[English] 日本語
Yorodumi
- PDB-2o01: The Structure of a plant photosystem I supercomplex at 3.4 Angstr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o01
TitleThe Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 9
  • AT3g54890
  • PSI light-harvesting antenna chlorophyll a/b-binding protein
  • PSI type III chlorophyll a/b-binding protein
  • Photosystem I iron-sulfur center
  • Photosystem I-N subunit
  • Type II chlorophyll a/b binding protein from photosystem I
KeywordsPHOTOSYNTHESIS / Membranal Super Complex
Function / homology
Function and homology information


response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I ...response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / molecular adaptor activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Chlorophyll a-b binding protein like / Single helix bin / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / 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 / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 ...Chlorophyll a-b binding protein like / Single helix bin / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / 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 / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 / 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 V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / 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 A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic ...BETA-CAROTENE / CHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I-N subunit / Photosystem I reaction center subunit IV A, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Spinacia oleracea (spinach)
Arabidopsis thaliana (thale cress)
Phaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsAmunts, A. / Drory, O. / Nelson, N.
CitationJournal: Nature / Year: 2007
Title: The structure of a plant photosystem I supercomplex at 3.4 A resolution.
Authors: Amunts, A. / Drory, O. / Nelson, N.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 2.0Aug 30, 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_conn_type / struct_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX determination method: author determined
Remark 700SHEET determination method: author determined
Remark 750TURN determination method: author determined
Remark 999SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment ...SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment is unclear and residues in coordinates were labeled as UNK. Proper sequence is LGAKCDFIGSSTNLIMVTSTTLMLFAGRFGLAPSANRKATAGLRLEARDSGLQ TGDPAGFTLADTLACGTVGHIIGVGVVLGLKNIGAI

-
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 reaction center subunit II, chloroplast
E: Photosystem I reaction center subunit IV A, chloroplast
F: Photosystem I reaction center subunit III, chloroplast
G: Photosystem I reaction center subunit V, chloroplast
H: Photosystem I reaction center subunit VI, chloroplast
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplast
L: Photosystem I reaction center subunit XI, chloroplast
N: Photosystem I-N subunit
1: AT3g54890
2: Type II chlorophyll a/b binding protein from photosystem I
3: PSI type III chlorophyll a/b-binding protein
4: PSI light-harvesting antenna chlorophyll a/b-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,246195
Polymers349,49917
Non-polymers154,747178
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.054, 188.784, 127.518
Angle α, β, γ (deg.)90.00, 95.19, 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: 83669.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Strain: alaska / References: UniProt: P05310
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB / PSI-B


Mass: 82226.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311

-
Protein , 6 types, 6 molecules CN1234

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


Mass: 8860.276 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) Phaseolus vulgaris (French bean) / References: UniProt: Q84U30
#14: Protein AT3g54890 / Chlorophyll A/B-binding protein / At3g54890/F28P10_130


Mass: 20415.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#15: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 20580.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038
#16: Protein PSI type III chlorophyll a/b-binding protein


Mass: 17929.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97
#17: Protein PSI light-harvesting antenna chlorophyll a/b-binding protein


Mass: 18561.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2

-
Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL

#4: Protein Photosystem I reaction center subunit II, chloroplast / / Photosystem I 20 kDa subunit / PSI-D


Mass: 15553.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12353
#5: Protein Photosystem I reaction center subunit IV A, chloroplast / / PSI-E A


Mass: 7127.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#6: Protein Photosystem I reaction center subunit III, chloroplast / / 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) Spinacia oleracea (spinach) / References: UniProt: P12355
#7: Protein Photosystem I reaction center subunit V, chloroplast / / PSI-G / Photosystem I 9 kDa protein


Mass: 10518.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12357
#8: Protein Photosystem I reaction center subunit VI, chloroplast / / PSI- H / Light-harvesting complex I 11 kDa protein


Mass: 8143.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P22179
#9: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 3270.042 Da / Num. of mol.: 1 / 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: 4845.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17230
#11: Protein/peptide Photosystem I reaction center subunit psaK, chloroplast /


Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#12: Protein Photosystem I reaction center subunit XI, chloroplast / / PSI- L / PSI subunit V


Mass: 17479.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41385

-
Non-polymers , 4 types, 178 molecules

#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 168 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: 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
#20: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.875 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.875 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 70551 / % possible obs: 91.1 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 3.4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.41
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6034 / % possible all: 78.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1QZV
Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.778 / Cor.coef. Fo:Fc free: 0.707 / SU B: 34.519 / SU ML: 0.625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.975 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.409 3516 5 %RANDOM
Rwork0.348 ---
obs0.351 70551 90.85 %-
all-69817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å22.78 Å2
2--0.74 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23599 0 6247 0 29846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02131845
X-RAY DIFFRACTIONr_angle_refined_deg4.1012.22245477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.28453024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.94623.2851032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.622153623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.58815103
X-RAY DIFFRACTIONr_chiral_restr0.2160.23853
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231360
X-RAY DIFFRACTIONr_nbd_refined0.3880.224775
X-RAY DIFFRACTIONr_nbtor_refined0.3340.219001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3370.21577
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4110.2238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.212
X-RAY DIFFRACTIONr_mcbond_it0.5631.515464
X-RAY DIFFRACTIONr_mcangle_it0.878224032
X-RAY DIFFRACTIONr_scbond_it1.334352416
X-RAY DIFFRACTIONr_scangle_it1.6974.521073
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 190 -
Rwork0.292 4106 -
obs-4296 75.93 %

+
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