[English] 日本語
Yorodumi
- PDB-8ddy: Helical rods of far-red light-absorbing allophycocyanin in Synech... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ddy
TitleHelical rods of far-red light-absorbing allophycocyanin in Synechococcus sp.
Components
  • Allophycocyanin subunit alpha
  • Allophycocyanin subunit beta
KeywordsPHOTOSYNTHESIS / Allophycocyanin / phycobiliprotein / photosystem / energy transfer / cyanobacteria / far-red light / FaRLiP / LoLiP
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin subunit beta / Allophycocyanin subunit alpha
Similarity search - Component
Biological speciesSynechococcus sp. 63AY4M1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsGisriel, C.J. / Shen, G.S. / Soulier, N.T. / Flesher, D.A. / Brudvig, G.W. / Bryant, D.A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
Department of Energy (DOE, United States)DE-SC0001423 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008283 United States
CitationJournal: Sci Adv / Year: 2023
Title: Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium.
Authors: Christopher J Gisriel / Eduard Elias / Gaozhong Shen / Nathan T Soulier / David A Flesher / M R Gunner / Gary W Brudvig / Roberta Croce / Donald A Bryant /
Abstract: To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using ...To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo-electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a-containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.
History
DepositionJun 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Allophycocyanin subunit alpha
B: Allophycocyanin subunit beta
C: Allophycocyanin subunit alpha
D: Allophycocyanin subunit beta
E: Allophycocyanin subunit alpha
F: Allophycocyanin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35515
Polymers114,7166
Non-polymers3,6399
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E"
d_2ens_1chain "C"
d_3ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "B"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERPHEPHEEE27 - 18427 - 184
d_12ens_1CYCCYCCYCCYCEM201
d_21ens_1SERSERPHEPHECC27 - 18427 - 184
d_22ens_1CYCCYCCYCCYCCJ201
d_31ens_1SERSERPHEPHEAA27 - 18427 - 184
d_32ens_1CYCCYCCYCCYCAG201
d_11ens_2METMETLEULEUDD1 - 1601 - 160
d_12ens_2CYCCYCCYCCYCDK201
d_21ens_2METMETLEULEUBB1 - 1601 - 160
d_22ens_2CYCCYCCYCCYCBH201
d_31ens_2METMETLEULEUFF1 - 1601 - 160
d_32ens_2CYCCYCCYCCYCFN201

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.203266180814, 0.979123513455, -7.16761279866E-5), (-0.979120616455, -0.203265756465, -0.00241881809332), (-0.00238289097231, -0.000421484341294, 0.999997072086)17.6705594243, 135.812816772, 10.5186055414
2given(-0.918749770196, -0.394818197726, -0.00417738068615), (0.394814330994, -0.918759266, 0.00174790753813), (-0.004528112917, -4.3400111928E-5, 0.999989747102)147.011100554, 91.0873506759, 21.0294920698
3given(-0.204125925499, 0.978935861413, -0.00414557349127), (-0.978944300512, -0.2041205022, 0.00169619497228), (0.00081426954337, 0.00440452291018, 0.999989968521)17.8392255653, 135.674689049, 10.1250485548
4given(-0.197611778999, -0.980269464735, 0.00462182958105), (0.980277307196, -0.1975971999, 0.00342747550534), (-0.00244658899538, 0.00520798418811, 0.999983445414)136.030315089, 9.90767661163, -10.3218166517

-
Components

#1: Protein Allophycocyanin subunit alpha


Mass: 20526.518 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. 63AY4M1 (bacteria) / Gene: SYN60AY4M2_00015 / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: A0A2G8PAX6
#2: Protein Allophycocyanin subunit beta


Mass: 17712.303 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. 63AY4M1 (bacteria) / Gene: SYN60AY4M2_00020 / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: A0A2G8PA94
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Far-red light allophycocyanin / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Synechococcus sp. 63AY4M1 (bacteria)
Source (recombinant)Organism: Synechococcus sp. PCC 7002 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding 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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 59.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74095 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01057764
ELECTRON MICROSCOPYf_angle_d1.642710518
ELECTRON MICROSCOPYf_chiral_restr0.0641176
ELECTRON MICROSCOPYf_plane_restr0.00931335
ELECTRON MICROSCOPYf_dihedral_angle_d23.89642907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints0.000711175053831
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000696727699685
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.0051991330527
ens_2d_3FELECTRON MICROSCOPYNCS constraints0.0033362234522

+
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://pdbjlvh1.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