[English] 日本語
Yorodumi
- EMDB-16732: Cryo-EM structure of the Photosystem I - LHCI supercomplex from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16732
TitleCryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Map data
Sample
  • Complex: Coelastrella sp. Photosystem I
    • Protein or peptide: x 19 types
  • Protein or peptide: x 1 types
  • Ligand: x 24 types
KeywordsGreen alga / PSI / Coelastrella / membrane protein / Cryo-EM / PHOTOSYNTHESIS
Biological speciesCoelastrella (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsFadeeva M / Klaiman D / Nelson N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Authors: Fadeeva M / Klaiman D / Nelson N
History
DepositionFeb 20, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16732.png

Downloads & links

-
Map

FileDownload / File: emd_16732.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 325.5 Å		0.65 Å/pix.
x 500 pix.
= 325.5 Å		0.65 Å/pix.
x 500 pix.
= 325.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.012152449 - 0.031648654
Average (Standard dev.)0.000095737065 (±0.0013488486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 325.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_16732_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16732_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Coelastrella sp. Photosystem I

EntireName: Coelastrella sp. Photosystem I
Components
  • Complex: Coelastrella sp. Photosystem I
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1 PsaA
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 PsaB
    • Protein or peptide: Photosystem I subunit VII PsaC
    • Protein or peptide: Photosystem I reaction center subunit II PsaD
    • Protein or peptide: Photosystem I reaction center subunit IV PsaE
    • Protein or peptide: Photosystem I reaction center subunit III PsaF
    • Protein or peptide: Photosystem I reaction center subunit V PsaG
    • Protein or peptide: Photosystem I reaction center subunit VIII PsaI
    • Protein or peptide: Photosystem I subunit IX PsaJ
    • Protein or peptide: Photosystem I reaction center subunit X psaK
    • Protein or peptide: Photosystem I reaction centre subunit XI PsaL
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca1
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca3
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca7
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca8
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca4
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca5
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca6
    • Protein or peptide: Light-harvesting protein of photosystem I Lhca9
  • Protein or peptide: Light-harvesting protein of photosystem I Lhca2 partial
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
  • Ligand: DIACYL GLYCEROLDiglyceride
  • Ligand: OCTANOIC ACID (CAPRYLIC ACID)
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: CALCIUM IONCalcium
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Phosphatidylinositol
  • Ligand: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
  • Ligand: LAURIC ACID
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: CHLOROPHYLL B
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: SPHINGOSINE
  • Ligand: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
  • Ligand: water

+
Supramolecule #1: Coelastrella sp. Photosystem I

SupramoleculeName: Coelastrella sp. Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19 / Details: Contains 11 core subunits and 10 antenna proteins
Source (natural)Organism: Coelastrella (plant) / Organelle: Chloroplast / Location in cell: Thylakoid membrane
Molecular weightTheoretical: 900 KDa

+
Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1 PsaA

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 PsaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 82.115883 KDa
SequenceString: KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGVIFIWLSG MYFHGARFS NYEAWLSDPV HIKPSAQVVW PVVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL YTTAIGGLVM A AAMFFAGW ...String:
KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGVIFIWLSG MYFHGARFS NYEAWLSDPV HIKPSAQVVW PVVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL YTTAIGGLVM A AAMFFAGW FHYHKAAPKL EWFQNVESML NHHLAGLLGL GSLSWAGHQI HVSLPVNKLL DAGVDPKEIP LPHEFLLNRQ IM QDLYPSF AKGLAPFFTL QWGEYSDFLT FNGGLNPVTG GLWLSDTAHH HLAIAVLFLV AGHMYRTNWG IGHSMKEILE AHK GPFTGE GHVGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYSMPP YPYLATDYGT QLSLFTHHNW IGGFCIVGAG AHAA IFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQPVFAQ WIQKT HFLA PQLTAPTALA ATSATWGGDV VAVGGKVAMM PISLGTSDFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIAIFHFSWK MQSDVWGTVT ASGVSHITGG NFAQSANTIN GWLRDFL WA QSSQVIQSYG SALSAYGLMF LGAHFVWAFS LMFLFSGRGY WQELIESIIW AHSKLKVAPS IQPRALSITQ GRAVGVAH Y LLGGIATTWS FFLARIIAV

+
Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2 PsaB

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 PsaB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 81.680602 KDa
SequenceString: ATKLFPKFSQ GLAQDPTTRR IWFGLAVAHD FESHDGMTEE NLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEQWGAD PIHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFASWLHLQP S FTPSLSWF ...String:
ATKLFPKFSQ GLAQDPTTRR IWFGLAVAHD FESHDGMTEE NLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEQWGAD PIHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFASWLHLQP S FTPSLSWF KDAESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGKHVG WDNFLTQLPH PQGLTPFWTG NWAAYAQNPD SA SHVFGTS DGAGEAILTF LGGFHPQTQS LWLTDMAHHH LAIAVIFIVA GHMYRTNFGI GHRMSAILDA HVAPSGRLGA GHK GLFETV NNSLHFQLGL ALASVGTICS LVAQHMYSLP PYAFLANDFT TQASLYTHHQ YIAGFIMCGA FAHGAIFWIR DYDP EQNKG NVLARMLDHK EAIISHLSWV SLFLGFHTLG LYVHNDVMQA FGTPEKQILI EPVFAQWIQA AHGKAFYGFD LLLSS SSSS AASASQTLWL PGWLDAINNN QNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAY DAFYLAVFWM LNTIGWVTFY FHWKHLTLWQ GNVSQFDESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWIFLF GHLVYATGFM FLISWRGYWQ ELIETLVWAH EKTPLANLVY WKDKPVALSI VQARLVGLTH FSVGYVFT Y AAFLIASTSG K

+
Macromolecule #3: Photosystem I subunit VII PsaC

MacromoleculeName: Photosystem I subunit VII PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 8.78017 KDa
SequenceString:
SHIVKIYDTC IGCTQCVRAC PLDVLEMVPW NGCKANQMAS APRTEDCVGC KRCETACPTD FLSVRVYLGS ESTRSMGLSY

+
Macromolecule #4: Photosystem I reaction center subunit II PsaD

MacromoleculeName: Photosystem I reaction center subunit II PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 16.034349 KDa
SequenceString:
WTEPTLNPDT PSPIFGGSTG GLLRKAQVEE FYVITWESNK EQIFEMPTGG AAIMRKGPNL LKFARKEQCL ALTTQLRTKF KFTPCFYRV YPSGEVQYLH PKDGVYPEKV NAGRPGVNQN FRRIGENVNP IKVKFTGNGT MDI

+
Macromolecule #5: Photosystem I reaction center subunit IV PsaE

MacromoleculeName: Photosystem I reaction center subunit IV PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 6.850657 KDa
SequenceString:
VGPKRGSQVK ILRPESYWYN QTGKVVSVDQ SGILYPVVVR FETQNYAGVT TNNFALDEVQ P

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

MacromoleculeName: Photosystem I reaction center subunit III PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 17.94968 KDa
SequenceString:
DIAGLTPCSE SAAYAKRLKN EVKGLNKRLK NYEADSAPAI ALKATIERTQ NRFANYAKAG LLCGADGLPH LISDPGLALK YGHAGEVFI PTFGFLYVAG WIGYVGRLYL NMVKGEAKPT EKEIIIDVPA ALRLTWQGAT WPVQVVAELR ANTLTEKAEN I TISPR

+
Macromolecule #7: Photosystem I reaction center subunit V PsaG

MacromoleculeName: Photosystem I reaction center subunit V PsaG / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 9.806025 KDa
SequenceString:
GLEPYLQVCA GTATMLAVGR FAFLPLHRRD LERSAATAGP KTTGSTYFDS LQQEASFITS TNDPAGFTLI DTMAWGALGH ALGFAFLAA SSLQ

+
Macromolecule #8: Photosystem I reaction center subunit VIII PsaI

MacromoleculeName: Photosystem I reaction center subunit VIII PsaI / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 4.352075 KDa
SequenceString:
AAGSYPFVPP SWAPSVFVPL TGLVLPAIAM ATLFVYIEKD N

+
Macromolecule #9: Photosystem I subunit IX PsaJ

MacromoleculeName: Photosystem I subunit IX PsaJ / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 4.50828 KDa
SequenceString:
MKNFTTYLST APVVALAWFT VTAALLIEIN RFFPDPLVFS

+
Macromolecule #10: Photosystem I reaction center subunit X psaK

MacromoleculeName: Photosystem I reaction center subunit X psaK / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 8.79409 KDa
SequenceString:
RADGFIGSTT NLIMVASTAA FLAAGKFGLA PTVKRGTDAA CKLVDRPNAA GLISNDPSGF TAVDTLAFGA LGHIAGVGIV LGLRATGNL

+
Macromolecule #11: Photosystem I reaction centre subunit XI PsaL

MacromoleculeName: Photosystem I reaction centre subunit XI PsaL / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 12.735546 KDa
SequenceString:
MLETPVTSTP EVASYLSNLP AYRTGVAPLL RGVEIGRAHG FFLPGPFIKL GPLRNVEGAA EIAGCLSAAG LVIILAAALS IYGSAMFQG EPRDPLQSAE GWNEFTSGFT VGALSGVAWA FACT

+
Macromolecule #12: Light-harvesting protein of photosystem I Lhca1

MacromoleculeName: Light-harvesting protein of photosystem I Lhca1 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 20.67143 KDa
SequenceString: RAGNWLPGSD APAWLPDDLP GNYGFDPLGL CKDPASLKRF TESEVIHCRW AMLGAAGCLG VEALGFGNWY DAPLWAINGG SPTWFGISV PFDLNTLLAV EFVAMAAAES RRGDETDAAK RIYPGGAFDP LNFAKGDIET LKLKEIKNGR LAMMACLGFV A QHAATGKT ...String:
RAGNWLPGSD APAWLPDDLP GNYGFDPLGL CKDPASLKRF TESEVIHCRW AMLGAAGCLG VEALGFGNWY DAPLWAINGG SPTWFGISV PFDLNTLLAV EFVAMAAAES RRGDETDAAK RIYPGGAFDP LNFAKGDIET LKLKEIKNGR LAMMACLGFV A QHAATGKT PLQALGDHIG NPWGSNFATN GVSLPF

+
Macromolecule #13: Light-harvesting protein of photosystem I Lhca3

MacromoleculeName: Light-harvesting protein of photosystem I Lhca3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 23.971211 KDa
SequenceString: QLYFTSESTL QYLDGTLPGD FGFDPLGLLD PVNSGGFVTP QWLAYSEVIH CRWAMLGAAG CIAPEILGKA GVGVDIRWFE TGVIPPAGT YDKYWTDPYS LFFIEVIAMQ FAELRRWQDF KYPGSMSKQY FVGLEAVQGG SGDPAYPGGP WFNLFNLGAK S EADMKKLK ...String:
QLYFTSESTL QYLDGTLPGD FGFDPLGLLD PVNSGGFVTP QWLAYSEVIH CRWAMLGAAG CIAPEILGKA GVGVDIRWFE TGVIPPAGT YDKYWTDPYS LFFIEVIAMQ FAELRRWQDF KYPGSMSKQY FVGLEAVQGG SGDPAYPGGP WFNLFNLGAK S EADMKKLK LNEIKNGRLA MLAVFGYGAQ AVLTGKGPYE NLLDHLADPV NNNILTNFGK

+
Macromolecule #14: Light-harvesting protein of photosystem I Lhca7

MacromoleculeName: Light-harvesting protein of photosystem I Lhca7 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 24.091938 KDa
SequenceString: AYGPDRPLWY PGNPAPAYLD GTLAGDYGFD PLGLSSDPET MRWMVHAELQ NARWAMLGAA GVLLTSIGAA VGLPFPEWYE AGAAPLPST VHGDWSFGTL TATMFLLFHW AEQKRIMDFR NPGSQGDGSF FGITDDFKSK ENGYPGGRLF DPIGFSRGDE A MYKKYKQN ...String:
AYGPDRPLWY PGNPAPAYLD GTLAGDYGFD PLGLSSDPET MRWMVHAELQ NARWAMLGAA GVLLTSIGAA VGLPFPEWYE AGAAPLPST VHGDWSFGTL TATMFLLFHW AEQKRIMDFR NPGSQGDGSF FGITDDFKSK ENGYPGGRLF DPIGFSRGDE A MYKKYKQN EIVNGRLAMV ANLGFWAQYA ATGKGPIQNL ADHLADPYHT TFTTNGVSVP FY

+
Macromolecule #15: Light-harvesting protein of photosystem I Lhca8

MacromoleculeName: Light-harvesting protein of photosystem I Lhca8 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 22.796273 KDa
SequenceString: RPLWMPGATV PAHLKGELAG DFGFDPLNLG KDPQALRWYQ QAELVHGRTA MTAVAGILIP GLLTKAGVLN VPEWYEAGKV SAEQTGIAL GPLLAVQLFM CGFVEGKRWM DFLKPGSQSE AGSFLGFEAS FKGTDNGYPG GPFDPMGMCN ESEAKTKDLK L KEIKNGRL ...String:
RPLWMPGATV PAHLKGELAG DFGFDPLNLG KDPQALRWYQ QAELVHGRTA MTAVAGILIP GLLTKAGVLN VPEWYEAGKV SAEQTGIAL GPLLAVQLFM CGFVEGKRWM DFLKPGSQSE AGSFLGFEAS FKGTDNGYPG GPFDPMGMCN ESEAKTKDLK L KEIKNGRL AMLACLGFAA QYGATGKGPL DNLADHLAAP LKTTFVDNGI SIPIHL

+
Macromolecule #16: Light-harvesting protein of photosystem I Lhca4

MacromoleculeName: Light-harvesting protein of photosystem I Lhca4 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 22.609793 KDa
SequenceString: ANRPSWFPGS KFPAHLDGTL PGDHGFDPLS LGVDPAKLKW YQQAELQNGR WAMLGAAGIL VPDLLRAVGM GGPAAQVPWF EAGKYEYFA PPSALFASMM FLFAFVEFRR LQDIRKPGSA NQDPIFTNNK LPAGEVGYPG GIFDPLGYSK GNMETLKLKE I KNARLAML ...String:
ANRPSWFPGS KFPAHLDGTL PGDHGFDPLS LGVDPAKLKW YQQAELQNGR WAMLGAAGIL VPDLLRAVGM GGPAAQVPWF EAGKYEYFA PPSALFASMM FLFAFVEFRR LQDIRKPGSA NQDPIFTNNK LPAGEVGYPG GIFDPLGYSK GNMETLKLKE I KNARLAML GFAGFVAQYQ TTGKTPLQNL SDHLANPWST TVLSNDLAR

+
Macromolecule #17: Light-harvesting protein of photosystem I Lhca5

MacromoleculeName: Light-harvesting protein of photosystem I Lhca5 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 24.988355 KDa
SequenceString: DRKLWAPTVD SPSYLNGELA GDYGFDPLGL GADPVALKWY RQSELVHARW AMLGVAGVLG QEILRPDVFW YEAGEPQNLP GPFQNINMG GLLAWEFLLM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPLGFSKGNR KELQTKEIKN G RIAMIAFM ...String:
DRKLWAPTVD SPSYLNGELA GDYGFDPLGL GADPVALKWY RQSELVHARW AMLGVAGVLG QEILRPDVFW YEAGEPQNLP GPFQNINMG GLLAWEFLLM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPLGFSKGNR KELQTKEIKN G RIAMIAFM SFVVQAQATG KGPLANLADH LSNPGANNWV SNINHCVTPS SVDVQGLTIP LTCLWPGS

+
Macromolecule #18: Light-harvesting protein of photosystem I Lhca6

MacromoleculeName: Light-harvesting protein of photosystem I Lhca6 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 24.911811 KDa
SequenceString: RPLWRPGSAP PAHLNGELPG DFGFDPLGLG ANPESLKWFA ESERVHARWA MLAVAGILVQ EVVKPDVFWY DAPTKIDLPF NIVGLLAFE FFAMHFVELK RWQDFRNPGS VDADPLFPSN KLAPHEVGYP GFAPFVPGPM EELKVKEIKN GRLAMLAFIG F TMAAQVTG ...String:
RPLWRPGSAP PAHLNGELPG DFGFDPLGLG ANPESLKWFA ESERVHARWA MLAVAGILVQ EVVKPDVFWY DAPTKIDLPF NIVGLLAFE FFAMHFVELK RWQDFRNPGS VDADPLFPSN KLAPHEVGYP GFAPFVPGPM EELKVKEIKN GRLAMLAFIG F TMAAQVTG KGPLAALSEH LADPMGTTIF SKAVVVPGQV VQPECKIPQF TDFQGTKIFT PCLFQGLW

+
Macromolecule #19: Light-harvesting protein of photosystem I Lhca9

MacromoleculeName: Light-harvesting protein of photosystem I Lhca9 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 20.119057 KDa
SequenceString:
RPTWLPNLNP PAHLKGEMAG DFGFDPLGLG ADPARLKWFA EAEKTNGRWA MMAVVGILGQ ELLGVQPSWW NAGAKDYGVA MGPLTAMEF LIMGFLETKR YQGFKETGSS GLINQFPFDP AGMYSKDMAV KEVKNGRLAM VAFVGFAVQA LASRTGPIEG L TKHLSNPG YNITYNLTHL QDVNTY

+
Macromolecule #20: Light-harvesting protein of photosystem I Lhca2 partial

MacromoleculeName: Light-harvesting protein of photosystem I Lhca2 partial
type: protein_or_peptide / ID: 20 / Details: partial / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coelastrella (plant)
Molecular weightTheoretical: 7.528819 KDa
SequenceString:
GRLAMLAFIG FCSQAAVRGK GPIDCLKDHI ADPWNNNIYT SSVGKETCVT VALLCVWPII IEATKSLNKG

+
Macromolecule #21: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 21 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

+
Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 213 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #23: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 23 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 30 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 25 / Number of copies: 15 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #26: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate

MacromoleculeName: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
type: ligand / ID: 26 / Number of copies: 2 / Formula: NKP
Molecular weightTheoretical: 436.52 Da
Chemical component information

ChemComp-NKP:
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate

+
Macromolecule #27: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 27 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

+
Macromolecule #28: OCTANOIC ACID (CAPRYLIC ACID)

MacromoleculeName: OCTANOIC ACID (CAPRYLIC ACID) / type: ligand / ID: 28 / Number of copies: 1 / Formula: OCA
Molecular weightTheoretical: 144.211 Da
Chemical component information

ChemComp-OCA:
OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid

+
Macromolecule #29: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 29 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #30: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #32: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 32 / Number of copies: 1 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol / Β-Cryptoxanthin

+
Macromolecule #33: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 33 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #34: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 34 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #35: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 35 / Number of copies: 1 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

+
Macromolecule #36: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca- ...Name: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 36 / Number of copies: 2 / Formula: C7Z
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-C7Z:
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol

+
Macromolecule #37: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 37 / Number of copies: 1 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID / Lauric acid

+
Macromolecule #38: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 38 / Number of copies: 18 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Lutein

+
Macromolecule #39: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 39 / Number of copies: 22 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

+
Macromolecule #40: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 40 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #41: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 41 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

+
Macromolecule #42: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 42 / Number of copies: 2 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

+
Macromolecule #43: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypro...

MacromoleculeName: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
type: ligand / ID: 43 / Number of copies: 1 / Formula: LPX
Molecular weightTheoretical: 453.55 Da
Chemical component information

ChemComp-LPX:
(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate

+
Macromolecule #44: water

MacromoleculeName: water / type: ligand / ID: 44 / Number of copies: 68 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 1.0 kPa / Details: Harrick Plasma cleaner PDC-32G-2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: blot for 3 seconds before plunging.
DetailsChlorophyll concentration was provided

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 31707 / Average exposure time: 1.38 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 2972135
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 56000
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 167160
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50
Output model

PDB-8cmo:
Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.

+
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