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- EMDB-14248: Chlamydomonas reinhardtii TSP9 mutant small Photosystem I complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14248
TitleChlamydomonas reinhardtii TSP9 mutant small Photosystem I complex
Map data
Sample
  • Complex: C. reinhardtii Photosystem I supercomplex
    • Protein or peptide: x 17 types
  • Ligand: x 22 types
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily ...Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 VIII / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center ...Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsKlaiman D / Schwartz T / Nelson N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: Biomolecules / Year: 2023
Title: Structure of Photosystem I Supercomplex Isolated from a Cytochrome b6f Temperature-Sensitive Mutant.
Authors: Tom Schwartz / Mariia Fadeeva / Daniel Klaiman / Nathan Nelson /
Abstract: The unicellular green alga, , has been widely used as a model system to study photosynthesis. Its possibility to generate and analyze specific mutants has made it an excellent tool for mechanistic ...The unicellular green alga, , has been widely used as a model system to study photosynthesis. Its possibility to generate and analyze specific mutants has made it an excellent tool for mechanistic and biogenesis studies. Using negative selection of ultraviolet (UV) irradiation-mutated cells, we isolated a mutant (TSP9) with a single amino acid mutation in the Rieske protein of the cytochrome b6f complex. The W143R mutation in the petC gene resulted in total loss of cytochrome b6f complex function at the non-permissive temperature of 37 °C and recovery at the permissive temperature of 25 °C. We then isolated photosystem I (PSI) and photosystem II (PSII) supercomplexes from cells grown at the non-permissive temperature and determined the PSI structure with high-resolution cryogenic electron microscopy. There were several structural alterations compared with the structures obtained from wild-type cells. Our structural data suggest that the mutant responded by excluding the Lhca2, Lhca9, PsaL, and PsaH subunits. This structural alteration prevents state two transition, where LHCII migrates from PSII to bind to the PSI complex. We propose this as a possible response mechanism triggered by the TSP9 phenotype at the non-permissive temperature.
History
DepositionFeb 7, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14248.png

Downloads & links

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Map

FileDownload / File: emd_14248.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 390 pix.
= 327.6 Å		0.84 Å/pix.
x 390 pix.
= 327.6 Å		0.84 Å/pix.
x 390 pix.
= 327.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.015943617 - 0.054983288
Average (Standard dev.)0.0002272367 (±0.0021505384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 327.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14248_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14248_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : C. reinhardtii Photosystem I supercomplex

EntireName: C. reinhardtii Photosystem I supercomplex
Components
  • Complex: C. reinhardtii Photosystem I supercomplex
    • 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, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit psaK, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic (Lhca4)
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM IONCalcium
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: LAURIC ACID
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: CHLOROPHYLL B
  • Ligand: SPHINGOSINE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: DIACYL GLYCEROLDiglyceride
  • Ligand: PALMITIC ACID
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: ERGOSTEROL
  • Ligand: water

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Supramolecule #1: C. reinhardtii Photosystem I supercomplex

SupramoleculeName: C. reinhardtii Photosystem I supercomplex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#17 / Details: Contains 10 core subunits and 8 antenna proteins
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Chloroplast / Location in cell: Chloroplast thylakoid membrane
Molecular weightTheoretical: 780 KDa

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 83.239203 KDa
SequenceString: MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV ...String:
MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV MAAAMFFAGW FHYHKAAPKL EWFQNVESML NHHLGGLLGL GSLAWAGHQI HVSLPVNKLL DAGVDPKEIP LP HDLLLNR AIMADLYPSF AKGIAPFFTL NWSEYSDFLT FKGGLNPVTG GLWLSDTAHH HVAIAVLFLV AGHMYRTNWG IGH SMKEIL EAHRGPFTGE GHVGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHTW IGGF CIVGA GAHAAIFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQ PVFA QWIQNTHFLA PQLTAPNALA ATSLTWGGDL VAVGGKVAMM PISLGTSDFM VHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVT ASGVSHITGG NFAQSAN TI NGWLRDFLWA QSSQVIQSYG SALSAYGLIF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSI T QGRAVGVAHY LLGGIATTWS FFLARIISVG

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 82.184266 KDa
SequenceString: MATKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHVA WQGNFEQWVT DPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG SVFLALVSAI FLFAGWLHLQ P NFQPSLSW ...String:
MATKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHVA WQGNFEQWVT DPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG SVFLALVSAI FLFAGWLHLQ P NFQPSLSW FKDAESRLNH HLSGLFGVSS LAWTGHLVHV AIPESRGQHV GWDNFLSVLP HPQGLTPFFT GNWAAYAQSP DT ASHVFGT AQGSGQAILT FLGGFHPQTQ SLWLTDMAHH HLAIAVIFIV AGHMYRTNFG IGHRMQAILE AHTPPSGSLG AGH KGLFDT VNNSLHFQLG LALASVGTIT SLVAQHMYSL PPYAFQAIDF TTQAALYTHH QYIAGFIMCG AFAHGAIFFI RDYD PEQNK GNVLARMLDH KEALISHLSW VSLFLGFHTL GLYVHNDVMQ AFGTPEKQIL IEPVFAQWIQ AAHGKALYGF DFLLS SKTS AAFANGQSLW LPGWLDAINN NQNSLFLTIG PGDFLVHHAI ALGLHTTTLI LVKGALDARG SKLMPDKKDF GYSFPC DGP GRGGTCDISA YDAFYLAVFW MLNTIGWVTF YWHWKHLTLW QGNVAQFDES STYLMGWLRD YLWLNSSQLI NGYNPFG MN SLSVWAWTFL FGHLIYATGF MFLISWRGYW QELIETLVWA HEKTPLANLV YWKDKPVALS IVQARLVGLA HFSVGYIF T YAAFLIASTS GRFG

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 8.869325 KDa
SequenceString:
MAHIVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKASQMA SAPRTEDCVG CKRCETACPT DFLSVRVYLG SESTRSMGLS Y

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Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 21.401885 KDa
SequenceString: MAVMMRTQAP AATRASSRVA VAARPAARRA VVVRAEAEAA PAAAKKAAEK PAWTVPTLNP DTPSPIFGGS TGGLLRKAQT EEFYVITWE AKKEQIFEMP TGGAAIMRQG PNLLKFGKKE QCLALTTQLR NKFKLTP(SNC)FY RVFPDGKVQY LHPADGV YP EKVNAGRVGA ...String:
MAVMMRTQAP AATRASSRVA VAARPAARRA VVVRAEAEAA PAAAKKAAEK PAWTVPTLNP DTPSPIFGGS TGGLLRKAQT EEFYVITWE AKKEQIFEMP TGGAAIMRQG PNLLKFGKKE QCLALTTQLR NKFKLTP(SNC)FY RVFPDGKVQY LHPADGV YP EKVNAGRVGA NQNMRRIGQN VNPIKVKFSG RMMSPAEI

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Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 10.786395 KDa
SequenceString:
MQALSSRVNI AAKPQRAQRL VVRAEEVKAA PKKEVGPKRG SLVKILRPES YWFNQVGKVV SVDQSGVRYP VVVRFENQNY AGVTTNNYA LDEVVAAK

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Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 24.088936 KDa
SequenceString: MALTMRNPAV KASSRVAPSS RRALRVACQA QKNETASKVG TALAASALAA AVSLSAPSAA MADIAGLTPC SESKAYAKLE KKELKTLEK RLKQYEADSA PAVALKATME RTKARFANYA KAGLLCGNDG LPHLIADPGL ALKYGHAGEV FIPTFGFLYV A GYIGYVGR ...String:
MALTMRNPAV KASSRVAPSS RRALRVACQA QKNETASKVG TALAASALAA AVSLSAPSAA MADIAGLTPC SESKAYAKLE KKELKTLEK RLKQYEADSA PAVALKATME RTKARFANYA KAGLLCGNDG LPHLIADPGL ALKYGHAGEV FIPTFGFLYV A GYIGYVGR QYLIAVKGEA KPTDKEIIID VPLATKLAWQ GAGWPLAAVQ ELQRGTLLEK EENITVSPR

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Macromolecule #7: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 13.236007 KDa
SequenceString:
MQTLASRPSL RASARVAPRR APRVAVVTKA ALDPQIVISG STAAFLAIGR FVFLGYQRRE ANFDSTVGPK TTGATYFDDL QKNSTIFAT NDPAGFNIID VAGWGALGHA VGFAVLAINS LQGANLS

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Macromolecule #8: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 10.586388 KDa
SequenceString:
MALRAVSAKS AVRPTVARAS VKPVAALKPA QKMALAGAAS VALLAASSSS AEASQVIATV ASAAQGYPFV PPSWAPSVFV PLTGLVLPA IAMATLFVYI EKEAPSS

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Macromolecule #9: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 4.750509 KDa
SequenceString:
MKDFTTYLST APVIATIWFT FTAGLLIEIN RYFPDPLVFS F

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Macromolecule #10: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 11.214084 KDa
SequenceString:
MQALATRPSA IRPTKAARRS SVVVRADGFI GSSTNLIMVA STTATLAAAR FGLAPTVKKN TTAGLKLVDS KNSAGVISND PAGFTIVDV LAMGAAGHGL GVGIVLGLKG IGAL

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Macromolecule #11: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 23.923205 KDa
SequenceString: MALSMRTLSA RTAAPRGFSG RRVAAVSNGS RVTMKAGNWL PGSDAPAWLP DDLPGNYGFD PLSLGKEPAS LKRFTESEVI HGRWAMLGV AGSLAVELLG YGNWYDAPLW AVNGGKATWF GIEVPFDLNA LLAFEFVAMA AAEGQRGDAG GVVYPGGAFD P LGFAKDSS ...String:
MALSMRTLSA RTAAPRGFSG RRVAAVSNGS RVTMKAGNWL PGSDAPAWLP DDLPGNYGFD PLSLGKEPAS LKRFTESEVI HGRWAMLGV AGSLAVELLG YGNWYDAPLW AVNGGKATWF GIEVPFDLNA LLAFEFVAMA AAEGQRGDAG GVVYPGGAFD P LGFAKDSS KSGELKLKEI KNGRLAMVAF LGFVAQHAAT GKGPIAALGE HLANPWGANF ATNGISVPFF

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Macromolecule #12: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 32.629486 KDa
SequenceString: MMLTKSAQAA FSGKVARPAK ANRARLVCRA EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQY SEVIHARWAM LGAAGCIAPE VLGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE L RRLQDFRY ...String:
MMLTKSAQAA FSGKVARPAK ANRARLVCRA EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQY SEVIHARWAM LGAAGCIAPE VLGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE L RRLQDFRY PGSMGQQYFL GLEAIFKGSG DAAYPGGPFF NLFNLGKTEA AMKELKLKEI KNGRLAMLAM LGYGAQAVMT GK GPFQNLV EHLADPVNNN ILTNFAGRVS GSSQPWRPHG WWRRRYRSVA ALALIRNRSV C

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Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 26.248869 KDa
SequenceString: MALSMIAQRR AGAFSARQAP RAVRAQAAVR PVWFPGNPPP AHLDGSLAGD YGFDPLFLGQ EPQTLKWYVQ AELVHGRFAM LGAAGIILT SIGAKVGLGF PEWYDAGKVV VEKNNIDFPT LMVIQFYLMG WAETKRWYDF KNPGSQADGS FLGFTEEFKG L ENGYPGGR ...String:
MALSMIAQRR AGAFSARQAP RAVRAQAAVR PVWFPGNPPP AHLDGSLAGD YGFDPLFLGQ EPQTLKWYVQ AELVHGRFAM LGAAGIILT SIGAKVGLGF PEWYDAGKVV VEKNNIDFPT LMVIQFYLMG WAETKRWYDF KNPGSQADGS FLGFTEEFKG L ENGYPGGR FFDPMGLSRG DAAKYQEYKQ KEVKNGRLAM IACLGFAAQY AATGKGPLDN LADHLADPNH VNFATNGVSI PI A

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Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 25.948812 KDa
SequenceString: MALTMKRSGV AARSASSRKS VVTCVARQSW LPGSQIPAHL DTPAAQALAG NFGFDPLGLG KDPVALRWYQ QAELIHCRTA MAGVAGILI PGLLTKAGAL NVPEWYDAGK VAIENSFAPW GSLLAVQLFL CGFVEAKRWQ DIRKPGSQGE PGSFLGFEAS L KGTSELGY ...String:
MALTMKRSGV AARSASSRKS VVTCVARQSW LPGSQIPAHL DTPAAQALAG NFGFDPLGLG KDPVALRWYQ QAELIHCRTA MAGVAGILI PGLLTKAGAL NVPEWYDAGK VAIENSFAPW GSLLAVQLFL CGFVEAKRWQ DIRKPGSQGE PGSFLGFEAS L KGTSELGY PGGPFDPLGL SKEADKWADW KLKEVKNGRL AMLAFLGFVA QKYATGAGPV DNLAAHLKDP WHVNYATNGV SL PFL

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic (Lhca4)

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic (Lhca4)
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 28.729822 KDa
SequenceString: MAFVLAKSSA FGVAAKPVSR RSSVAVKASA VPENVKEARE WIDAWKSKSG GAKRDAALPS WMPGADLPGY LNGTLPGDFG FDPLYLGQD PVKLKWYAQA ELMNARFAML AVAGILVPEL LSNIGFSWPG AGVAWYDAGK FEYFAPASSL FGVQMLLFAW V EIRRYQDF ...String:
MAFVLAKSSA FGVAAKPVSR RSSVAVKASA VPENVKEARE WIDAWKSKSG GAKRDAALPS WMPGADLPGY LNGTLPGDFG FDPLYLGQD PVKLKWYAQA ELMNARFAML AVAGILVPEL LSNIGFSWPG AGVAWYDAGK FEYFAPASSL FGVQMLLFAW V EIRRYQDF VKPGSANQDP IFTNNKLPDG NEPGYPGGIF DPFGWSKGDI KSLKLKEIKN GRLAMLAFAG FIGQAYTTGT TP LKNLSTH LADPWSTTVW QNDLARL

+
Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 28.257555 KDa
SequenceString: MAALMQKSAL SRPACSTRSS RRAVVVRAAA DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVL VQEIVKPDVY FYEAGLPQNL PEPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN P EMGYPGGI ...String:
MAALMQKSAL SRPACSTRSS RRAVVVRAAA DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVL VQEIVKPDVY FYEAGLPQNL PEPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN P EMGYPGGI FDPFGFSKGN LKELQTKEIK NGRLAMIAYM AFILQAQATG KGPLAALSAH LSNPFGNNIL KNIGTCTVPH SV DVQGLTI PLTCLWPGSQ

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Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: Chloroplast
Molecular weightTheoretical: 27.812373 KDa
SequenceString: MMLVAKNAVA ARPSARSARR SVVAKASSRP LWLPGSTPPA HLKGDLPGDF GFDPLGLGAN AESLKWFKES ELVHSRWAMA AVAGILVQE IVRPDVFWYN AGKEVESPLG PLGLLAVEFF LMHWVEVRRW QDLRKPGSVD QDPIFSQYKL PPHEVGYPGG V FAPFIPGD ...String:
MMLVAKNAVA ARPSARSARR SVVAKASSRP LWLPGSTPPA HLKGDLPGDF GFDPLGLGAN AESLKWFKES ELVHSRWAMA AVAGILVQE IVRPDVFWYN AGKEVESPLG PLGLLAVEFF LMHWVEVRRW QDLRKPGSVD QDPIFSQYKL PPHEVGYPGG V FAPFIPGD LAELKVKEIK NGRLAMLAFV GFVMAAQVTG KGPIAALQEH LADPWGTTIF SKAAVVPGQA VAPPCKIPAS VS YKGIEIP TPCFLQGLWP

+
Macromolecule #18: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 18 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 186 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 28 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #24: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 16 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 25 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #26: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 26 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #27: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 27 / Number of copies: 3 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

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

+
Macromolecule #28: (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: 28 / Number of copies: 3 / 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 #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #30: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 30 / Number of copies: 1 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID / Lauric acid

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Macromolecule #31: (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: 31 / Number of copies: 14 / 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 #32: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 32 / Number of copies: 28 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #33: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 33 / Number of copies: 3 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

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Macromolecule #34: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 34 / 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 #35: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 35 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

+
Macromolecule #36: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 36 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #37: 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: 37 / 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

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Macromolecule #38: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 38 / Number of copies: 2 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL / Ergosterol

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Macromolecule #39: water

MacromoleculeName: water / type: ligand / ID: 39 / Number of copies: 570 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 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: 12.0 nm / 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: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13173 / Average exposure time: 2.6 sec. / Average electron dose: 57.74 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1009378
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 20000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 173187
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6jo5

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7r3k:
Chlamydomonas reinhardtii TSP9 mutant small Photosystem I complex

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