[English] 日本語
Yorodumi
- PDB-4kt0: Crystal structure of a virus like photosystem I from the cyanobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kt0
TitleCrystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • (Photosystem I subunit ...) x 2
  • Photosystem I iron-sulfur center
KeywordsELECTRON TRANSPORT / photosynthetic reaction center / membrane complex / plastocyanin / cytochrome C6 / Ferredoxin
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Alpha-t-alpha / Photosystem I PsaK, reaction centre / 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 reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK ...Alpha-t-alpha / Photosystem I PsaK, reaction centre / 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 reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Alpha-Beta Plaits - #20 / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII / Photosystem I subunit II / Photosystem I reaction center subunit ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII / Photosystem I subunit II / Photosystem I reaction center subunit / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I subunit III / Photosystem I subunit X / Photosystem I reaction center subunit IV / Photosystem I subunit VII / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMazor, Y. / Nataf, D. / Toporik, H. / Nelson, N.
CitationJournal: Elife / Year: 2014
Title: Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803.
Authors: Mazor, Y. / Nataf, D. / Toporik, H. / Nelson, N.
History
DepositionMay 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / 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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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: Photosystem I subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I subunit III
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,998131
Polymers236,9789
Non-polymers98,020122
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.179, 173.308, 179.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR STATED THAT THERE IS NO QUATERNARY STRUCTURE FOR THIS ENTRY. PISA FAILED TO GENERATE ASSEMBLY. THEREFORE THE ASU IS INDICATED AS ASSEMBLY TEMPORARILY.

-
Components

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

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


Mass: 83036.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 10HIS tag was added to the C terminus of PsaL. The mutated chain is lost during purification.
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: Synechocystis sp. PCC 6803 / Gene: BEST7613_2234, MYO_18690, psaA
References: UniProt: L8AHT3, UniProt: P29254*PLUS, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81369.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaB, BEST7613_2235, MYO_18700 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AIC0, UniProt: P29255*PLUS, photosystem I

-
Photosystem I subunit ... , 2 types, 2 molecules DF

#4: Protein Photosystem I subunit II


Mass: 15663.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaD, BEST7613_1459, MYO_11100 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AFM8, UniProt: P19569*PLUS, photosystem I
#6: Protein Photosystem I subunit III


Mass: 18267.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaF, BEST7613_2928 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AII8, UniProt: P29256*PLUS, photosystem I

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

#5: Protein Photosystem I reaction center subunit IV


Mass: 8154.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaE, BEST7613_5968, MYO_118260 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8ASH8, UniProt: P12975*PLUS, photosystem I
#7: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4535.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaJ, BEST7613_2927, MYO_115450 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AGL9, UniProt: Q55329*PLUS, photosystem I
#8: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 13732.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaK, BEST7613_4536, MYO_129960 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8APJ0, UniProt: P74564*PLUS, photosystem I
#9: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3382.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psbM, psaM, BEST7613_1787, MYO_14340 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8ADF9, UniProt: P72986*PLUS, photosystem I

-
Protein / Sugars , 2 types, 3 molecules C

#16: 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
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8837.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaC, BEST7613_5694, MYO_120930 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AST2, UniProt: P32422*PLUS, photosystem I

-
Non-polymers , 9 types, 149 molecules

#10: 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
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C40H56
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#18: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4.5% PEG3350, 30mM Tricine-NaOH pH8, 55mM NaCl, 50mM Glycine, 0.005% Nonyl- beta -D-Maltoside., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 92450 / Num. obs: 91895 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.382 / Mean I/σ(I) obs: 1.1

-
Processing

Software
NameClassification
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JB0 with truncated side chains and chlorophyll tails

1jb0


Resolution: 2.8→29.977 Å / SU ML: 0.4 / Isotropic thermal model: single parameter per residue. / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 4558 5 %
Rwork0.1977 --
obs0.2 91218 98.61 %
all-92518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15758 0 6264 29 22051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423288
X-RAY DIFFRACTIONf_angle_d1.73433063
X-RAY DIFFRACTIONf_dihedral_angle_d28.2499045
X-RAY DIFFRACTIONf_chiral_restr0.0462902
X-RAY DIFFRACTIONf_plane_restr0.0123907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.38171400.35042428X-RAY DIFFRACTION85
2.8318-2.86510.35951490.32962743X-RAY DIFFRACTION95
2.8651-2.90.35061560.31332826X-RAY DIFFRACTION98
2.9-2.93670.34541460.30722912X-RAY DIFFRACTION99
2.9367-2.97530.38311430.29312842X-RAY DIFFRACTION99
2.9753-3.0160.3661560.28942894X-RAY DIFFRACTION99
3.016-3.05910.35521450.27412881X-RAY DIFFRACTION100
3.0591-3.10470.34281530.26992888X-RAY DIFFRACTION100
3.1047-3.15310.36171560.27062896X-RAY DIFFRACTION100
3.1531-3.20480.32021560.2572895X-RAY DIFFRACTION100
3.2048-3.260.30711610.23852888X-RAY DIFFRACTION100
3.26-3.31920.27591440.2382907X-RAY DIFFRACTION100
3.3192-3.38290.29411530.23412871X-RAY DIFFRACTION100
3.3829-3.45190.30451450.22922862X-RAY DIFFRACTION98
3.4519-3.52680.28431600.21352877X-RAY DIFFRACTION99
3.5268-3.60870.27211670.19942883X-RAY DIFFRACTION100
3.6087-3.69880.24161760.19112851X-RAY DIFFRACTION100
3.6988-3.79860.27971460.18312933X-RAY DIFFRACTION100
3.7986-3.91020.20651620.17942901X-RAY DIFFRACTION100
3.9102-4.03610.20411390.16562918X-RAY DIFFRACTION99
4.0361-4.180.19131450.16012906X-RAY DIFFRACTION100
4.18-4.34690.2041570.16252941X-RAY DIFFRACTION100
4.3469-4.54410.20981530.16112898X-RAY DIFFRACTION99
4.5441-4.78270.20451610.15672914X-RAY DIFFRACTION99
4.7827-5.0810.20421300.15932969X-RAY DIFFRACTION100
5.081-5.47120.23131370.16532961X-RAY DIFFRACTION100
5.4712-6.01770.22941590.18182985X-RAY DIFFRACTION100
6.0177-6.87930.21571350.18312929X-RAY DIFFRACTION98
6.8793-8.63280.22161840.17582977X-RAY DIFFRACTION99
8.6328-29.97880.21911440.22213084X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -9.005 Å / Origin y: -7.8261 Å / Origin z: 21.7491 Å
111213212223313233
T0.6394 Å20.1236 Å2-0.1111 Å2-0.5398 Å2-0.0396 Å2--0.6407 Å2
L1.0077 °20.0284 °20.0181 °2-0.6814 °20.1622 °2--1.5999 °2
S0.0244 Å °-0.0161 Å °-0.0826 Å °0.1128 Å °0.0938 Å °-0.1135 Å °0.2188 Å °0.2096 Å °0.0099 Å °
Refinement TLS groupSelection details: chain A or chain B or chain C or chain D or chain E or chain F or chain J or chain K or chain M

+
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