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Entry
Database: PDB / ID: 5zji
TitleStructure of photosystem I supercomplex with light-harvesting complexes I and II
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 5
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 10
  • 16kDa membrane protein
  • Chlorophyll a-b binding protein 1, chloroplastic
  • photosystem I subunit VII
KeywordsMEMBRANE PROTEIN / Photosystem / Antenna / Supercomplex / State transition
Function / homology
Function and homology information


plastoglobule / thylakoid membrane / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I ...plastoglobule / thylakoid membrane / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / : / 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 / Photosystem I PsaO / Single helix bin ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / : / 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 / Photosystem I PsaO / Single helix bin / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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 / Electron transport accessory-like domain superfamily / 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 / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV A / Photosystem I reaction center subunit II / 16kDa membrane protein / PSI-F / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Photosystem I reaction center subunit N / PSI-G / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX
Similarity search - Component
Biological speciesZea mays (maize)
Zea mays subsp. mays (maize)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPan, X.W. / Ma, J. / Su, X.D. / Cao, P. / Liu, Z.F. / Zhang, X.Z. / Li, M.
Funding support China, 10items
OrganizationGrant numberCountry
the National Key R&D Program of China2017YFA0503702 China
the National Key R&D Program of China2017YFA0504700 China
the National Key R&D Program of China2016YFA0502900 China
the Strategic Priority Research Program of CASXDB08020302 China
the Strategic Priority Research Program of CASXDB08030204 China
the Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National Natural Science Foundation of China31770778 China
National Natural Science Foundation of China31700649 China
National Natural Science Foundation of China31600609 China
National Thousand (Young) Talents Program China
CitationJournal: Science / Year: 2018
Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.
Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light- ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Advisory / Data collection / Category: database_PDB_caveat / pdbx_validate_chiral
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: photosystem I subunit VII
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV A
F: Photosystem I reaction center subunit III
G: Photosystem I reaction center subunit V
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK
L: Photosystem I reaction center subunit XI
O: 16kDa membrane protein
N: Photosystem I reaction center subunit N
X: Chlorophyll a-b binding protein 1, chloroplastic
Y: Chlorophyll a-b binding protein, chloroplastic
Z: Chlorophyll a-b binding protein 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)747,990292
Polymers526,26521
Non-polymers221,725271
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area383070 Å2
ΔGint-3480 kcal/mol
Surface area141810 Å2

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Components

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Chlorophyll a-b binding protein, ... , 5 types, 5 molecules 1234Y

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


Mass: 26335.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6SSN3
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29237.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6T892
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29011.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6SUC4
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27406.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6SZR1
#20: Protein Chlorophyll a-b binding protein, chloroplastic / photosystem II light harvesting complex gene 2.1


Mass: 24780.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6T1H1, UniProt: B6SZT9*PLUS

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 83193.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P04966, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82648.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays subsp. mays (maize) / References: UniProt: A0A059Q6U2, photosystem I

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Protein , 3 types, 4 molecules COXZ

#7: Protein photosystem I subunit VII /


Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays subsp. mays (maize) / References: UniProt: A0A172FJJ4*PLUS
#17: Protein 16kDa membrane protein


Mass: 14381.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6SQZ7
#19: Protein Chlorophyll a-b binding protein 1, chloroplastic / LHCII type I CAB-1 / LHCP


Mass: 24879.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P12329

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Photosystem I reaction center subunit ... , 10 types, 10 molecules DEFGHIJKLN

#8: Protein Photosystem I reaction center subunit II / / Photosystem I reaction center subunit II-1 chloroplastic


Mass: 21603.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B4FAW3
#9: Protein Photosystem I reaction center subunit IV A /


Mass: 14429.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: A0A1D6HY75
#10: Protein Photosystem I reaction center subunit III /


Mass: 23833.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6SRI3
#11: Protein Photosystem I reaction center subunit V /


Mass: 15329.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6U534
#12: Protein Photosystem I reaction center subunit VI, chloroplastic / / PSI-H / Light-harvesting complex I 11 kDa protein


Mass: 14948.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: O65101
#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 4029.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P30980
#14: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4747.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P62596
#15: Protein Photosystem I reaction center subunit psaK / / Photosystem I reaction center6


Mass: 13668.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6TR16
#16: Protein Photosystem I reaction center subunit XI /


Mass: 22347.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6STT2
#18: Protein Photosystem I reaction center subunit N /


Mass: 15663.827 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: B6TXS5

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Sugars , 2 types, 4 molecules

#31: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#32: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


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

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Non-polymers , 11 types, 267 molecules

#21: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 171 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: 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.: 11 / Source method: obtained synthetically / Formula: C40H56O2
#24: 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.: 7 / Source method: obtained synthetically / Formula: C40H56O4
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H56
#26: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10
#28: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#29: 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
#30: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#33: 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.: 3 / Source method: obtained synthetically / Formula: C40H56O4

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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: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Zea mays (maize)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 635845 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01147570
ELECTRON MICROSCOPYf_angle_d2.17467792
ELECTRON MICROSCOPYf_dihedral_angle_d13.8722073
ELECTRON MICROSCOPYf_chiral_restr0.0925767
ELECTRON MICROSCOPYf_plane_restr0.0098965

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