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- EMDB-0727: Structure of PSI from H. hongdechloris grown under far-red light ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0727
TitleStructure of PSI from H. hongdechloris grown under far-red light condition
Map data
Sample
  • Complex: far-red PSI
    • Protein or peptide: x 9 types
  • Ligand: x 12 types
KeywordsPhotosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / 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 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 center subunit PsaK / Photosystem I reaction centre subunit PsaK / 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 superfamily / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / 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 II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I iron-sulfur center / Photosystem I reaction center subunit PsaK
Similarity search - Component
Biological speciesHalomicronema hongdechloris (bacteria) / Halomicronema hongdechloris C2206 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsKato K / Nagao R
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Authors: Koji Kato / Toshiyuki Shinoda / Ryo Nagao / Seiji Akimoto / Takehiro Suzuki / Naoshi Dohmae / Min Chen / Suleyman I Allakhverdiev / Jian-Ren Shen / Fusamichi Akita / Naoyuki Miyazaki / Tatsuya Tomo /
Abstract: Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first ...Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
History
DepositionAug 1, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kmx
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0727.png

Downloads & links

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Map

FileDownload / File: emd_0727.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.30953747 - 0.91508144
Average (Standard dev.)0.0009085082 (±0.013346554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z313.200313.200313.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3100.9150.001

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Supplemental data

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Sample components

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Entire : far-red PSI

EntireName: far-red PSI
Components
  • Complex: far-red PSI
    • 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 VIII
    • Protein or peptide: Photosystem I reaction center subunit PsaK
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll F
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: UNKNOWN LIGAND
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: far-red PSI

SupramoleculeName: far-red PSI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Halomicronema hongdechloris (bacteria)

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 87.406258 KDa
SequenceString: MTTSPPEQRQ RVRVEVDQNP NPTSFEKWAK PGHFERSLAR GPKTTTWIWD LHADAHDFDS HTTDLEDISR KIFSAHFGHL AVIFLWLSG MYFHGARFSN FSSWMTDPIH IKPSAQVVWP IFGQEILNAD MGDGFRGIQI TSGLFQMWRG EGFTHEFQLF W TAIGALVM ...String:
MTTSPPEQRQ RVRVEVDQNP NPTSFEKWAK PGHFERSLAR GPKTTTWIWD LHADAHDFDS HTTDLEDISR KIFSAHFGHL AVIFLWLSG MYFHGARFSN FSSWMTDPIH IKPSAQVVWP IFGQEILNAD MGDGFRGIQI TSGLFQMWRG EGFTHEFQLF W TAIGALVM AALMMFAGWF HYHVRAPKLD WFRNWESMMN HHLAGLLGLG SLGWAGHLIH VALPTNKLLD AGVPLEDIPL PH EFILNKS LMVDLYPSFA EGVKPFFTLN WSAYADFLTF KGGLNPVTGG LWMTDIAHHH VAIAVLFIIA GHFYRTNWGI GHS FRELLD DARTPKMLPI FNFIGPVGHR GLDKIFETSW HANLAIHLVQ FGTASLLVAH HMYAMPPYPY LATDYATVTS LFTH HVWIA GFCIVGGAAH AAIFLVRDYN PADHVNNVLD RTLRHRDTVV SHLAWVCQFL GFHSFAMYCH NDTMRAFGRP QDMFS DTGI QLQPIFAQWV QQIQTMAVGA NLQAAEPLGN VFGGLRNIDL AGVGVTAPGL GGPVSHAFGG GVVAIGDKIA MMPIQL GTA DFLIHHIHAF TIHVTVLVLL KGVLFSRNSR LIPDKGELGF RFPCDGPGRG GTCQVSAWDH VFLGLFWMYN SLSIVIF HF FWKMQSDVWG TVGADGTISH ITGGNFAQAS ITNNGWLRDF LWAQASQVIG SYGSALSAYG LFFLAGHFIF GFSLMFLF S GRGYWQELIE SIVWAHNKLK ITTAIQPRAL SITQGRAVGV AHYLLGGIVT TWAFFLARMA AIG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 83.287695 KDa
SequenceString: MATKFPKFSQ DLQRDPTTRR LFYAIATAHD FESHDGMSEE NLYQRIFASH FGHLAIIFLW ISGILFHVAW QGNFEQWIQD PLNNSPIAH AIWDAQFGPP AIAAYTQAGA MNPVDICYSG VYHWWYTIGM RTNNDLFMGS IFLLLLSSVM LYAGWLHLQP R FRPGLAWF ...String:
MATKFPKFSQ DLQRDPTTRR LFYAIATAHD FESHDGMSEE NLYQRIFASH FGHLAIIFLW ISGILFHVAW QGNFEQWIQD PLNNSPIAH AIWDAQFGPP AIAAYTQAGA MNPVDICYSG VYHWWYTIGM RTNNDLFMGS IFLLLLSSVM LYAGWLHLQP R FRPGLAWF KNAESRLNHH LAGLFGVSSL AWTGHLVHVA LPESRGQHVG WDNFLSIRPH PEGLAPLFTG NWGAYAQNPD TA EHAFGTA QGAGSAILTF LGGFHPQTES LWLTDMAHHH LAIAVIFIVA GHMYRTNFGI GHNIKEMTEA LQGPGRSGFF IAP RTGRGH KGIYDTYNNS LHFQLGWHLA CLGVITSLVA QHMYAMPPYA FMARDYTTMS ALYTHHQYIA GFLMIGAFAH GAIF LIRDY DPEANRDNVL ARMLAHKEAI ISHLSWVSLF LGFHTLGLYV HNDCEVALGS PEKQILIEPV FAQWTQAFHG KALYG INSL LSNPDSVAST AWPNYGNVWL SGWLEAVNNG ANSLFLTIGP GDLLVHHAIA LGLHVTTLIL VKGALDARGS KLMPDK KDF GYSFPCDGPG RGGTCDISAW DAFYLATFWM LNTLGWVTFY WHWKHLSVWS GNVAQFNESS TYLMGWFRDY LWANSAQ LI NGYSPAGTNS LAVWAWMFLF GHLAWAVSFM FLITWRGYWQ ELIETLMWAH ENTPLSFGYP KDKPVALSIV QARLVGLT H FTVGYIATYG AFLIASTSSR FP

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 8.782184 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAGSIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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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 / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 15.7238 KDa
SequenceString:
MAETLTGKTP VFGGSTGGLL TRAAVEEKYA ITWTSTKQQV FEMPTGGAAI MHEGENLLYL ARKEQCLALG TQLRSKFKPK IEDYKIYRI YPNGETQYVH PADGVFPEKV NEGREYNGKI DRNIGANPDP ATVKFSGKAP YEV

UniProtKB: Photosystem I reaction center subunit II

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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: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 7.907028 KDa
SequenceString:
MVQRGSKVRI LRPESYWYRD IGTVATVDQS GIRYPAIVRF DKVNYYGISS NNFALSELEE VEPPKKKK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 7.136356 KDa
SequenceString:
MADMTQLTGA YAAPWLPWIM IPLIFYILPF PIFAIIFLWI EREGNGVNDM GGEPMKSDGN YPV

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #7: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 9.726539 KDa
SequenceString:
MFGFGIAGFN GGLLAQASPQ TAEWSLSIAV IMVVCNLFVL AIGKYAIQRP GAGPELPVQL PMLFAGFGLP ELLATASLGH ILGAGMILG LGNAGLL

UniProtKB: Photosystem I reaction center subunit PsaK

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Macromolecule #8: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 20.191928 KDa
SequenceString:
MTNTETSTWV DAYDQKDIIQ PYRGNPELGN LATPVNSSNL VKTYINNLPA YRPGLTPFLR GLEIGMAHGY FLVGPEVVVG PLRETAHGA NLSGLITAIY ITVSACLGIS IFALATFQGD PRGAYNSNSP DRLRPLRSKD GWFQLSGGIL LGSMGGAIFA Y VLLENFGD LDAILRGAVN VSQWLGGGVM G

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #9: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Halomicronema hongdechloris C2206 (bacteria)
Molecular weightTheoretical: 3.440141 KDa
SequenceString:
MTLSETQVFV ALVIALVPAI LAFRLSTELY K

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Macromolecule #10: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 10 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #11: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 246 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #12: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 12 / Number of copies: 21 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
Chlorophyll F

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Macromolecule #13: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 13 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 51 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 17 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 18 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #19: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 19 / Number of copies: 15 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #20: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 20 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 636 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.071 mg/mL
BufferpH: 6.5 / Component:
ConcentrationName
20.0 mMMES-NaOH
0.04 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 311993
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1jb0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6kmx:
Structure of PSI from H. hongdechloris grown under far-red light condition

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