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- EMDB-0726: Structure of PSI from H. hongdechloris grown under white light co... -

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Basic information

Entry
Database: EMDB / ID: EMD-0726
TitleStructure of PSI from H. hongdechloris grown under white light condition
Map data
Sample
  • Complex: white PSI
    • Protein or peptide: x 8 types
  • Ligand: x 11 types
KeywordsPhotosystem I / ELECTRON TRANSPORT
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 / oxidoreductase 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 / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
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 / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD ...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 / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / 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/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 reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / 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 VIII
Similarity search - Component
Biological speciesHalomicronema hongdechloris C2206 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsKato K / Nagao R
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Authors: Koji Kato / Toshiyuki Shinoda / Ryo Nagao / Seiji Akimoto / Takehiro Suzuki / Naoshi Dohmae / Min Chen / Suleyman I Allakhverdiev / Jian-Ren Shen / Fusamichi Akita / Naoyuki Miyazaki / Tatsuya Tomo /
Abstract: Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first ...Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
History
DepositionAug 1, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kmw
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0726.png

Downloads & links

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Map

FileDownload / File: emd_0726.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.2670965 - 0.4529732
Average (Standard dev.)0.00079463935 (±0.012903853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z313.200313.200313.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2670.4530.001

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Supplemental data

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Sample components

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Entire : white PSI

EntireName: white PSI
Components
  • Complex: white PSI
    • 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 reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: UNKNOWN LIGAND
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: white PSI

SupramoleculeName: white PSI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Halomicronema hongdechloris C2206 (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: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 84.273633 KDa
SequenceString: MTISPPEPGR KVKVVVDSDP VNTSFERWAK PGHFERSLSK GPKTTTWIWD LHADAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG MYFHGAKFSN YEAWLSNPTG IKPSAQVVWP IFGQEILNGD VGGGFHGIQI TSGLFQMWRA NGITNSFELY C TAIGALVM ...String:
MTISPPEPGR KVKVVVDSDP VNTSFERWAK PGHFERSLSK GPKTTTWIWD LHADAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG MYFHGAKFSN YEAWLSNPTG IKPSAQVVWP IFGQEILNGD VGGGFHGIQI TSGLFQMWRA NGITNSFELY C TAIGALVM AGLMLFAGWF HYHKKAPKLE WFQNVESMMN HHLAGLLGLG CLGYAGQQIH VSLPINACLD AIDAGKPLTV GG KVIDSVA AIPLPHEWIL NPSLMTDIYP SFAEGLKPFF TLNWSVYADF LTFNGGLNPQ TGGLWLTDTA HHHLALAVLF IVA GHFYRT NWGIGHSFKE VLEAHKGPVT GEGHKGMYEI FTTSWHCQLS WNLAWIGSLS ILVAHHMYSM PPYPYIATDY PTQL SLFTH HMWIGGFLIV GAGAHAAIFM VRDYDPATHI NNLLDRVIRH RDAIISHLNW VCIFLGFHSF GLYVHNDTMR AFGRP QDMF SDTGIQLQPV FAQWVQNLHA AAAGGTAPNA AAGVSPAFGG DILAVVGKVA MMPITLGTAD FLVHHIHAFT IHVTVL ILL KGVLFARNSR LIPDKGELGF RFPCDGPGRG GTCQVSGWDH VFLGLFWMYN SLSIVIFHFS WKMQSDVWGS VSPDGSV SH ITAGNFAQSA ITINGWLRDF LWAQASQVIG SYGSALSAYG LLFLGAHFVW AFSLMFLFSG RGYWQELIES IVWAHNKL K VAPAIQPRAL SITQGRAVGV AHFLLGGIAT TWAFFLARII AVG

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: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 83.080469 KDa
SequenceString: MATKFPKFSQ DLASDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFQQWVKD PLNISPIAH AIWDPQFGQS AVEAFSQAGA NYPVDIAYSG VYHWWYTIGM RTAGDLYGGA LFLMIMAAVF LFAGWLHLQP R FRPSLAWF ...String:
MATKFPKFSQ DLASDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFQQWVKD PLNISPIAH AIWDPQFGQS AVEAFSQAGA NYPVDIAYSG VYHWWYTIGM RTAGDLYGGA LFLMIMAAVF LFAGWLHLQP R FRPSLAWF KNAESRMNHH LAGLFGVSSL AWAGHLIHVA IPESRGQHVG WDNFLFTPPH PAGLTPFFTG NWGVYAQNPD TA SHVFGSS TGAGSAILTF LGGFHPQTES LWLTDMAHHH LAIAVLFIVA GHMYRTNFGI GHNMKEIMNA HNPPQGTPFG GMI GEGHKG MYDTYNNSLH FQLGWHLACL GVITSLVAQH MYSLPPYAFL AKSYTTQAAL YTHHQYIAGF IMVGAFAHGA IFLI RDYDP ASNSNNVLDR VLQHKEAIIS HLSWVSLFLG FHTLGLYVHN DVMVAFGTPE KQILVEPVFA QWIQAAHGKL LYGFD TLLS NPGSIASTAW PNYGNVWLSG WLDAINSGDN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKD FGY SFPCDGPGRG GTCDISAWDA FYLAVFWMLN TIGWVTFYWH WKHLAIWQGN VAQFNESSTY LMGWLRDYLW LNSSQLI NG YNPYGMNNLA VWAWMFLLGH LVWATGFMFL ISWRGYWQEL IETLVWAHER TPLANLVRWK DKPVALSIVQ ARLVGLAH F SVGYIITYAA FLIASTSSRF G

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: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 8.782184 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAGSIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 15.7238 KDa
SequenceString:
MAETLTGKTP VFGGSTGGLL TRAAVEEKYA ITWTSTKQQV FEMPTGGAAI MHEGENLLYL ARKEQCLALG TQLRSKFKPK IEDYKIYRI YPNGETQYVH PADGVFPEKV NEGREYNGKI DRNIGANPDP ATVKFSGKAP YEV

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: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 7.907028 KDa
SequenceString:
MVQRGSKVRI LRPESYWYRD IGTVATVDQS GIRYPAIVRF DKVNYYGISS NNFALSELEE VEPPKKKK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 4.318124 KDa
SequenceString:
MDGTYAASWL PWLLIPVVTW LMPAVVMGLL FFYIESDA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #7: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 16.871471 KDa
SequenceString:
MTNQVVKPYL DEPELGHLST PISDSAFVRS FIGNLPAYRK GMAPITRGLE IGLAHGYFLV GPEIIVGALR DYAPAPYLGG LVTAIAIVL LGTTGMGAHG LVSLKPVAES SPKTDALMTS EGWSEMTAGF FLGGMSGAFM AYFLLSHFSE IDAIFRGFVN

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #8: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 3.440141 KDa
SequenceString:
MTLSETQVFV ALVIALVPAI LAFRLSTELY K

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Macromolecule #9: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 9 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #10: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 10 / Number of copies: 267 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #11: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 11 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #12: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 12 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #13: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 13 / Number of copies: 51 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #14: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 14 / 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 #15: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 15 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 16 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #17: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 17 / Number of copies: 15 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #18: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 18 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 627 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

Concentration0.032 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES-NaOH
0.04 %DDMDDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 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: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 546366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1jb0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6kmw:
Structure of PSI from H. hongdechloris grown under white light condition

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