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- EMDB-37674: the structure of PsaQ -

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Basic information

Entry
Database: EMDB / ID: EMD-37674
Titlethe structure of PsaQ
Map data
Sample
  • Complex: pigment binding protein
    • Protein or peptide: PsaQ
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A
  • Ligand: water
Keywordsphotosynthesis / chlorophyll / alloxanthin / growth phase
Biological speciesRhodomonas salina (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang SM / Si L / Li M
Funding support China, 2 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2024
Title: Growth phase-dependent reorganization of cryptophyte photosystem I antennae.
Authors: Shumeng Zhang / Long Si / Xiaodong Su / Xuelin Zhao / Xiaomin An / Mei Li /
Abstract: Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. ...Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems.
History
DepositionOct 6, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37674.png

Downloads & links

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Map

FileDownload / File: emd_37674.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04004 Å
Density
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.094304815 - 0.16515547
Average (Standard dev.)0.000011560649 (±0.0009134931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.41473 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37674_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37674_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pigment binding protein

EntireName: pigment binding protein
Components
  • Complex: pigment binding protein
    • Protein or peptide: PsaQ
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A
  • Ligand: water

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Supramolecule #1: pigment binding protein

SupramoleculeName: pigment binding protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhodomonas salina (eukaryote)

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Macromolecule #1: PsaQ

MacromoleculeName: PsaQ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 23.834393 KDa
SequenceString: RTAAYVALAA ASAEAFSTPA LSGLKMAEPA QISRKDVLTT AAGAAIIAMP TLAGAASLDP KTGFPIQGGS REKLCGGSAS AGCQPMTQA ASILDKQRTV LAGKITVAAN KVPVLTAAVD KMKTAKKPKL DRDYVLRYSA LYLTTLVDAM EQYCLRDANG A KAAGGAGL ...String:
RTAAYVALAA ASAEAFSTPA LSGLKMAEPA QISRKDVLTT AAGAAIIAMP TLAGAASLDP KTGFPIQGGS REKLCGGSAS AGCQPMTQA ASILDKQRTV LAGKITVAAN KVPVLTAAVD KMKTAKKPKL DRDYVLRYSA LYLTTLVDAM EQYCLRDANG A KAAGGAGL PKFKETLKPA SSSSLYSYVD TVKSGIAAVS AAAKAGDFDG VNKAAGDIKT AADSFLSTAN PPIIFN

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Macromolecule #2: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #3: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38675
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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