[English] 日本語
Yorodumi
- EMDB-26601: Energetic robustness to large scale structural dynamics in a phot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26601
TitleEnergetic robustness to large scale structural dynamics in a photosynthetic supercomplex
Map dataPSI-IsiA complex
Sample
  • Complex: PSI-IsiA
    • Protein or peptide: x 12 types
  • Ligand: x 13 types
Keywordsphotosystem I / antenna / cyanobacteria / photosynthesis / membrane complex
Function / homology
Function and homology information


plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis ...plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / 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 / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / Iron stress-induced chlorophyll-binding protein ...Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / Iron stress-induced chlorophyll-binding protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHarris D / Toporik H / Schlau-Cohen GS / Mazor Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2034021 United States
CitationJournal: Nat Commun / Year: 2023
Title: Energetic robustness to large scale structural fluctuations in a photosynthetic supercomplex.
Authors: Dvir Harris / Hila Toporik / Gabriela S Schlau-Cohen / Yuval Mazor /
Abstract: Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position ...Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position chlorophylls to tight tolerances considered critical for fast and efficient energy transfer. The variability in protein organization within the supercomplexes, and how efficiency is maintained despite variability, had been unresolved. Here, we report on structural heterogeneity in the 2-MDa cyanobacterial PSI-IsiA photosynthetic supercomplex observed using Cryo-EM, revealing large-scale variances in the positions of IsiA relative to PSI. Single-molecule measurements found efficient IsiA-to-PSI energy transfer across all conformations, along with signatures of transiently decoupled IsiA. Structure based calculations showed that rapid IsiA-to-PSI energy transfer is always maintained, and even increases by three-fold in rare conformations via IsiA-specific chls. We postulate that antennae design mitigates structural fluctuations, providing a mechanism for robust energy transfer in the flexible membrane.
History
DepositionApr 7, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26601.png

Downloads & links

-
Map

FileDownload / File: emd_26601.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSI-IsiA complex
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 9.199999999999999
Minimum - Maximum-42.667392999999997 - 70.466194000000002
Average (Standard dev.)-0.0007194118 (±2.3053522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : PSI-IsiA

EntireName: PSI-IsiA
Components
  • Complex: PSI-IsiA
    • 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 III
    • 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 1
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Iron stress-induced chlorophyll-binding protein
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: beta,beta-caroten-4-one
  • Ligand: CALCIUM IONCalcium
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: water

+
Supramolecule #1: PSI-IsiA

SupramoleculeName: PSI-IsiA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12 / Details: PSI-IsiA from cyanobacteria
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 2 MDa

+
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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 83.036398 KDa
SequenceString: MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM ...String:
MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM AALMLFAGWF HYHVKAPKLE WFQNVESMMN HHLAGLLGLG SLGWAGHQIH VSMPINKLLD AGVAPKDIPL PH EFILEPS KMAELYPSFA QGLTPFFTLN WGVYSDFLTF KGGLNPVTGG LWLSDTAHHH LAIAVLFIIA GHMYRTNWGI GHS MKEILE AHKGPFTGEG HKGLYEILTT SWHAQLAINL ALLGSLTIIV AQHMYAMPPY PYQAIDYATQ LSLFTHHMWI GGFL IVGAG AHGAIFMVRD YDPAKNVNNL LDRMLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMRALG RPQDMFSDTA IQLQP IFAQ WVQHLHTLAP GATAPNALAT ASYAFGGETI AVAGKVAMMP ITLGTADFMV HHIHAFTIHV TALILLKGVL YARSSR LVP DKANLGFRFP CDGPGRGGTC QVSGWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVSP DGSVTHVTLG NFAQSAI TI NGWLRDFLWA QAANVINSYG SALSAYGIMF LAGHFVFAFS LMFLFSGRGY WQELIESIVW AHNKLNVAPA IQPRALSI I QGRAVGVAHY LLGGIVTTWA FFLARSLSIG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

+
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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 81.369531 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF KNAESRLNHH LAGLFGVSSL AWAGHLVHVA IPEARGQHVG WDNFLSTPPH PAGLMPFFTG NWGVYAADPD TA GHIFGTS EGAGTAILTF LGGFHPQTES LWLTDIAHHH LAIAVIFIIA GHMYRTNWGI GHSIKEILNA HKGPLTGAGH TNL YDTINN SLHFQLGLAL ASLGVITSLV AQHMYSLPSY AFIAQDHTTQ AALYTHHQYI AGFLMVGAFA HGAIFFVRDY DPVA NKDNV LARMLEHKEA LISHLSWVSL FLGFHTLGLY VHNDVVVAFG TPEKQILIEP VFAQWIQATS GKALYGFDVL LSNPD SIAS TTGAAWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTALILIKG ALDARGSKLM PDKKDFGYSF PCDGPG RGG TCDISAWDAF YLAMFWMLNT LGWLTFYWHW KHLGVWSGNV AQFNENSTYL MGWFRDYLWA NSAQLINGYN PYGVNNL SV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETIVWAHERT PLANLVRWKD KPVALSIVQA RLVGLAHFTV GYVLTYAA F LIASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

+
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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 8.837261 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAAQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

+
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
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 15.663749 KDa
SequenceString:
MTELSGQPPK FGGSTGGLLS KANREEKYAI TWTSASEQVF EMPTGGAAIM NEGENLLYLA RKEQCLALGT QLRTKFKPKI QDYKIYRVY PSGEVQYLHP ADGVFPEKVN EGREAQGTKT RRIGQNPEPV TIKFSGKAPY EV

UniProtKB: Photosystem I reaction center subunit II

+
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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 8.154086 KDa
SequenceString:
MALNRGDKVR IKRTESYWYG DVGTVASVEK SGILYPVIVR FDRVNYNGFS GSASGVNTNN FAENELELVQ AAAK

UniProtKB: Photosystem I reaction center subunit IV

+
Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 18.267082 KDa
SequenceString:
MKHLLALLLA FTLWFNFAPS ASADDFANLT PCSENPAYLA KSKNFLNTTN DPNSGKIRAE RYASALCGPE GYPHLIVDGR FTHAGDFLI PSILFLYIAG WIGWVGRSYL IEIRESKNPE MQEVVINVPL AIKKMLGGFL WPLAAVGEYT SGKLVMKDSE I PTSPR

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 4.414148 KDa
SequenceString:
MDGSYAASYL PWILIPMVGW LFPAVTMGLL FIHIESEGEG

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 4.535415 KDa
SequenceString:
MDGLKSFLST APVMIMALLT FTAGILIEFN RFYPDLLFHP

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #9: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 8.649268 KDa
SequenceString:
MHSFLLATAV PATLSWSPKV AGVMIACNIL AIAFGKLTIK QQNVGTPMPS SNFFGGFGLG AVLGTASFGH ILGAGVILGL ANMGVL

UniProtKB: Photosystem I reaction center subunit PsaK 1

+
Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 16.631795 KDa
SequenceString:
MAESNQVVQA YNGDPFVGHL STPISDSAFT RTFIGNLPAY RKGLSPILRG LEVGMAHGYF LIGPWTLLGP LRDSEYQYIG GLIGALALI LVATAALSSY GLVTFQGEQG SGDTLQTADG WSQFAAGFFV GGMGGAFVAY FLLENLSVVD GIFRGLFN

UniProtKB: Photosystem I reaction center subunit XI

+
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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 3.382063 KDa
SequenceString:
MALSDTQILA ALVVALLPAF LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

+
Macromolecule #12: Iron stress-induced chlorophyll-binding protein

MacromoleculeName: Iron stress-induced chlorophyll-binding protein / type: protein_or_peptide / ID: 12 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 37.250734 KDa
SequenceString: MQTYGNDTVQ YEWWAGNARF ADQSGLFIAA HVAQAALTAF WAGAFTLFEI SRFDPTQAMG DQGLILLPHL ATLGWGVGDG GQIVDTYPY FVIGSIHLIA SAVLGAGALF HTLRAPADLS TLKGQGKKFH FTWENPQQLG IILGHHLLFL GAGALLLAGK A MYWGGLYD ...String:
MQTYGNDTVQ YEWWAGNARF ADQSGLFIAA HVAQAALTAF WAGAFTLFEI SRFDPTQAMG DQGLILLPHL ATLGWGVGDG GQIVDTYPY FVIGSIHLIA SAVLGAGALF HTLRAPADLS TLKGQGKKFH FTWENPQQLG IILGHHLLFL GAGALLLAGK A MYWGGLYD ATTQTVRLVS QPTLDPLVIY GYQTHFASIS SLEDLVGGHI FVGFLLIGGG IWHILVPPLG WAKKVLLFSG EA ILSYSLG GIALAGFVAA YFCAVNTLAY PPEFYGPPLA IKLGIFPYFA DTVELPMHAH TSRAWLANAH FFLAFFFLQG HLW HALRAL GFDFKRVEQA FDSLQT

UniProtKB: Iron stress-induced chlorophyll-binding protein

+
Macromolecule #13: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 13 / Number of copies: 21 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #14: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 14 / Number of copies: 15 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #15: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 15 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

+
Macromolecule #16: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 16 / Number of copies: 591 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #17: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 17 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #18: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 18 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #19: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 19 / Number of copies: 123 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #20: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 20 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #21: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 21 / Number of copies: 9 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one / Echinenone

+
Macromolecule #22: CALCIUM ION

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

+
Macromolecule #23: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 23 / Number of copies: 9 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

+
Macromolecule #24: (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: 24 / Number of copies: 3 / 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 #25: water

MacromoleculeName: water / type: ligand / ID: 25 / Number of copies: 461 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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 / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1114567
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.02)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.02)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.03) / Number images used: 143739

-
Atomic model buiding 1

Initial modelPDB ID:

6nwa

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 61.76
Output model

PDB-7umh:
Energetic robustness to large scale structural dynamics in a photosynthetic supercomplex

+
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