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- PDB-7yca: Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreoco... -

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Basic information

Entry
Database: PDB / ID: 7yca
TitleCryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri
Components
  • (Chlorophyll a-b binding protein, ...) x 6
  • (Photosystem I ...) x 12
  • Lhca1
  • Lhca6
  • PSI subunit V
  • PsaG
  • PsaO
KeywordsPHOTOSYNTHESIS / Complex / Electron transport
Function / homology
Function and homology information


chloroplast 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 ...chloroplast 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 / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IWJ / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IWJ / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX / PHYLLOQUINONE / Chem-Q6L / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I PsaN, reaction centre subunit N / Photosystem I PsaG/PsaK protein / Unnamed product / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I PsaE, reaction centre subunit IV / Chlorophyll a-b binding protein, chloroplastic / PSI-G / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / 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 speciesOstreococcus tauri (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsShan, J. / Sheng, X. / Ishii, A. / Watanabe, A. / Song, C. / Murata, K. / Minagawa, J. / Liu, Z.
Funding support Japan, China, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H04778 and 21H05040 Japan
Chinese Academy of SciencesXDB37020101 and YSBR-015 China
National Natural Science Foundation of China (NSFC)31925024 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
CitationJournal: Elife / Year: 2023
Title: The photosystem I supercomplex from a primordial green alga harbors three light-harvesting complex trimers.
Authors: Asako Ishii / Jianyu Shan / Xin Sheng / Eunchul Kim / Akimasa Watanabe / Makio Yokono / Chiyo Noda / Chihong Song / Kazuyoshi Murata / Zhenfeng Liu / Jun Minagawa /
Abstract: As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in ...As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll 603-609 pair in Lhca1-4.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Lhca6
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction centre subunit IV
F: Photosystem I reaction center subunit III
G: PsaG
H: Photosystem I PsaH, reaction centre subunit VI
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I PsaG/PsaK protein
L: PSI subunit V
M: Photosystem I reaction center subunit XII
N: Photosystem I PsaN, reaction centre subunit N
O: PsaO
P: Chlorophyll a-b binding protein, chloroplastic
Q: Chlorophyll a-b binding protein, chloroplastic
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Chlorophyll a-b binding protein, chloroplastic
U: Chlorophyll a-b binding protein, chloroplastic
V: Chlorophyll a-b binding protein, chloroplastic
W: Chlorophyll a-b binding protein, chloroplastic
X: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,076,390479
Polymers715,92830
Non-polymers360,462449
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules 16GLO

#1: Protein Lhca1


Mass: 24128.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U3
#6: Protein Lhca6


Mass: 26742.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A1Y5IA87
#13: Protein PsaG


Mass: 14124.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q019T9
#18: Protein PSI subunit V


Mass: 21526.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090M7B0
#21: Protein PsaO


Mass: 15020.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096P9N0

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Chlorophyll a-b binding protein, ... , 6 types, 13 molecules 2345PRSTUVWXQ

#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26404.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A454XUD2
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29432.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U5
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25924.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9V1
#5: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23401.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090M1L8
#22: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 24689.807 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9U7
#23: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24161.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090LYE8

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Photosystem I ... , 12 types, 12 molecules ABCDEFHIJKMN

#7: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 83249.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K1, photosystem I
#8: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 81421.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K2, photosystem I
#9: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8751.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3P1, photosystem I
#10: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 20560.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A1Y5I5Y8
#11: Protein Photosystem I reaction centre subunit IV


Mass: 11278.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A454XT75
#12: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 24593.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q01B61
#14: Protein Photosystem I PsaH, reaction centre subunit VI


Mass: 17797.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096PAU9
#15: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3766.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3K0
#16: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4731.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3J4
#17: Protein Photosystem I PsaG/PsaK protein


Mass: 13573.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A096P8E8
#19: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3413.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q0P3J8
#20: Protein Photosystem I PsaN, reaction centre subunit N


Mass: 14405.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: A0A090N3J0

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Sugars , 1 types, 2 molecules

#36: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 451 molecules

#24: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 245 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical...
ChemComp-IWJ / (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one / Prasinoxanthin


Mass: 600.870 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#28: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#29: Chemical...
ChemComp-Q6L / (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol


Mass: 570.887 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C40H58O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C40H56
#31: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#33: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C31H46O2
#35: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#37: Chemical
ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#38: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#39: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: photosystem I-light-harvesting complex I-prasinophyte-specific Lhc protein (PSI-LHCI-Lhcp) supercomplex
Type: COMPLEX / Entity ID: #1-#22 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ostreococcus tauri (plant) / Strain: OTH95 / Cellular location: thylakoid membrane / Organelle: chloroplast
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.1particle selectionTemplate picker was used to automatically select particle images
4cryoSPARC3.3.1CTF correction
5MotionCorr21.3CTF correction
8UCSF Chimera1.16model fittingUCSF Chimera was used to maunnally fit model and map
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
14PHENIX1.19.2model refinementPhenix 1.19. 2 was used to automatically refined in real space
Image processingDetails: The selected images were normalized
CTF correctionType: NONE
Particle selectionNum. of particles selected: 5288217
Details: Template picker was used to automatically select particle images
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80366 / Symmetry type: POINT
Atomic model buildingB value: 110.967 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Details: Initial local fitting was done using Chimera and then Wincoot was usd for flexible fitting
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
15ZJI

5zji

A5ZJIA1
25ZJI

5zji

B5ZJIB1
35ZJI

5zji

C5ZJIC1
45ZJI

5zji

D5ZJID1
55ZJI

5zji

E5ZJIE1
65ZJI

5zji

F5ZJIF1
75ZJI

5zji

G5ZJIG1
85ZJI

5zji

H5ZJIH1
95ZJI

5zji

I5ZJII1
105ZJI

5zji

J5ZJIJ1
115ZJI

5zji

K5ZJIK1
125ZJI

5zji

L5ZJIL1
135ZJI

5zji

O5ZJIO1
147D0J

7d0j

Q7D0JQ2
157D0J

7d0j

P7D0JP2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01268761
ELECTRON MICROSCOPYf_angle_d1.65998641
ELECTRON MICROSCOPYf_dihedral_angle_d18.38511647
ELECTRON MICROSCOPYf_chiral_restr0.0838110
ELECTRON MICROSCOPYf_plane_restr0.01113006

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  • 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

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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

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