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- EMDB-13110: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-13110

Title

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

Map data

3d map

Sample

Complex: RC-LH1 from rhodospirillum rubrum
- Protein or peptide: x 6 types
Ligand: x 12 types

Function / homology

Function and homology information

organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 2.5 Å

Authors

Qian P / Croll TI / Castro HP / Moriarty NW / sader K / Hunter CN

Funding support

United Kingdom, European Union, 3 items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M000265/1	United Kingdom
European Research Council (ERC)	Synergy Award 854126	European Union
Wellcome Trust	209407/Z/17/Z	United Kingdom

Citation

Journal: Biochem J / Year: 2021
Title: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 Å.
Authors: Pu Qian / Tristan I Croll / David J K Swainsbury / Pablo Castro-Hartmann / Nigel W Moriarty / Kasim Sader / C Neil Hunter /

Abstract: The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 ...

History

Deposition	Jun 23, 2021	-
Header (metadata) release	Sep 22, 2021	-
Map release	Sep 22, 2021	-
Update	Sep 22, 2021	-
Current status	Sep 22, 2021	Processing site: PDBe / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.02 Imaged by UCSF Chimera Download Surface view colored by height Surface level: 0.02 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7oy8 Surface level: 0.02 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_13110.png

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Downloads & links

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EMDB archive

Map data	emd_13110.map.gz	2.5 MB		EMDB map data format
Header (meta data)	emd-13110-v30.xml emd-13110.xml	24.6 KB 24.6 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_13110_fsc.xml	18.2 KB	Display	FSC data file
Images	emd_13110.png	83.3 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-13110 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13110	HTTPS FTP

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Validation report

Summary document	emd_13110_validation.pdf.gz	252.1 KB	Display	EMDB validaton report
Full document	emd_13110_full_validation.pdf.gz	251.2 KB	Display
Data in XML	emd_13110_validation.xml.gz	13.8 KB	Display
Data in CIF	emd_13110_validation.cif.gz	19.1 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13110 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13110	HTTPS FTP

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Related structure data

Related structure data	7oy8MC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	7eqd-d 31258 7oy8-d 11080 30656 6z5r-d 6z5s-d 7ddq-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#22 - Oct 2001 Photosystem I similarity (14) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (4) #59 - Nov 2004 Photosystem II similarity (4)

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Map

File

Download / File: emd_13110.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

3d map

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	1.3 Å/pix. x 256 pix. = 332.8 Å	1.3 Å/pix. x 256 pix. = 332.8 Å	1.3 Å/pix. x 256 pix. = 332.8 Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 1.3 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.0165 / Movie #1: 0.02
Minimum - Maximum	-0.07090002 - 0.16119713
Average (Standard dev.)	0.00027483224 (±0.0032619392)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	256	256	256
Spacing	256	256	256

Cell

A=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.3	1.3	1.3
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	332.800	332.800	332.800
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	256	256	256
D min/max/mean	-0.071	0.161	0.000

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Supplemental data

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Sample components

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Entire : RC-LH1 from rhodospirillum rubrum

Entire	Name: RC-LH1 from rhodospirillum rubrum
Components	Complex: RC-LH1 from rhodospirillum rubrum Protein or peptide: Light-harvesting protein B-870 beta chain Protein or peptide: Antenna complex, alpha/beta subunit Protein or peptide: Photosynthetic reaction center, H-chain Protein or peptide: Photosynthetic reaction center L subunit Protein or peptide: Reaction center protein M chain Protein or peptide: Antenna complex, alpha/beta subunit Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A Ligand: SPIRILLOXANTHIN Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate Ligand: BACTERIOPHEOPHYTIN A Ligand: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione Ligand: UBIQUINONE-10 Ligand: FE (III) ION Ligand: CHLORIDE ION Ligand: PHOSPHATE ION Ligand: DODECYL-BETA-D-MALTOSIDE Ligand: water

Entire

Name: RC-LH1 from rhodospirillum rubrum

Components

Complex: RC-LH1 from rhodospirillum rubrum
- Protein or peptide: Light-harvesting protein B-870 beta chain
- Protein or peptide: Antenna complex, alpha/beta subunit
- Protein or peptide: Photosynthetic reaction center, H-chain
- Protein or peptide: Photosynthetic reaction center L subunit
- Protein or peptide: Reaction center protein M chain
- Protein or peptide: Antenna complex, alpha/beta subunit
Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
Ligand: SPIRILLOXANTHIN
Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
Ligand: BACTERIOPHEOPHYTIN A
Ligand: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
Ligand: UBIQUINONE-10
Ligand: FE (III) ION
Ligand: CHLORIDE ION
Ligand: PHOSPHATE ION
Ligand: DODECYL-BETA-D-MALTOSIDE
Ligand: water

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Supramolecule #1: RC-LH1 from rhodospirillum rubrum

Supramolecule	Name: RC-LH1 from rhodospirillum rubrum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 Details: A reaction centre light harvesting core complex from purple bacterium ops. rubrum.
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: S1
Molecular weight	Experimental: 297.7 kDa/nm

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Macromolecule #1: Light-harvesting protein B-870 beta chain

Macromolecule	Name: Light-harvesting protein B-870 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 6.083941 KDa
Sequence	String: EVKQESLSGI TEGEAKEFHK IFTSSILVFF GVAAFAHLLV WIWRPWVPGP NGYS

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Macromolecule #2: Antenna complex, alpha/beta subunit

Macromolecule	Name: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 5.920986 KDa
Sequence	String: (FME)WRIWQLFDP RQALVGLATF LFVLALLIHF ILLSTERFNW LEGASTKPVQ

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Macromolecule #3: Photosynthetic reaction center, H-chain

Macromolecule	Name: Photosynthetic reaction center, H-chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 27.976193 KDa
Sequence	String: MNKGDITGYM DVAQVVLYAF WIFFAGLIIY LRREDRREGY PLEDAISGKI NSLQGLGSVF SIARPKIFKL KTGATYAAPN FKRDAVAIK ATRTAPTAGA PFEPTGNPMT DAVGPAAYAL RDELPDLTLG GQPAIVPLRV APTFSVAAED TDPRGLPVVD R KGAVAGKV ...String: MNKGDITGYM DVAQVVLYAF WIFFAGLIIY LRREDRREGY PLEDAISGKI NSLQGLGSVF SIARPKIFKL KTGATYAAPN FKRDAVAIK ATRTAPTAGA PFEPTGNPMT DAVGPAAYAL RDELPDLTLG GQPAIVPLRV APTFSVAAED TDPRGLPVVD R KGAVAGKV TDLWIDRASI AIRYLEVELA ATPGRKVLLP FAATRINAKT KSKTVTVQSI LARHFANVPT IAKTDSITRR EE DKVMAYY SSGYLYSDRV

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Macromolecule #4: Photosynthetic reaction center L subunit

Macromolecule	Name: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 30.660688 KDa
Sequence	String: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTL LFTVLGTALI VWGAALGPSW TFWQISINPP DVSYGLAMAP MAKGGLWQI ITFSAIGAFV SWALREVEIC RKLGIGYHIP FAFGFAILAY VSLVVIRPVM MGAWGYGFPY GFMTHLDWVS N TGYQYANF ...String: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTL LFTVLGTALI VWGAALGPSW TFWQISINPP DVSYGLAMAP MAKGGLWQI ITFSAIGAFV SWALREVEIC RKLGIGYHIP FAFGFAILAY VSLVVIRPVM MGAWGYGFPY GFMTHLDWVS N TGYQYANF HYNPAHMLGI TLFFTTCLAL ALHGSLILSA ANPGKGEVVK GPEHENTYFQ DTIGYSVGTL GIHRVGLILA LS AVVWSII CMILSGPIYT GSWPDWWLWW QKLPFWNHG

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Macromolecule #5: Reaction center protein M chain

Macromolecule	Name: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 34.234547 KDa
Sequence	String: MSEYQNILTG VQVRTAPHSA PIAKGIFPRL GKPGFSYWLG KIGDAQIGPI YLGTTGVLSL VFGFFAIEII GFNLLASVNW SPMEFGRQF FWLGLEPPAA EYGLGFAPLA EGGWWQIAGF FLTTSILLWW VRMYRRARAL KMGTHTAWAF ASAIFLFLSL G FIRPLLMG ...String: MSEYQNILTG VQVRTAPHSA PIAKGIFPRL GKPGFSYWLG KIGDAQIGPI YLGTTGVLSL VFGFFAIEII GFNLLASVNW SPMEFGRQF FWLGLEPPAA EYGLGFAPLA EGGWWQIAGF FLTTSILLWW VRMYRRARAL KMGTHTAWAF ASAIFLFLSL G FIRPLLMG NFSESVPFGI FPHLEWTNSF SLNYGNFFYN PFHMLSIAFL YGSALLFAMH GATILAVSRL GGDREVEQIT DR GTAAERA ALFWRWTMGF NATMESIHRW AWWFAVLCTF TGAIGILLTG TVVDNWFEWG VKHGLAPAP

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Macromolecule #6: Antenna complex, alpha/beta subunit

Macromolecule	Name: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria) Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weight	Theoretical: 7.112404 KDa
Sequence	String: MWRIWQLFDP RQALVGLATF LFVLALLIHF ILLSTERFNW LEGASTKPVQ TSMVMPSSDL AV

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Macromolecule #7: Trans-Geranyl BACTERIOCHLOROPHYLL A

Macromolecule	Name: Trans-Geranyl BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 37 / Formula: 07D
Molecular weight	Theoretical: 901.425 Da
Chemical component information	ChemComp-07D: Trans-Geranyl BACTERIOCHLOROPHYLL A

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Macromolecule #8: SPIRILLOXANTHIN

Macromolecule	Name: SPIRILLOXANTHIN / type: ligand / ID: 8 / Number of copies: 17 / Formula: CRT
Molecular weight	Theoretical: 596.925 Da
Chemical component information	ChemComp-CRT: SPIRILLOXANTHIN

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Macromolecule #9: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

Macromolecule	Name: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 9 / Number of copies: 2 / Formula: PGW
Molecular weight	Theoretical: 749.007 Da

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Macromolecule #10: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

Macromolecule	Name: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate type: ligand / ID: 10 / Number of copies: 2 / Formula: CD4
Molecular weight	Theoretical: 1.241633 KDa
Chemical component information	ChemComp-CD4: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

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Macromolecule #11: BACTERIOPHEOPHYTIN A

Macromolecule	Name: BACTERIOPHEOPHYTIN A / type: ligand / ID: 11 / Number of copies: 2 / Formula: BPH
Molecular weight	Theoretical: 889.215 Da
Chemical component information	ChemComp-BPH: BACTERIOPHEOPHYTIN A

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Macromolecule #12: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E}...

Macromolecule	Name: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6- ...Name: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione type: ligand / ID: 12 / Number of copies: 1 / Formula: RQ0
Molecular weight	Theoretical: 844.3 Da
Chemical component information	ChemComp-RQ0: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione

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Macromolecule #13: UBIQUINONE-10

Macromolecule	Name: UBIQUINONE-10 / type: ligand / ID: 13 / Number of copies: 3 / Formula: U10
Molecular weight	Theoretical: 863.343 Da
Chemical component information	ChemComp-U10: UBIQUINONE-10

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Macromolecule #14: FE (III) ION

Macromolecule	Name: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
Molecular weight	Theoretical: 55.845 Da

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Macromolecule #15: CHLORIDE ION

Macromolecule	Name: CHLORIDE ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: CL
Molecular weight	Theoretical: 35.453 Da

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Macromolecule #16: PHOSPHATE ION

Macromolecule	Name: PHOSPHATE ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: PO4
Molecular weight	Theoretical: 94.971 Da
Chemical component information	ChemComp-PO4: PHOSPHATE ION

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Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

Macromolecule	Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 17 / Number of copies: 1 / Formula: LMT
Molecular weight	Theoretical: 510.615 Da
Chemical component information	ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #18: water

Macromolecule	Name: water / type: ligand / ID: 18 / Number of copies: 372 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Concentration	4.0 mg/mL
Buffer	pH: 8 / Component - Concentration: 20.0 mM / Component - Formula: C₈H₁₈N₂O₄S / Component - Name: HEPES / Details: 20 mM HEPES, 0.03% beta DDM, pH 8.0
Grid	Model: Quantifoil / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Vitrification	Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Quantifiol R1.2/1.3 grid, glow discharged. bloting time: 2.5, bloting force 3, waiting time 0.
Details	The protein were solubilised using detergent beta DDM, and purified by the use of ion exchange column and size exclusion column. Monodisperse sample was used for cry-EM preparation.

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Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9024 / Average exposure time: 12.12 sec. / Average electron dose: 45.0 e/Å² Details: total dose of 45 was fractionated to 42 frames within 12.12 second.
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 120000
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Details	Images were motion corrected and CTF corrected.
Particle selection	Number selected: 1519688
CTF correction	Software - Name: CTFFIND
Startup model	Type of model: OTHER Details: Selected 2D classes were used to build up an initial model using EMAN2.
Final reconstruction	Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 519005
Initial angle assignment	Type: COMMON LINE / Software - Name: EMAN2
Final angle assignment	Type: COMMON LINE / Software - Name: RELION (ver. 3.1)
Final 3D classification	Number classes: 4 / Software - Name: RELION (ver. 3.1) / Details: A best 3D class was selected.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	(PDB ID: 1lgh , 3i4d )
Refinement	Space: REAL / Protocol: FLEXIBLE FIT
Output model	PDB-7oy8: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

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+Entire : RC-LH1 from rhodospirillum rubrum

+Supramolecule #1: RC-LH1 from rhodospirillum rubrum

+Macromolecule #1: Light-harvesting protein B-870 beta chain

+Macromolecule #2: Antenna complex, alpha/beta subunit

+Macromolecule #3: Photosynthetic reaction center, H-chain

+Macromolecule #4: Photosynthetic reaction center L subunit

+Macromolecule #5: Reaction center protein M chain

+Macromolecule #6: Antenna complex, alpha/beta subunit

+Macromolecule #7: Trans-Geranyl BACTERIOCHLOROPHYLL A

+Macromolecule #8: SPIRILLOXANTHIN

+Macromolecule #9: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

+Macromolecule #10: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

+Macromolecule #11: BACTERIOPHEOPHYTIN A

+Macromolecule #12: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E}...

+Macromolecule #13: UBIQUINONE-10

+Macromolecule #14: FE (III) ION

+Macromolecule #15: CHLORIDE ION

+Macromolecule #16: PHOSPHATE ION

+Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

+Macromolecule #18: water

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-Atomic model buiding 1

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