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- EMDB-31455: Cryo-EM Structure of primitive cyanobacterium photosystem I -

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Basic information

Entry
Database: EMDB / ID: EMD-31455
TitleCryo-EM Structure of primitive cyanobacterium photosystem I
Map data
Sample
  • Complex: PSI trimer
    • Protein or peptide: x 10 types
  • Ligand: x 8 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily ...Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 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 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 reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 Z / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria) / Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsKato K / Hamaguchi T
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI
Authors: Kato K / Hamaguchi T / Nagao R / Kawakami K / Ueno Y / Suzuki T / Uchida H / Murakami A / Nakajima Y / Yokono M / Akimoto S / Dohmae N / Yonekura K / Shen JR
History
DepositionJun 21, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_31455.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.823 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.23874322 - 0.46545348
Average (Standard dev.)0.00047807692 (±0.008708103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PSI trimer

EntireName: PSI trimer
Components
  • Complex: PSI trimer
    • 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 Z
    • Protein or peptide: Unknown protein
    • 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: Menaquinone-4
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: water

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Supramolecule #1: PSI trimer

SupramoleculeName: PSI trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 1.1 MDa

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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: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 86.505219 KDa
SequenceString: MSTTPQEREK PVRVLVDNDP VPTSTEKWGK PGWFERNLAR GPKTTTWIWD LHALAHDFET HTSDKEEISR KIFSAHFGHL AVVCVWLSG MFWHGAYFSN FTAWMENPLG LKPSAQTVWP VFGQEILNDP STVAKGFEQG GIVITSGLFH LWRAVGFTTT G QLAAMSIA ...String:
MSTTPQEREK PVRVLVDNDP VPTSTEKWGK PGWFERNLAR GPKTTTWIWD LHALAHDFET HTSDKEEISR KIFSAHFGHL AVVCVWLSG MFWHGAYFSN FTAWMENPLG LKPSAQTVWP VFGQEILNDP STVAKGFEQG GIVITSGLFH LWRAVGFTTT G QLAAMSIA MLIIAALFLF AGWFHYHKRA PKLEWFQNVE SMLNHHLAGL FGLGSLFWTG HLIHVALPVK AQLDAGIAPA QV NPFAGLD YGLMGQYFPK GFGPNGGLGA FFTLNWGQFT DFLTFKGGLE PATGALYLTD IAHHHLAIAT LFIIAGHMYR TNW GIGHSI KEMLEAHKGP LTGEGHRGLY EVLTTSWHAQ LAINLAMAGS ITIIVAHHMY AMNPYPYMGT DYATQISLFT HHMW IGGFL IVGAGAHAAI FMVRDYDPVT NQNNLLDRVL RHRDAIISHL NWVTLFLGFH SFGLYVHNDT MQALGRPRDM FADFA IPLQ PVFAQWIQNI HAAAPGGATA PWVGGTSPTW YTGALSSAAT LQANQVLALA NDKISISPIH LGTADFMVHH IFALCI HVT VLILLKGVLF ARSSRLIPDK ANLGFRFPCD GPGRGGTCQS SAWDHVFLGL FWMYNTISVV IFHFSWKMQS DVWGTVD RS TGAVNHIIGN TDVLLGGQTV ALSQYAASSI NINGWLRDFL WAQSSAVINS YGGPLSAYGL MFLGAHFIWA FSLMFLFS G RGYWQELIES IVWAHNKLKV APAIQPRALS ITQGRAVGVA HYLLGGIATT WAFFLARFLA LP

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: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 96.166758 KDa
SequenceString: MATRFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE SLYQKLFATH FGHLAIIFLW SSGNLFHIAW QGNFEQWVSN PTGVVPIAH AIWDPHFGKG AVEAFTPEGG AGPVNAAYSG LYYLYYTLGM RFNSDLYQGS IFLMVLATVF LIAGWLHLQP R FRPSLAWF ...String:
MATRFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE SLYQKLFATH FGHLAIIFLW SSGNLFHIAW QGNFEQWVSN PTGVVPIAH AIWDPHFGKG AVEAFTPEGG AGPVNAAYSG LYYLYYTLGM RFNSDLYQGS IFLMVLATVF LIAGWLHLQP R FRPSLAWF KNAESRLNHH LSALFGVSSL AFAGHMIHVA IPAARGQRVD WSNFLNTLPH PAGLAPFFTG NWGVYADPQA GP PILTFIG GLNPATGTLW LTDIAHHHLA IAVIFIIAGH MYRTNFGIGH SIKEILDAHK GPLTGEGHRG LYDTINNSLH FQL GLALAS LGVVTSLVAQ HTYALPAYFY MPQDHTTMAA LYTHHQYIAG FLMVGAFAHG AIFFVRDYDP KANENNVLAR MLEH KEALI SHLSWVSLFL GFHTLGLYVH NDVMLAFGRP EDQLLIEPVF AQFVQVQSGK IIEGIPALFG GPGVTAPGEF LTGWL GSVN ANNSPIFLPI GPGDFLVHHA IALGLHTTTL ILVKGALDAR GSKLMPDKKD FGFAFPCDGP GRGGTCDISA WDAFYL AVF WMLNTIGWVT FYWHWKWISI WGDNVAQFNA SSTYLMGWLR DYLWANSAPL IGGYSPSGGT NALSVWAWMF LFGHLVW AT GFMFLIAWRG YWQELIETLV WAHERTPLAN LVRWKDKPVA MSIVQGRLVG LAHFTIGYIL TYAAFLIAST AALYPNGP A AFTPAISAEQ AKGVLSEFKA KPVPGGVMLL LPENIVFDFD KSSVKLDADP ALNRVVGVIQ FYGSEPVEIL GHTDSLGED AYNQKLSEER ASAVKAFFEK KGIEAERLTA KGYGETKPVA PNAKPDGSDN PDGRQQNRRV EILIKTEVVP VS

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: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 8.80717 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGNKAGTIA 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
Source (natural)Organism: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 15.952242 KDa
SequenceString:
MADVKELPFG GSTPLFGGST GGLLRKAQIE EKYLIVWNSK EEQVFEMPTG GAATMVAGTN VLYLARKEQC HALHRQLVST FKIRDSKIY RVYPNGEQVL IFPMDGVPSE KSNPGREVVG YVPRKIGDNP NPVDVKFTGK ETFDV

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: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 7.468415 KDa
SequenceString:
MAIERGAKVR ILRKESYWYR EVGTVASVDK SEKTIYPVTV RFEKVNYSGI NTNNFGVSEL EEVEA

UniProtKB: Photosystem I reaction center subunit IV

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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: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 19.931127 KDa
SequenceString:
MSNKQSRVPF GAALLGILTL LLLFETGAFA QTQVKDPLKL CKDVPAYQEL KTQRLEAAQK AQADGKPVTF NEAGTKQKFE RYDTAYCGQ DGYPHLITSG QLDRAGDFLI PSVLFLWIAG ALGWAGRLYL AESKGPEDEI IIDLPKAIKC LLLGLIWPVQ A IPELISGK IRVPEDRVTI SPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit Z

MacromoleculeName: Photosystem I reaction center subunit Z / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 3.853611 KDa
SequenceString:
MQSYNVFPAL VIITTLVVPF MAAAALLFII ERDPS

UniProtKB: Photosystem I reaction center subunit Z

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Macromolecule #8: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 2.826475 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #9: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 15.806324 KDa
SequenceString:
MTLARYVYTP DPQEGTLLTP VNNSTAIRWF IDNLPINRVG MDEFTRGLEI GMAHGYWLIG PFALLGPLRN TELGLVAGLV STIGLLLIS TIGLSGYASL VEDVPTEFDR KGWSRLAGGF LVGGVGGAIF AFAILQFFPL VSAIARIP

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #10: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421
Molecular weightTheoretical: 3.212907 KDa
SequenceString:
MAATVVSGAQ VAIAFVVALI AGIAALLLST ALGK

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #11: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 11 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 264 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #13: Menaquinone-4

MacromoleculeName: Menaquinone-4 / type: ligand / ID: 13 / Number of copies: 6 / Formula: 1L3
Molecular weightTheoretical: 444.648 Da
Chemical component information

ChemComp-1L3:
Menaquinone-4

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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: 60 / 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: 9 / 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 17 / 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 #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 402 / 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

Concentration1.68 mg/mL
BufferpH: 6.5 / Component:
ConcentrationFormula
20.0 mMMES-NaOH
0.03 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / 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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 70.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: An initial model was generated de novo from 2D classification.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 261743
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7f4v:
Cryo-EM structure of a primordial cyanobacterial photosystem I

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