[English] 日本語
Yorodumi
- PDB-5l8r: The structure of plant photosystem I super-complex at 2.6 angstro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l8r
TitleThe structure of plant photosystem I super-complex at 2.6 angstrom resolution.
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • (Putative uncharacterized ...) x 2
  • Chlorophyll a-b binding protein, chloroplastic
  • Lhca1
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaG
KeywordsOXIDOREDUCTASE / photosynthesis / membrane complex / chlorophyll / light harvesting
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / chloroplast envelope / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / magnesium ion binding / metal ion binding / nucleus
Similarity search - Function
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 / Single helix bin / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI ...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 / 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 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 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 / Chlorophyll A-B binding protein, plant and chromista / Alpha-Beta Plaits - #20 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit IX / PsaJ / PsaD / 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. / 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 B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Chem-ZEX / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N.
Funding support Israel, 3items
OrganizationGrant numberCountry
European Research Council293579 Israel
ISF71/14 Israel
I-CORE1775/12 Israel
CitationJournal: Nat Plants / Year: 2017
Title: Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution.
Authors: Mazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Structure summary / Category: entity
Item: _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Apr 24, 2019Group: Advisory / Author supporting evidence / Data collection
Category: database_PDB_caveat / pdbx_audit_support ...database_PDB_caveat / pdbx_audit_support / pdbx_seq_map_depositor_info / pdbx_validate_chiral
Item: _pdbx_audit_support.funding_organization / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

-
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: Putative uncharacterized protein
F: Photosystem I reaction center subunit III
G: PsaG
H: Photosystem I reaction center subunit VI
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)564,878258
Polymers372,37116
Non-polymers192,507242
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.611, 200.994, 212.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 5 types, 5 molecules 12CDG

#1: Protein Lhca1


Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 28912.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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 natural source / Source: (natural) 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 natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS
#11: Protein PsaG


Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9S7N7*PLUS

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

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


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


Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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: 84265.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310, 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 natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0F6NGI2, photosystem I

-
Putative uncharacterized ... , 2 types, 2 molecules EL

#9: Protein Putative uncharacterized protein


Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6
#16: Protein Putative uncharacterized protein


Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1

-
Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK

#10: Protein Photosystem I reaction center subunit III /


Mass: 17238.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12
#12: Protein Photosystem I reaction center subunit VI /


Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL10
#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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 natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3
#15: Protein Photosystem I reaction center subunit X psaK /


Mass: 7988.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3

-
Sugars , 2 types, 15 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#26: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 13 types, 436 molecules

#17: 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 / Lutein


Mass: 568.871 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H56O2
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 142 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#20: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#21: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


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


Mass: 787.158 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C45H86O10
#23: 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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4
#25: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#27: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: 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
#30: Chemical ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#31: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.75
Details: 30mM Tris-Hcl pH8.75, 50mM KH2PO4, 0.03% Octyl Glucose Neopentyl Glycol, 14% PEG400, 2mM glutathione

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 248807 / % possible obs: 99.9 % / Redundancy: 84.6 % / CC1/2: 0.997 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 83.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→39.906 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2323 4916 1.98 %
Rwork0.2105 --
obs0.2109 247956 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→39.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25275 0 12099 209 37583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00639485
X-RAY DIFFRACTIONf_angle_d1.84655777
X-RAY DIFFRACTIONf_dihedral_angle_d20.31421909
X-RAY DIFFRACTIONf_chiral_restr0.1164963
X-RAY DIFFRACTIONf_plane_restr0.0167070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.46011740.41468004X-RAY DIFFRACTION100
2.6295-2.66050.43381600.38918060X-RAY DIFFRACTION100
2.6605-2.69290.40651710.37198029X-RAY DIFFRACTION100
2.6929-2.7270.37311720.34957992X-RAY DIFFRACTION100
2.727-2.76290.37141280.33268128X-RAY DIFFRACTION100
2.7629-2.80070.30491580.32088025X-RAY DIFFRACTION100
2.8007-2.84070.33221810.30538040X-RAY DIFFRACTION100
2.8407-2.88310.30661700.29138054X-RAY DIFFRACTION100
2.8831-2.92810.29731500.28498028X-RAY DIFFRACTION100
2.9281-2.97610.30191790.27098072X-RAY DIFFRACTION100
2.9761-3.02740.28931720.26478027X-RAY DIFFRACTION100
3.0274-3.08250.28911410.26228073X-RAY DIFFRACTION99
3.0825-3.14170.27571700.24858070X-RAY DIFFRACTION100
3.1417-3.20580.29541790.24438039X-RAY DIFFRACTION100
3.2058-3.27550.30761440.23218082X-RAY DIFFRACTION100
3.2755-3.35170.25421740.22538064X-RAY DIFFRACTION100
3.3517-3.43540.26361380.22268061X-RAY DIFFRACTION99
3.4354-3.52830.28211640.2198059X-RAY DIFFRACTION99
3.5283-3.6320.27231460.21888028X-RAY DIFFRACTION99
3.632-3.74920.22681740.19258062X-RAY DIFFRACTION99
3.7492-3.88310.19531530.17988109X-RAY DIFFRACTION100
3.8831-4.03840.17831680.17558104X-RAY DIFFRACTION100
4.0384-4.2220.21391440.17238125X-RAY DIFFRACTION100
4.222-4.44430.20871570.16458168X-RAY DIFFRACTION100
4.4443-4.72230.18581500.16638103X-RAY DIFFRACTION99
4.7223-5.08630.18771740.16368160X-RAY DIFFRACTION100
5.0863-5.59690.19951750.17438214X-RAY DIFFRACTION100
5.5969-6.40390.22351830.18518211X-RAY DIFFRACTION100
6.4039-8.05730.19871860.18618280X-RAY DIFFRACTION100
8.0573-39.9110.19441810.21698569X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.038 Å / Origin y: 7.6729 Å / Origin z: 64.5628 Å
111213212223313233
T0.5119 Å20.0885 Å2-0.1498 Å2-0.5604 Å20.0489 Å2--0.5651 Å2
L0.6916 °2-0.026 °2-0.019 °2-1.2618 °2-0.0499 °2--0.7382 °2
S-0.0523 Å °-0.0784 Å °0.0985 Å °-0.0292 Å °0.0776 Å °0.2026 Å °-0.0384 Å °-0.0046 Å °0.0059 Å °
Refinement TLS groupSelection details: all

+
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