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- EMDB-20397: Structure of Photosystem I Acclimated to Far-red Light -

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Basic information

Entry
Database: EMDB / ID: EMD-20397
TitleStructure of Photosystem I Acclimated to Far-red Light
Map dataMap of trimeric photosystem I acclimated to far-red light
Sample
  • Complex: Photosystem I from far-red light-adapted Fischerella thermalis PCC 7521
    • Protein or peptide: x 12 types
  • Ligand: x 10 types
Keywordstrimeric alpha helical complex / PHOTOSYNTHESIS
Function / homology
Function and homology information


: / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis ...: / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center protein subunit XI / Uncharacterized protein / Uncharacterized protein / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV ...Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center protein subunit XI / Uncharacterized protein / Uncharacterized protein / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV / Photosystem one PsaX / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesFischerella thermalis PCC 7521 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsGisriel CJ / Shen G
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613022 United States
National Science Foundation (NSF, United States)1531991 United States
Department of Energy (DOE, United States)DE-SC 0001035 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41-GM103311 United States
CitationJournal: Sci Adv / Year: 2020
Title: The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis.
Authors: Christopher Gisriel / Gaozhong Shen / Vasily Kurashov / Ming-Yang Ho / Shangji Zhang / Dewight Williams / John H Golbeck / Petra Fromme / Donald A Bryant /
Abstract: Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria ...Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium PCC 7521 by single-particle, cryo-electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature.
History
DepositionJul 2, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseFeb 12, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0293
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0293
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pnj
  • Surface level: 0.0293
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20397.png

Downloads & links

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Map

FileDownload / File: emd_20397.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of trimeric photosystem I acclimated to far-red light
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0293 / Movie #1: 0.0293
Minimum - Maximum-0.16519657 - 0.2507048
Average (Standard dev.)0.000016519209 (±0.0058539025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1650.2510.000

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Supplemental data

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Sample components

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Entire : Photosystem I from far-red light-adapted Fischerella thermalis PC...

EntireName: Photosystem I from far-red light-adapted Fischerella thermalis PCC 7521
Components
  • Complex: Photosystem I from far-red light-adapted Fischerella thermalis PCC 7521
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I protein PsaD
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center protein PsaF subunit III
    • Protein or peptide: photosystem I subunit VIII
    • Protein or peptide: Photosystem I reaction centre subunit IX / PsaJ
    • Protein or peptide: photosystem I reaction center subunit PsaK
    • Protein or peptide: Photosystem I reaction center protein subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem one PsaX
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll F
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CALCIUM ION

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Supramolecule #1: Photosystem I from far-red light-adapted Fischerella thermalis PC...

SupramoleculeName: Photosystem I from far-red light-adapted Fischerella thermalis PCC 7521
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Fischerella thermalis PCC 7521 (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: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 87.627914 KDa
SequenceString: MTLTPEREQE VRVVVDNDPV PTSFQKWSQP GHFDRTLAKG AKTTTWIWNL HANAHDFDTH TSDLEDISRK IFAAHFGHLA VVFIWLSGM YFHGARFSNF EAWMANPTGI KPSAQVVWPI FGQEILNGDM GGGFHGIQIT SGLFQMWRAA GFTNTFQLYC T AIGGLVMA ...String:
MTLTPEREQE VRVVVDNDPV PTSFQKWSQP GHFDRTLAKG AKTTTWIWNL HANAHDFDTH TSDLEDISRK IFAAHFGHLA VVFIWLSGM YFHGARFSNF EAWMANPTGI KPSAQVVWPI FGQEILNGDM GGGFHGIQIT SGLFQMWRAA GFTNTFQLYC T AIGGLVMA ALMLFAGWFH YHKRAPKLEW FQNTQSMLNH HLAGLLGLGS LGWTGHLIHV SLPTNKLLDT GVALKDIPLP HE FILNPSL MNKLYPHADW GFVKGVVPFF TLQWGHFTDF LTFKGGLNPV TGGLWLTDVA HHHLAIAVMF IIAGHMYRTN WGI GHSIKE MLDDARTPNM LPFLSFIGPV GHKGLFEVLT TSWHAQLSIN LAMLGSLSII IAHHMYAMPP YPYLATDYGT VVSL FTHHV WIGGFLIVGG AAHAAIYMVR DYDPEQNFNN VLDRVLRHRD AIISHLAWVC QFLGFHSFAM YCHNDTMRAF GRPQD MFSD TGIQLQPVFA QWLQHIHTMT IGNPSLQVAA PLGHAFGGLR NLELTGLGTA APNLHDPVSY AFGGGVVAVG GKVAMM PIT LGTADFLIHH IHAFTIHVTV LVLLKGVLFA RSSRLIPDKA NLGFRFPCDG PGRGGTCQVS AWDHVFLGLF WMYNSLS MV IFHFFWKMQS DVWGTVGADG VVTHITGGNF ATSSITNNGW LRDFLWAQST QVITSYNTSL SAYGLMFLGG HFIFGFSL M FLFSGRGYWQ ELIESIVWAH NKLKVAPAIQ PRALSIIHGR AVGVAHYLLG GIVTTWAFFL ARMTAFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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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: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 83.450969 KDa
SequenceString: MATKFPKFSQ DLANDPTTRR IFYAIATAHD FESHDGMTEE NLYQRIFASH FGHLAIIFLW ASGILFHVAW QGNFEVWIKD PVHVRPIAH AIWDAQFGPG AIKAFTQAGA RNPVDICYSG VYHWWYTIGL RTNTELYVGA LFLILLAAVF LFAGWLHLQP R YRPNLGWF ...String:
MATKFPKFSQ DLANDPTTRR IFYAIATAHD FESHDGMTEE NLYQRIFASH FGHLAIIFLW ASGILFHVAW QGNFEVWIKD PVHVRPIAH AIWDAQFGPG AIKAFTQAGA RNPVDICYSG VYHWWYTIGL RTNTELYVGA LFLILLAAVF LFAGWLHLQP R YRPNLGWF KNSEARLNHH LAGLFGVSSL AWAGHLVHVA IPESRGQHVG WDNFLSTPPH PAGLWAFFTG NWGAYAQNPD TA EHVFSTS QGAGTAILTF LGGFHPQTQS LWLTDMAHHH LAIAVVLIIA GHMYRTNWRI GHSIKEMMDS KTFFGRKVEG PFN LPHQGL YETVNNSLHF QLSLALACLG VASSLTAQHM YSMPPYAFIA KDFTTMAALY THHQYIAGFL MVGAFSHAAI FWIK DYDPE QNKGNVLERV LKHKEAIIAH LSWVSLFLGF HTLGLYVHND VEVAFGAADK QILIEPVFAQ FIQSANGKIL YGFHT LLSN PDSIAFTAWP NHANVWLPGW LDAINNGTNS LFLTIGPGDF YVHHAIALGL HVTTLILVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDAS YLAVFWMLNT LGWVTFYWHW KHLSIWQGNV AQFNESSTYL MGWFRDYLWA NSAQLIN GY NPYGTNNLAV WAWMFLFGHL AWAVSFMFLI TWRGYWQELI ETLAWAHEQT PLSFGYWRDK PVALSIVQAR LVGLTHFT V GYIATYGAFL IASTASKFGQ

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 8.853221 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCRAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I protein PsaD

MacromoleculeName: Photosystem I protein PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 17.776348 KDa
SequenceString:
MSPSAVLGCR KNVERRFMAE TLSGQTPIFG GSTGGLLKKA EVEEKYAITW TSPKEQVFEM PTGGAAIMRQ GQNLLYLARK EQCIALGGQ LRKFKITDYK IYRIYPNGET VYIHPADGVF PEKVNQGREK VRYNDRRIGQ NPSPSKVKFS GIATYDAPNS

UniProtKB: Photosystem I reaction center subunit II

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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: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 8.070138 KDa
SequenceString:
MVQRGSKVRI LRPESYWFQD VGTVASIEQG GTSRYPVIVR FDKVNYAGVN TNNFAQDELV EVEAPKAKAK KA

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center protein PsaF subunit III

MacromoleculeName: Photosystem I reaction center protein PsaF subunit III
type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 17.788021 KDa
SequenceString:
MKRIFALILA IFIWFSAVST ALAENTTLVP CYKSPAFVER MKNAPDSYYT TKPLKAYSQL LCGEDGLPRI ALDRLSLAVD VAIPIAIFL YTAGFIGWSG RSYLQAIKKQ DKAEEKEVFI DVPLFISCMV MALFWPMAVI KELLAGELVA KDEEIPISVR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: photosystem I subunit VIII

MacromoleculeName: photosystem I subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 7.735956 KDa
SequenceString:
MMVDMTQLTG DYAASWLPWI MIPLVFYILP FPVFAILFLW IQKEASEEIK ETDNNLAEIG ELEVPNS

UniProtKB: Uncharacterized protein

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Macromolecule #8: Photosystem I reaction centre subunit IX / PsaJ

MacromoleculeName: Photosystem I reaction centre subunit IX / PsaJ / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 5.435492 KDa
SequenceString:
MEARYLFRYL SSAPVVATLA LIIISVILIV LNYLFPGLQY GTFFHSLP

UniProtKB: Photosystem I reaction centre subunit IX / PsaJ

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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: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 3.615425 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) VAA MAFGHVIGVA IVLGLTNIGK

UniProtKB: Photosystem I reaction center subunit PsaK

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Macromolecule #10: Photosystem I reaction center protein subunit XI

MacromoleculeName: Photosystem I reaction center protein subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 18.543229 KDa
SequenceString:
MSNTVDTVDN DIIKPFKGDP CLGNLSTPIN DSPLAKAFIN NLPAYRKGLT PFMRGLEIGM AHGYFLVGPE VVIGPLRESA HGANLSGLI TAIYIAVSAC LGISIFAITT FQGNPKGSYS SYSKDSLRPL RTREEWSQLN GGIFLGAMGG AIFAYLLLEN F DALDAILR GAVNAS

UniProtKB: Photosystem I reaction center protein subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 3.471115 KDa
SequenceString:
MSISDTQVYI ALVVALVPGF LAWRLATELY K

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Photosystem one PsaX

MacromoleculeName: Photosystem one PsaX / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Molecular weightTheoretical: 11.132814 KDa
SequenceString:
MPGKESTALP RLHTLPTSLP LATQNHENIF NESGELGHLF GISEEVLKLG VHFMAKADTT ADLPVAKSTT AKPPYTFRTA WALLLLAIN FIVAAYYFHI IE

UniProtKB: Photosystem one PsaX

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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

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 252 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #15: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 15 / Number of copies: 12 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
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

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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

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Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 63 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-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: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 20 / Number of copies: 12 / 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: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #22: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 22 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMC6H13NO5tricine
50.0 mMNaClsodium chloride
0.02 %BDDM
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5252 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 178666
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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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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