[English] 日本語
Yorodumi
- PDB-3lw5: Improved model of plant photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lw5
TitleImproved model of plant photosystem I
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • (Putative uncharacterized ...) x 5
  • AT3g54890
  • CHAIN R
  • Photosystem I iron-sulfur center
  • Photosystem I-N subunit
  • Type II chlorophyll a/b binding protein from photosystem I
KeywordsPHOTOSYNTHESIS / Electron transfer / Membrane proteins / Large / 2 Complexes / Chlorophyll / Chloroplast / Chromophore / Electron transport / Iron / Iron-sulfur / Magnesium / Membrane / Metal-binding / Photosystem I / Thylakoid / Transmembrane / Transport
Function / homology
Function and homology information


chloroplast photosystem I / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II ...chloroplast photosystem I / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting / 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 / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 ...Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 / GTP Cyclohydrolase I; Chain A, domain 1 / Single helix bin / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / 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 / SH3 type barrels. - #50 / Photosystem I reaction centre subunit PsaK superfamily / 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 / 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. / Few Secondary Structures / Irregular / 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 A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit IV / Photosystem I-N subunit / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit IX ...BETA-CAROTENE / CHLOROPHYLL A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit IV / Photosystem I-N subunit / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit IX / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit V / 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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsNelson, N. / Toporik, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure determination and improved model of plant photosystem I
Authors: Amunts, A. / Toporik, H. / Borovikova, A. / Nelson, N.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 1, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.0Sep 22, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / database_2 ...chem_comp / database_2 / database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Photosystem I reaction center subunit III, chloroplastic
G: Putative uncharacterized protein
H: Putative uncharacterized protein
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: Putative uncharacterized protein
N: Photosystem I-N subunit
R: CHAIN R
1: AT3g54890
2: Type II chlorophyll a/b binding protein from photosystem I
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)550,200270
Polymers354,72618
Non-polymers195,474252
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.655, 189.086, 129.388
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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

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


Mass: 82022.758 Da / Num. of mol.: 1 / Fragment: residues 21-758 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB / PSI-B


Mass: 82359.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311

-
Protein , 5 types, 5 molecules CNR12

#3: Protein Photosystem I iron-sulfur center / Photosystem I subunit VII / 9 kDa polypeptide / PSI-C / PsaC


Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793
#13: Protein Photosystem I-N subunit


Mass: 9767.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K7*PLUS
#14: Protein CHAIN R


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others)
#15: Protein AT3g54890


Mass: 18616.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS
#16: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 19528.191 Da / Num. of mol.: 1 / Fragment: residues 94-269 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038

-
Putative uncharacterized ... , 5 types, 5 molecules DEGHL

#4: Protein Putative uncharacterized protein / Photosystem I subunit PsaD


Mass: 15557.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS
#5: Protein Putative uncharacterized protein


Mass: 7270.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS
#7: Protein Putative uncharacterized protein


Mass: 10456.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P20120*PLUS
#8: Protein Putative uncharacterized protein


Mass: 7314.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K9*PLUS
#12: Protein Putative uncharacterized protein


Mass: 17059.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1*PLUS

-
Photosystem I reaction center subunit ... , 4 types, 4 molecules FIJK

#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17299.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P12355*PLUS
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3270.042 Da / Num. of mol.: 1 / Fragment: residues 1-30 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4793.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L0*PLUS
#11: Protein Photosystem I reaction center subunit X psaK


Mass: 8462.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3*PLUS

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

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


Mass: 18723.426 Da / Num. of mol.: 1 / Fragment: residues 84-255 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904
#18: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 18704.330 Da / Num. of mol.: 1 / Fragment: residues 81-246 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2

-
Sugars , 1 types, 53 molecules

#22: Sugar...
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 5 types, 199 molecules

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


Mass: 893.489 Da / Num. of mol.: 174 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#20: 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
#21: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#24: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10

-
Details

Sequence detailsMISSING ALANINE OF THIS POSITION IN CHAIN 4 IS CORRECT BECAUSE IN ALL THE OTHER PLANTS INCLUDING ...MISSING ALANINE OF THIS POSITION IN CHAIN 4 IS CORRECT BECAUSE IN ALL THE OTHER PLANTS INCLUDING ARABIDOPSIS IT IS MISSING. THE AUTHOR CAN NOT ASSIGN TO THE SEQRES OF CHAIN R. ABOUT CHAIN D, E, F, G, H, J, K, L, N, 1, THE SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PEA DOES NOT CURRENTLY EXIST.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 22.5mM MES BIS-TRIS, 10mM SUCCINIC ACID, 6% PEG6000, 0.015% DTM, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 82447

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5 Å49.14 Å
Translation5 Å49.14 Å

-
Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WSC

2wsc


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.792 / Cor.coef. Fo:Fc free: 0.743 / Occupancy max: 1 / Occupancy min: 1 / SU B: 50.537 / SU ML: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.857 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.383 4344 5 %RANDOM
Rwork0.349 ---
obs0.351 82447 99.46 %-
Displacement parametersBiso max: 75.43 Å2 / Biso mean: 23.073 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å2-1.43 Å2
2---7.81 Å20 Å2
3---9.37 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24732 0 11638 0 36370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02138548
X-RAY DIFFRACTIONr_angle_refined_deg4.7572.33654957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg26.85253108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19723.4381085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.575153836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.06615105
X-RAY DIFFRACTIONr_chiral_restr0.5150.25004
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02135040
X-RAY DIFFRACTIONr_mcbond_it0.4161.515697
X-RAY DIFFRACTIONr_mcangle_it0.612225009
X-RAY DIFFRACTIONr_scbond_it3.568322362
X-RAY DIFFRACTIONr_scangle_it4.4124.528722
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 276 -
Rwork0.496 5893 -
all-6169 -
obs--97.44 %

+
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