG FHSFAMYCHN DTMRAFGRPQ DMFSD TGIQ LQPIFAQWVQ HIQTMAVGSA QVAEPLGDAL GGIQNIALSG VGTTAPGVAS PASYAFGGGL VAVGGKVAMM PISLGT ADF LIHHIHAFTI HVTVLVLLKG VLFARNSRLI PDKSELGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSI AMVIFHF FW KMQSDVWGAV DANGTVSHIT GGNFAQSSIT INGWLRDFLW AQATQVISSY GSALSAYGLM FLAGHFVFAF SLMFLFSG R GYWQELIESI VWAHNKLRIT TAIQPRALSI TQGRAVGAAH YLLGSIVTTW AFFLARMAAI G

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 83.207648 KDa
SequenceString: MATKFPKFSQ ELQQDPTTRR IFYSLATAHD FESHDGMTEE SLYQRIFASH FGHLAIIFLW TSGILFHVAW QGNFEAWIKD PLNISPIAH AIWDPQFGPA AMDAFTPAGA GNPVNFCYSG VYHWWYTIGL RTNGDLFAGA MFLLLLAAVM LYAGWLHLQP R YRPSLAWF ...String:
MATKFPKFSQ ELQQDPTTRR IFYSLATAHD FESHDGMTEE SLYQRIFASH FGHLAIIFLW TSGILFHVAW QGNFEAWIKD PLNISPIAH AIWDPQFGPA AMDAFTPAGA GNPVNFCYSG VYHWWYTIGL RTNGDLFAGA MFLLLLAAVM LYAGWLHLQP R YRPSLAWF KNAESRLNHH LAGLFGVSSL AWTGHLVHVA IPESRGQHVG WDNFLSMPPH PEGLKPFFTG NWGAYALNPD TS EHLFNTS QGAGTAILTF LGGFHPQTES LWLTDMAHHH LAIAVIFIIA GHMYRTNFGI GHSIKEMTES LQGPGWTGFF IAP NTGRGH KGIYDAYNNS LHFQLGWHLA CLGVVTSLVA QHMYAMPPYA FIARDYTTTA ALYTHHQYIA GFLMLGAFAH GGIF LIRDY DPVANENNVL ARVLDHKEAI ISHLSWVSLF LGFHTLALYV HNDCEVAFGS PDKQILVEPV FAQWIQAVHG KALYG ISSL LSNPDSIAST AWPNHANVWL PGWLEAINNG TNSLFLAIGP GDFLVHHAIA LGLHVTTLIL VKGALDARGS KLMPDK KDF GYAFPCDGPG RGGTCDISAW DSVYLATFWM LNTLGWVTFY WHWKHLAIWS GNVAQFNEGS TYLMGWFRDY LWLNSAQ LI NGYNPYGTNN LAIWAWIFLF GHLVWAISFM FLITWRGYWQ ELIETLMWAH ENTPLSFGYP KDKPVALSIV QARLVGLV H FTVGYIATYG AFLIASTGSR FP

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Macromolecule #3: PsaC

MacromoleculeName: PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 8.809169 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCRAGQIA ASPRTEDCVG CKRCETACPT DFLSIRVYLG AETSRSMGLA Y

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Macromolecule #4: Photosystem I 16 kDa polypeptide

MacromoleculeName: Photosystem I 16 kDa polypeptide / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 17.051336 KDa
SequenceString:
MALTGSMPKF GGSTGGLLTA AFVEERYAIT WTSSKEQVFE MPTGGAATMN EGENLLELAR KEQCLALGAQ LRTKFKPKIT DYKIYRIFP NGETTFIHPA DGVFPEKVNE GRGYSGKKDR RIGENPNPAT IKFSGQNTFE TDMKSTDVKT TGLPRP

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 7.955112 KDa
SequenceString:
MVQRGSKVRI LRPESYWFRE VGSVASVDQS GIKYPVVVRF SKVNYAGVNT NNFSEAELVE VEAPPKKAAK K

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Macromolecule #6: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 18.569213 KDa
SequenceString:
MHKTIRKFFS LLLAAFVWLS VVSPAVAASE GYTDTHLVPC ASSPAFNERM QNAPEGYYFD TPYQSYAANL LCGAEGLPHQ QLRFDRAID VLIPFGIFFY VAGFIGWSGR AYLISSNRNS KPEETEIFID VALAIKSFVQ GLLWPLLAVK ELTTGELTAP V SEVSVSPR

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Macromolecule #7: PsaI2

MacromoleculeName: PsaI2 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 7.668838 KDa
SequenceString:
MVDATQLEGA YAAAWLPWIM IPMITYILPF PIFAIAFLWI EREGGEGGLD IDVMGSNAMS NEAMGRDISS

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 5.170094 KDa
SequenceString:
MKYFAKYLTS APIMATVALV SLSVVLIELN HFFPGLQYGT YFHSVP

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Macromolecule #9: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 8.195834 KDa
SequenceString:
MLSLVAAAGV VPNTVTWGPN VAIVMIICNL IAFAIGKQVI QIPDAGPAPG TFLGLGLPAL LGVTSLGHAI GVGAILGLAN IGVL

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Macromolecule #10: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 18.632201 KDa
SequenceString:
MSASDAYISD DPIQPYQGNP QLGNLATPIN SSNLAKAFIN NLPAYRPGLT PFLRGLEIGM AHGYFLVGPE VVFGPLKEGS HGANLSGLI TAIYITVSAC LGISIFALAT FQGDPRGTYN SHSRDRLRPL RKKEDWYQLS GGILMGSLGG AIFAYALLEN F ELLDSILR GAVNVG

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Macromolecule #11: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 3.366065 KDa
SequenceString:
MALSDSQIFL ALALALIPGF LALRLATELY K

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Macromolecule #12: 2Fe-2S ferredoxin-type domain-containing protein

MacromoleculeName: 2Fe-2S ferredoxin-type domain-containing protein / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 10.835725 KDa
SequenceString:
MASYKVTLVN ETENLNTTIE VADDEYILDA AEEQGIDLPY SCRAGACSTC AGKLTEGTVD QSDQSFLDDD QIEAGYVLTC VAYPTSDCT VMTHQEEELY

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Macromolecule #13: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 13 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 255 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #15: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 15 / Number of copies: 18 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
Chlorophyll F / Chlorophyll f

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Macromolecule #16: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 16 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 57 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

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Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 20 / Number of copies: 9 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #21: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 21 / Number of copies: 39 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #22: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 22 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #23: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 23 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 24 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #25: water

MacromoleculeName: water / type: ligand / ID: 25 / Number of copies: 333 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 6.5
VitrificationCryogen name: ETHANE

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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: 40.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 286672
FSC plot (resolution estimation)

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  • 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

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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

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