[English] 日本語
Yorodumi
- PDB-6igz: Structure of PSI-LHCI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6igz
TitleStructure of PSI-LHCI
Components
  • Lhca-a
  • Lhca-b
  • Lhca-c
  • Lhca-d
  • Lhca-g
  • Lhca-h
  • Lhca-i
  • Lhca-j
  • Photosystem I reaction center subunit XII
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
KeywordsPLANT PROTEIN / PSI-LHCI
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / 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 / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant ...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 / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Alpha-Beta Plaits - #20 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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 / Helicase, Ruva Protein; domain 3 / 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 / 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
Chem-8CT / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I reaction center subunit XII ...Chem-8CT / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / PsaK / 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 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / photosystem I / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / PsaE / Photosystem I reaction center subunit III / PsaH / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsXiong, P. / Xiaochun, Q.
CitationJournal: Nat Plants / Year: 2019
Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.
Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui /
Abstract: Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an ...Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 Å resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution.
History
DepositionSep 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Advisory / Data collection / Category: database_PDB_caveat / pdbx_validate_chiral
Revision 1.3Nov 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
Revision 1.4Mar 4, 2020Group: Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.5Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9670
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PsaA
B: PsaB
C: PsaC
D: PsaD
E: PsaE
F: PsaF
G: PsaG
H: PsaH
I: PsaI
J: PsaJ
K: PsaK
L: PsaL
1: Lhca-a
2: Lhca-c
3: Lhca-d
4: Lhca-b
6: Lhca-g
5: Lhca-a
7: Lhca-h
8: Lhca-b
9: Lhca-i
0: Lhca-j
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)841,704343
Polymers579,24923
Non-polymers262,455320
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 18 types, 20 molecules ABCDEFGHKL1523486790

#1: Protein PsaA


Mass: 83412.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ2*PLUS
#2: Protein PsaB


Mass: 82164.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H003*PLUS
#3: Protein PsaC


Mass: 8880.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H005*PLUS
#4: Protein PsaD


Mass: 21733.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H006*PLUS
#5: Protein PsaE


Mass: 10096.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H007*PLUS
#6: Protein PsaF


Mass: 25129.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H008*PLUS
#7: Protein PsaG


Mass: 18226.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#8: Protein PsaH


Mass: 14400.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H009*PLUS
#11: Protein PsaK


Mass: 12487.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ4*PLUS
#12: Protein PsaL


Mass: 21338.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ5*PLUS
#13: Protein Lhca-a


Mass: 24458.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ6*PLUS
#14: Protein Lhca-c


Mass: 27808.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ7*PLUS
#15: Protein Lhca-d


Mass: 30409.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ8*PLUS
#16: Protein Lhca-b


Mass: 26575.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ9*PLUS
#17: Protein Lhca-g


Mass: 29300.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H000*PLUS
#18: Protein Lhca-h


Mass: 28621.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H001*PLUS
#19: Protein Lhca-i


Mass: 24152.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H002*PLUS
#20: Protein Lhca-j


Mass: 26910.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H004*PLUS

-
Protein/peptide , 3 types, 3 molecules IJM

#9: Protein/peptide PsaI


Mass: 3859.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H010*PLUS
#10: Protein/peptide PsaJ


Mass: 4744.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ3*PLUS
#21: Protein/peptide Photosystem I reaction center subunit XII / PsaM / PSI-M


Mass: 3505.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0D6E2L8

-
Sugars , 2 types, 3 molecules

#26: Sugar ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#28: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 8 types, 317 molecules

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


Mass: 893.489 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: 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
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#25: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C40H56
#27: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#30: 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.: 20 / Source method: obtained synthetically / Formula: C40H56O4
#31: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: PSI-LHCI / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 FIELD
Image recordingElectron dose: 1.852 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59525 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00954746
ELECTRON MICROSCOPYf_angle_d1.96678218
ELECTRON MICROSCOPYf_dihedral_angle_d15.14832460
ELECTRON MICROSCOPYf_chiral_restr0.1126449
ELECTRON MICROSCOPYf_plane_restr0.00610222

+
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