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- EMDB-23563: Quantitative assessment of chlorophyll types in cryo-EM maps of p... -

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Basic information

Entry
Database: EMDB / ID: EMD-23563
TitleQuantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light
Map dataTrimeric photosystem I adapted to far-red light from Fischerella thermalis sp. PCC 7521
Sample
  • Complex: Photosystem I adapted to far-red light
    • Protein or peptide: x 12 types
  • Ligand: x 10 types
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / : / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / : / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaX / Photosystem I PsaM, reaction centre superfamily / Photosystem I protein M (PsaM) / Photosystem I PsaM, reaction centre / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI ...Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaX / Photosystem I PsaM, reaction centre superfamily / Photosystem I protein M (PsaM) / Photosystem I PsaM, reaction centre / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX / 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 protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaA/PsaB / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I iron-sulfur center / Photosystem one PsaX / PSI subunit V / Photosystem I P700 chlorophyll a apoprotein A1 / PSI-F / Photosystem I reaction centre subunit IX / PsaJ / Uncharacterized protein / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesFischerella thermalis PCC 7521 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsGisriel CJ / Wang J
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: BBA Adv / Year: 2021
Title: Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light
Authors: Gisriel CJ / Huang HL / Reiss KM / Flesher DA / Batista VS / Bryant DA / Brudvig GW / Wang J
History
DepositionMar 2, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lx0
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23563.png

Downloads & links

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Map

FileDownload / File: emd_23563.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTrimeric photosystem I adapted to far-red light from Fischerella thermalis sp. PCC 7521
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 256 pix.
= 381.601 Å		1.49 Å/pix.
x 256 pix.
= 381.601 Å		1.49 Å/pix.
x 256 pix.
= 381.601 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.15547588 - 0.32351974
Average (Standard dev.)0.0006775416 (±0.0107421875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 381.6013 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.490628906251.490628906251.49062890625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z381.601381.601381.601
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1550.3240.001

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Supplemental data

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Sample components

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Entire : Photosystem I adapted to far-red light

EntireName: Photosystem I adapted to far-red light
Components
  • Complex: Photosystem I adapted to far-red light
    • 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: PSI subunit V
    • 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: 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: CALCIUM IONCalcium

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Supramolecule #1: Photosystem I adapted to far-red light

SupramoleculeName: Photosystem I adapted to far-red light / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Fischerella thermalis PCC 7521 (Cyanobacteria)

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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 (Cyanobacteria)
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

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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 (Cyanobacteria)
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

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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 (Cyanobacteria)
Molecular weightTheoretical: 8.853221 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCRAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

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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 (Cyanobacteria)
Molecular weightTheoretical: 17.776348 KDa
SequenceString:
MSPSAVLGCR KNVERRFMAE TLSGQTPIFG GSTGGLLKKA EVEEKYAITW TSPKEQVFEM PTGGAAIMRQ GQNLLYLARK EQCIALGGQ LRKFKITDYK IYRIYPNGET VYIHPADGVF PEKVNQGREK VRYNDRRIGQ NPSPSKVKFS GIATYDAPNS

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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 (Cyanobacteria)
Molecular weightTheoretical: 8.070138 KDa
SequenceString:
MVQRGSKVRI LRPESYWFQD VGTVASIEQG GTSRYPVIVR FDKVNYAGVN TNNFAQDELV EVEAPKAKAK KA

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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 (Cyanobacteria)
Molecular weightTheoretical: 17.788021 KDa
SequenceString:
MKRIFALILA IFIWFSAVST ALAENTTLVP CYKSPAFVER MKNAPDSYYT TKPLKAYSQL LCGEDGLPRI ALDRLSLAVD VAIPIAIFL YTAGFIGWSG RSYLQAIKKQ DKAEEKEVFI DVPLFISCMV MALFWPMAVI KELLAGELVA KDEEIPISVR

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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 (Cyanobacteria)
Molecular weightTheoretical: 7.735956 KDa
SequenceString:
MMVDMTQLTG DYAASWLPWI MIPLVFYILP FPVFAILFLW IQKEASEEIK ETDNNLAEIG ELEVPNS

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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 (Cyanobacteria)
Molecular weightTheoretical: 5.435492 KDa
SequenceString:
MEARYLFRYL SSAPVVATLA LIIISVILIV LNYLFPGLQY GTFFHSLP

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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 (Cyanobacteria)
Molecular weightTheoretical: 4.494526 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)VAAM AFGHVIGVAI VLGLTNIGKI

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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: Fischerella thermalis PCC 7521 (Cyanobacteria)
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

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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 (Cyanobacteria)
Molecular weightTheoretical: 3.471115 KDa
SequenceString:
MSISDTQVYI ALVVALVPGF LAWRLATELY K

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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 (Cyanobacteria)
Molecular weightTheoretical: 11.132814 KDa
SequenceString:
MPGKESTALP RLHTLPTSLP LATQNHENIF NESGELGHLF GISEEVLKLG VHFMAKADTT ADLPVAKSTT AKPPYTFRTA WALLLLAIN FIVAAYYFHI IE

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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: 252 / 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: 15 / 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: 60 / 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: 6 / 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: 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

Concentration1.5 mg/mL
BufferpH: 7
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300
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 K2 SUMMIT (4k x 4k) / Average electron dose: 57.328 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201104
FSC plot (resolution estimation)

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