[English] 日本語
Yorodumi
- EMDB-35988: Cryo-EM structure of native RC-LH complex from Roseiflexus casten... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35988
TitleCryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux
Map data
Sample
  • Complex: the native RC-LH complex at 100lux
    • Protein or peptide: x 8 types
  • Ligand: x 7 types
KeywordsRC-LH core complex / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, L subunit / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Uncharacterized protein / Reaction center protein L chain / Alpha subunit of light-harvesting 1 / Beta subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii DSM 13941 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXu X / Xin J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2023
Title: Carotenoid assembly regulates quinone diffusion and the reaction center-light harvesting complex architecture.
Authors: Jiyu Xin / Yang Shi / Xin Zhang / Xinyi Yuan / Yueyong Xin / Huimin He / Jiejie Shen / Robert E Blankenship / Xiaoling Xu /
Abstract: Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships ...Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in , a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.
History
DepositionApr 24, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35988.png

Downloads & links

-
Map

FileDownload / File: emd_35988.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 264 pix.
= 235.752 Å		0.89 Å/pix.
x 264 pix.
= 235.752 Å		0.89 Å/pix.
x 264 pix.
= 235.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.893 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.12581758 - 0.23744218
Average (Standard dev.)0.0002489091 (±0.008848198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 235.752 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35988_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35988_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : the native RC-LH complex at 100lux

EntireName: the native RC-LH complex at 100lux
Components
  • Complex: the native RC-LH complex at 100lux
    • Protein or peptide: Beta subunit of light-harvesting 1
    • Protein or peptide: Alpha subunit of light-harvesting 1
    • Protein or peptide: MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Subunit X
    • Protein or peptide: Subunit Y
    • Protein or peptide: Subunit Z
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: beta,psi-caroten-4-one
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: FE (III) ION
  • Ligand: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione

+
Supramolecule #1: the native RC-LH complex at 100lux

SupramoleculeName: the native RC-LH complex at 100lux / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)

+
Macromolecule #1: Beta subunit of light-harvesting 1

MacromoleculeName: Beta subunit of light-harvesting 1 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 6.431528 KDa
SequenceString:
MTDKPQNDLV PDQWKPLFNN AQWLVHDIVV KTIYGGLIIA VIAHVLCWAW TPWIR

UniProtKB: Beta subunit of light-harvesting 1

+
Macromolecule #2: Alpha subunit of light-harvesting 1

MacromoleculeName: Alpha subunit of light-harvesting 1 / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 4.724656 KDa
SequenceString:
MKDRPFEFRT SVVVSTLLGL VMALLIHFVV LSSGAFNWLR AP

UniProtKB: Alpha subunit of light-harvesting 1

+
Macromolecule #3: MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN

MacromoleculeName: MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 34.923031 KDa
SequenceString: MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQ AVQVLKGMTT AQISAYMVAQ VSGGLKVDCS YCHNIANFAQ QDGYPNAAKK VTARKMMLMS ADLNQNYTAK L PASVGGYQ ...String:
MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQ AVQVLKGMTT AQISAYMVAQ VSGGLKVDCS YCHNIANFAQ QDGYPNAAKK VTARKMMLMS ADLNQNYTAK L PASVGGYQ ITCATCHNGK AAGLEPYPIE IMNTLPNDWR LPLELDYPGG LVVTGRKDVS NHEVEQNQFA MYHMNVSMGQ GC TFCHNAR YFPSYEIAQK NHSIIMLQMT KHIQETYVAP GGRIADGIMA GKSPSCWLCH QGANIPPGAA KPGQVPAVLS STP

UniProtKB: Uncharacterized protein

+
Macromolecule #4: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 4
Details: The L- and M-subunits of the RC are encoded by a fused gene pufLM but post-translational processed into two discrete subunits each containing six and five transmembrane helices
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 34.84423 KDa
SequenceString: MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLY EGVVNEGTLN ILAMRIEPPP VSQGLNVDPA QPGFFWFLTM VAATIAFVGW LLRQIDISLK LDMGMEVPIA F GAVVSSWI ...String:
MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLY EGVVNEGTLN ILAMRIEPPP VSQGLNVDPA QPGFFWFLTM VAATIAFVGW LLRQIDISLK LDMGMEVPIA F GAVVSSWI TLQWLRPIAM GAWGHGFPLG ITHHLDWVSN IGYQYYNFFY NPFHAIGITL LFASTLFLHM HGSAVLSEAK RN ISDQNIH VFWRNILGYS IGEIGIHRVA FWTGAASVLF SNLCIFLSGT FVKDWNAFWG FWDKMPIWNG VGQGALVA

UniProtKB: Reaction center protein L chain

+
Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5
Details: The L- and M-subunits of the RC are encoded by a fused gene pufLM but post-translational processed into two discrete subunits each containing six and five transmembrane helices
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 35.046078 KDa
SequenceString: PIDLHDEEYR DGLEGTIAKP PGHVGWMQRL LGEGQVGPIY VGLWGVISFI TFFASAFIIL VDYGRQVGWN PIIYLREFWN LAVYPPPTE YGLSWNVPWD KGGAWLAATF FLHISVLTWW ARLYTRAKAT GVGTQLAWGF ASALSLYFVI YLFHPLALGN W SAAPGHGF ...String:
PIDLHDEEYR DGLEGTIAKP PGHVGWMQRL LGEGQVGPIY VGLWGVISFI TFFASAFIIL VDYGRQVGWN PIIYLREFWN LAVYPPPTE YGLSWNVPWD KGGAWLAATF FLHISVLTWW ARLYTRAKAT GVGTQLAWGF ASALSLYFVI YLFHPLALGN W SAAPGHGF RAILDWTNYV SIHWGNFYYN PFHMLSIFFL LGSTLLLAMH GATIVATSKW KSEMEFTEMM AEGPGTQRAQ LF WRWVMGW NANSYNIHIW AWWFAAFTAI TGAIGLFLSG TLVPDWYAWG ETAKIVAPWP NPDWAQYVFR

UniProtKB: Reaction center protein L chain

+
Macromolecule #6: Subunit X

MacromoleculeName: Subunit X / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 3.628477 KDa
SequenceString:
MAPFLMAFFT IVLIVATLYF LSMIMSGKPE SR

+
Macromolecule #7: Subunit Y

MacromoleculeName: Subunit Y / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 4.493262 KDa
SequenceString:
MNWIVATFML MFVLVAFLPL VVSLAYTWVT NPETQSTEE

+
Macromolecule #8: Subunit Z

MacromoleculeName: Subunit Z / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Molecular weightTheoretical: 6.927004 KDa
SequenceString:
MDFLILLQAE PSPWPVWSGY ALCFVPLAAV ILGFIIAARF TDKQATSAYL RLDPAKANEP EQG

+
Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 48 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

+
Macromolecule #10: beta,psi-caroten-4-one

MacromoleculeName: beta,psi-caroten-4-one / type: ligand / ID: 10 / Number of copies: 30 / Formula: KGD
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-KGD:
beta,psi-caroten-4-one

+
Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #12: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 12 / Number of copies: 4 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

+
Macromolecule #13: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 13 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

+
Macromolecule #14: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #15: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,...

MacromoleculeName: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione
type: ligand / ID: 15 / Number of copies: 3 / Formula: MQE
Molecular weightTheoretical: 921.467 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 322595
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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