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- PDB-6qph: Dunaliella minimal PSI complex -

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Basic information

Entry
Database: PDB / ID: 6qph
TitleDunaliella minimal PSI complex
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I ...) x 4
  • Lhc2
  • Lhc4
  • PsaD
  • PsaE
  • PsaF
KeywordsPHOTOSYNTHESIS / Photosystem I / Dunaliella / Electron Transport
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / 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 / Alpha-Beta Plaits - #20 / 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 / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / CACODYLATE ION / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / GLUTATHIONE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT ...BETA-CAROTENE / CACODYLATE ION / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / GLUTATHIONE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2
Similarity search - Component
Biological speciesDunaliella salina (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKlaiman, D. / Caspy, I. / Nelson, N.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
Israel Science Foundation2716/17 Israel
CitationJournal: Nat Plants / Year: 2020
Title: Structure of a minimal photosystem I from the green alga Dunaliella salina.
Authors: Annemarie Perez-Boerema / Daniel Klaiman / Ido Caspy / Sigal Y Netzer-El / Alexey Amunts / Nathan Nelson /
Abstract: Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular ...Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein, chloroplastic
2: Lhc2
3: Chlorophyll a-b binding protein, chloroplastic
4: Lhc4
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PsaF
J: Photosystem I reaction center subunit IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,690214
Polymers308,45511
Non-polymers160,235203
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240160 Å2
ΔGint-2220 kcal/mol
Surface area115050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.881, 100.506, 191.040
Angle α, β, γ (deg.)90.00, 91.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 13

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


Mass: 21149.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K003
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22732.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K004

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Protein , 5 types, 5 molecules 24DEF

#2: Protein Lhc2


Mass: 23120.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#4: Protein Lhc4


Mass: 23131.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#8: Protein PsaD


Mass: 15989.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#9: Protein PsaE


Mass: 7297.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#10: Protein PsaF


Mass: 18212.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

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Photosystem I ... , 4 types, 4 molecules ABCJ

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


Mass: 81748.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXV2, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 81742.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ0, photosystem I
#7: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8717.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW7, photosystem I
#11: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4614.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW0

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Sugars , 2 types, 5 molecules

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


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15
#22: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 14 types, 198 molecules

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


Mass: 568.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O2
#13: 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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#14: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#16: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#17: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#19: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#20: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#23: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#24: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#26: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#27: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate 50mM, MgCl2 100mM, PEG1500 8-11%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 3.4→48.947 Å / Num. obs: 83250 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 109.15 Å2 / Rpim(I) all: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 3.4→3.5 Å / Num. unique obs: 4575 / Rpim(I) all: 0.636

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L8R

5l8r


Resolution: 3.4→48.947 Å / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 45.94
RfactorNum. reflection% reflection
Rfree0.3563 1593 1.92 %
Rwork0.3373 --
obs0.3377 82910 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→48.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21829 0 9009 0 30838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832704
X-RAY DIFFRACTIONf_angle_d1.87646651
X-RAY DIFFRACTIONf_dihedral_angle_d17.38517710
X-RAY DIFFRACTIONf_chiral_restr0.0723942
X-RAY DIFFRACTIONf_plane_restr0.0076087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.50980.47461400.41387330X-RAY DIFFRACTION99
3.5098-3.63520.42281330.3957315X-RAY DIFFRACTION100
3.6352-3.78070.3481510.37687375X-RAY DIFFRACTION100
3.7807-3.95270.39871550.36667301X-RAY DIFFRACTION100
3.9527-4.1610.39281200.36027406X-RAY DIFFRACTION100
4.161-4.42150.37691440.35237380X-RAY DIFFRACTION100
4.4215-4.76260.37971590.33827356X-RAY DIFFRACTION100
4.7626-5.24140.3421520.33677366X-RAY DIFFRACTION99
5.2414-5.99870.35621200.35477439X-RAY DIFFRACTION100
5.9987-7.55320.32511540.34097472X-RAY DIFFRACTION100
7.5532-48.95170.32511650.297577X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.3531 Å / Origin y: 1.1142 Å / Origin z: 44.127 Å
111213212223313233
T1.2549 Å2-0.0733 Å20.0825 Å2-0.8128 Å2-0.0849 Å2--1.3298 Å2
L0.4712 °20.08 °2-0.037 °2-1.1001 °2-0.14 °2--0.6526 °2
S0.0084 Å °-0.1035 Å °-0.1015 Å °0.3828 Å °-0.0278 Å °-0.4395 Å °-0.1525 Å °0.2044 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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