[English] 日本語
Yorodumi
- PDB-7dkz: Structure of plant photosystem I-light harvesting complex I super... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dkz
TitleStructure of plant photosystem I-light harvesting complex I supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 2
  • Chlorophyll a-b binding protein, chloroplastic
  • Lhca1
  • PSI-F
  • PSI-K
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaG
  • PsaH
  • PsaL
KeywordsPHOTOSYNTHESIS / PSI-LHCI high plants
Function / homology
Function and homology information


response to low light intensity stimulus / response to high light intensity / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II ...response to low light intensity stimulus / response to high light intensity / photosynthesis, light harvesting in 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 / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
Similarity search - Function
Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / PSI-K / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsWang, J. / Yu, L.J. / Wang, W.
CitationJournal: J Integr Plant Biol / Year: 2021
Title: Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 angstrom resolution.
Authors: Wang, J. / Yu, L.J. / Wang, W. / Yan, Q. / Kuang, T. / Qin, X. / Shen, J.R.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 2.0Jul 21, 2021Group: Data collection / Database references / Non-polymer description
Category: chem_comp / citation / pdbx_validate_chiral
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
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: PSI-F
G: PsaG
H: PsaH
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: PsaL
K: PSI-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,371231
Polymers372,52716
Non-polymers170,844215
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.652, 168.952, 185.224
Angle α, β, γ (deg.)90.000, 121.390, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 10 types, 10 molecules 12CDEFGHLK

#1: Protein Lhca1


Mass: 21477.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Tissue: leaf / Production host: Pisum sativum (garden pea)
#2: Protein Chlorophyll a-b binding protein, chloroplastic / Lhca2


Mass: 28912.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhaB / Production host: Pisum sativum (garden pea) / References: UniProt: Q41038
#7: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8991.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaC, frxA / Production host: Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I
#8: Protein PsaD


Mass: 16041.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#9: Protein PsaE


Mass: 7479.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: E1C9K6
#10: Protein PSI-F


Mass: 17238.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12
#11: Protein PsaG


Mass: 10678.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#12: Protein PsaH


Mass: 9491.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#15: Protein PsaL


Mass: 16564.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#16: Protein PSI-K / PsaK / Photosystem I subunit X


Mass: 7988.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: E1C9L3

-
Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34

#3: Protein Chlorophyll a-b binding protein 3, chloroplastic / Lhca3 / LHCII type III CAB-3


Mass: 29634.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhca3 / Production host: Pisum sativum (garden pea) / References: UniProt: Q32904
#4: Protein Chlorophyll a-b binding protein P4, chloroplastic / Lhca4 / LHCI type III CAB-P4


Mass: 21994.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhcA-P4 / Production host: Pisum sativum (garden pea) / References: UniProt: Q9SQL2

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

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


Mass: 84279.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaA / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0F6NFW5, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82512.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaB / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0F6NGI2, photosystem I

-
Photosystem I reaction center subunit ... , 2 types, 2 molecules IJ

#13: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4474.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaI / Production host: Pisum sativum (garden pea) / References: UniProt: P17227
#14: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4767.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaJ / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAL3

-
Sugars , 3 types, 12 molecules

#23: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#25: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#26: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 10 types, 296 molecules

#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#19: 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


Mass: 568.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O2
#20: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE


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


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: sodium chlotide, magnesium chloride, PEG 400 / PH range: 8.0-9.0

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→44.41 Å / Num. obs: 230250 / % possible obs: 98.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 65.37 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Net I/σ(I): 17.8
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 6.2 % / Num. unique obs: 21565 / CC1/2: 0.708 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XK8

4xk8


Resolution: 2.393→44.405 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 11603 5.04 %
Rwork0.189 218420 -
obs0.1909 230023 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.68 Å2 / Biso mean: 101.2191 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.393→44.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25009 0 10991 93 36093
Biso mean--102.45 77.66 -
Num. residues----3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838062
X-RAY DIFFRACTIONf_angle_d1.67654040
X-RAY DIFFRACTIONf_chiral_restr0.0764657
X-RAY DIFFRACTIONf_plane_restr0.0086697
X-RAY DIFFRACTIONf_dihedral_angle_d17.81218206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3932-2.42040.3383300.3065574279
2.4204-2.44890.33713640.31477383100
2.4489-2.47870.36544030.30517318100
2.4787-2.51010.31983810.2877730299
2.5101-2.54310.30874030.27967263100
2.5431-2.5780.29644050.26337364100
2.578-2.61480.30054070.2557322100
2.6148-2.65380.284150.24287303100
2.6538-2.69530.28033960.23547308100
2.6953-2.73950.29594080.23447273100
2.7395-2.78670.25623880.21947378100
2.7867-2.83740.25094240.2127309100
2.8374-2.89190.26383980.2047349100
2.8919-2.95090.25633570.20257370100
2.9509-3.01510.24613840.20567345100
3.0151-3.08520.28773920.21417325100
3.0852-3.16230.25673720.20397313100
3.1623-3.24780.24763850.19777364100
3.2478-3.34340.24333510.19737418100
3.3434-3.45120.2623820.20197331100
3.4512-3.57450.243730.18527326100
3.5745-3.71760.21013800.17937350100
3.7176-3.88670.20793920.17537336100
3.8867-4.09150.19983810.16937366100
4.0915-4.34760.19293780.1681732699
4.3476-4.68290.19063820.1667731099
4.6829-5.15360.20423930.168732999
5.1536-5.89780.22434400.1802732899
5.8978-7.4250.20543630.1705731798
7.425-44.4050.21723760.1853735298
Refinement TLS params.Method: refined / Origin x: 33.6643 Å / Origin y: 66.1507 Å / Origin z: 28.6623 Å
111213212223313233
T0.4627 Å20.0825 Å20.0257 Å2-0.5926 Å2-0.0416 Å2--0.4984 Å2
L0.7951 °2-0.0942 °20.1091 °2-0.4892 °20.0325 °2--0.394 °2
S-0.0477 Å °-0.3699 Å °-0.0704 Å °0.1592 Å °0.1478 Å °0.0545 Å °0.0252 Å °0.0825 Å °0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1all135 - 229
2X-RAY DIFFRACTION1all1301 - 404
3X-RAY DIFFRACTION1all252 - 255
4X-RAY DIFFRACTION1all2601 - 704
5X-RAY DIFFRACTION1all350 - 265
6X-RAY DIFFRACTION1all3301 - 403
7X-RAY DIFFRACTION1all453 - 709
8X-RAY DIFFRACTION1allA17 - 758
9X-RAY DIFFRACTION1allA801 - 933
10X-RAY DIFFRACTION1allB2 - 734
11X-RAY DIFFRACTION1allB801 - 954
12X-RAY DIFFRACTION1allC2 - 81
13X-RAY DIFFRACTION1allC101 - 103
14X-RAY DIFFRACTION1allD71 - 210
15X-RAY DIFFRACTION1allE1 - 63
16X-RAY DIFFRACTION1allF77 - 406
17X-RAY DIFFRACTION1allG2 - 96
18X-RAY DIFFRACTION1allG101 - 105
19X-RAY DIFFRACTION1allH56 - 143
20X-RAY DIFFRACTION1allI2 - 31
21X-RAY DIFFRACTION1allI101
22X-RAY DIFFRACTION1allJ1 - 39
23X-RAY DIFFRACTION1allJ3001 - 3004
24X-RAY DIFFRACTION1allL6 - 156
25X-RAY DIFFRACTION1allL201 - 301
26X-RAY DIFFRACTION1allK47 - 125
27X-RAY DIFFRACTION1allK201 - 205

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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

-
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

Read more