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- EMDB-12682: Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimo... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-12682

Title

Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A

Map data

Sample

Complex: RC-dLH model_2b
- Protein or peptide: x 11 types
Ligand: x 16 types

Function / homology

Function and homology information

organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...
Similarity search - Function

Biological species

Gemmatimonas phototrophica (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 2.44 Å

Authors

Qian P / Koblizek M

Funding support

Czech Republic,

United Kingdom, European Union, 7 items

Organization	Grant number	Country
Czech Science Foundation	19-28778X,19-28323X	Czech Republic
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M000265/1	United Kingdom
European Research Council (ERC)	854126	European Union
European Regional Development Fund	CZ.02.1.01/0.0/0.0/15_003/0000441	Czech Republic
Wellcome Trust	Wellcome Trust	United Kingdom
Medical Research Council (MRC, United Kingdom)	MC UP 120117	United Kingdom
Royal Society	UF160039	United Kingdom

Citation

Journal: Sci Adv / Year: 2022
Title: 2.4-Å structure of the double-ring photosystem.
Authors: Pu Qian / Alastair T Gardiner / Ivana Šímová / Katerina Naydenova / Tristan I Croll / Philip J Jackson / Nupur / Miroslav Kloz / Petra Čubáková / Marek Kuzma / Yonghui Zeng / Pablo ...
Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo- ...

History

Deposition	Mar 28, 2021	-
Header (metadata) release	Mar 2, 2022	-
Map release	Mar 2, 2022	-
Update	Mar 16, 2022	-
Current status	Mar 16, 2022	Processing site: PDBe / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.0292 Imaged by UCSF Chimera Download Surface view colored by cylindrical radius Surface level: 0.0292 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7o0x Surface level: 0.0292 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_12682.png

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Downloads & links

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EMDB archive

Map data	emd_12682.map.gz	19.4 MB		EMDB map data format
Header (meta data)	emd-12682-v30.xml emd-12682.xml	32.9 KB 32.9 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_12682_fsc.xml	14.1 KB	Display	FSC data file
Images	emd_12682.png	95.9 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-12682 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12682	HTTPS FTP

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Validation report

Summary document	emd_12682_validation.pdf.gz	347.9 KB	Display	EMDB validaton report
Full document	emd_12682_full_validation.pdf.gz	347.4 KB	Display
Data in XML	emd_12682_validation.xml.gz	13.4 KB	Display
Data in CIF	emd_12682_validation.cif.gz	17.8 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12682 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12682	HTTPS FTP

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Related structure data

Related structure data	7o0xMC 12679C 12680C 12681C 7o0uC 7o0vC 7o0wC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	12680 12679 12681 7o0u-d 7o0v-d 7o0x-d 7o0w-d 21296 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
EM raw data	EMPIAR-10681 (Title: Movies of a photosynthetic reaction centre - double light-harvesting 1 complex from the bacterium G. phototrophica Data size: 12.1 TB Data #1: Unaligned multi-frame micrographs of RC-dLH1 complexes on HexAuFoil support [micrographs - multiframe])

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#22 - Oct 2001 Photosystem I similarity (12) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (4) #59 - Nov 2004 Photosystem II similarity (4)

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Map

File

Download / File: emd_12682.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	1 Å/pix. x 400 pix. = 399.784 Å	1 Å/pix. x 400 pix. = 399.784 Å	1 Å/pix. x 400 pix. = 399.784 Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 0.99946 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.0292 / Movie #1: 0.0292
Minimum - Maximum	-0.061458874 - 0.20402716
Average (Standard dev.)	0.0005923907 (±0.0047766645)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	400	400	400
Spacing	400	400	400

Cell

A=B=C: 399.784 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	0.99946	0.99946	0.99946
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	399.784	399.784	399.784
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	512	512	512
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	400	400	400
D min/max/mean	-0.061	0.204	0.001

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Supplemental data

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Sample components

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Entire : RC-dLH model_2b

Entire	Name: RC-dLH model_2b
Components	Complex: RC-dLH model_2b Protein or peptide: LHh-alpha Protein or peptide: Light-harvesting protein B:885 subunit beta Protein or peptide: MULTIHEME_CYTC domain-containing protein Protein or peptide: RC-S Protein or peptide: RC-U Protein or peptide: PRCH domain-containing protein Protein or peptide: RC-Hc Protein or peptide: Photosynthetic reaction center L subunit Protein or peptide: RC-M Protein or peptide: LHC domain-containing protein Protein or peptide: LHC domain-containing protein Ligand: BACTERIOCHLOROPHYLL A Ligand: DODECYL-BETA-D-MALTOSIDE Ligand: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid Ligand: HEME C Ligand: 2-acetamido-2-deoxy-alpha-D-glucopyranose Ligand: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate Ligand: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-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: MENAQUINONE 8 Ligand: FE (III) ION Ligand: SPIRILLOXANTHIN Ligand: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate Ligand: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate Ligand: water

Entire

Name: RC-dLH model_2b

Components

Complex: RC-dLH model_2b
- Protein or peptide: LHh-alpha
- Protein or peptide: Light-harvesting protein B:885 subunit beta
- Protein or peptide: MULTIHEME_CYTC domain-containing protein
- Protein or peptide: RC-S
- Protein or peptide: RC-U
- Protein or peptide: PRCH domain-containing protein
- Protein or peptide: RC-Hc
- Protein or peptide: Photosynthetic reaction center L subunit
- Protein or peptide: RC-M
- Protein or peptide: LHC domain-containing protein
- Protein or peptide: LHC domain-containing protein
Ligand: BACTERIOCHLOROPHYLL A
Ligand: DODECYL-BETA-D-MALTOSIDE
Ligand: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid
Ligand: HEME C
Ligand: 2-acetamido-2-deoxy-alpha-D-glucopyranose
Ligand: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid
Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Ligand: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-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: MENAQUINONE 8
Ligand: FE (III) ION
Ligand: SPIRILLOXANTHIN
Ligand: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate
Ligand: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate
Ligand: water

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Supramolecule #1: RC-dLH model_2b

Supramolecule	Name: RC-dLH model_2b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 Details: Reaction centre light harvesting complex model_2b from Gemmatimonas phototrophic AP64
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weight	Theoretical: 800 KDa

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Macromolecule #1: LHh-alpha

Macromolecule	Name: LHh-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 6.061153 KDa
Sequence	String: (FME)HRIWMGTDP HIIMSALGSF LVGAVLVMHI WAYGQFNWPA TLKAKYATPP AATR

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Macromolecule #2: Light-harvesting protein B:885 subunit beta

Macromolecule	Name: Light-harvesting protein B:885 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 5.084809 KDa
Sequence	String: MSEKGGMTEE EARRFHGYMV TGTLGYVVVA SVAHFLAWSW RPWF

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Macromolecule #3: MULTIHEME_CYTC domain-containing protein

Macromolecule	Name: MULTIHEME_CYTC domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 38.457609 KDa
Sequence	String: MVPVSLLTLG ACGDAATDTV QVGYRGTAME QNYDHGDLKT KFAQVKLPQS PPPAGESPPG PLPWKNVQVL NDISIAEFNR TMIAMSTWV AGTGNCAYCH NVAAFQDDTL PNGKPLYTKI VARRMLQMTR NINGNYSQHV KNTGVTCYTC HMGKPLPNGL W FYSSQTDY ...String: MVPVSLLTLG ACGDAATDTV QVGYRGTAME QNYDHGDLKT KFAQVKLPQS PPPAGESPPG PLPWKNVQVL NDISIAEFNR TMIAMSTWV AGTGNCAYCH NVAAFQDDTL PNGKPLYTKI VARRMLQMTR NINGNYSQHV KNTGVTCYTC HMGKPLPNGL W FYSSQTDY LRHYLDRDGA RVITQGVAPS NANRSSTKQA EWTYALMISQ SRSLGVNCTY CHNTRQFASW REAPPARVTA YH GILMLRD VNQNYLAPLQ PVYPAVRLGA MGDAPKAQCV TCHNGAYKPL YGAQMAKDFP AMWGRADWNG VPFPGIMRVA ADS TKTDST VVAAPAAAPA QRTSARPGSV TTPVGGVN

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Macromolecule #4: RC-S

Macromolecule	Name: RC-S / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 21.079074 KDa
Sequence	String: MPASPSPLPR SSRVRNAAVV VALVAVGLAA RGRDAQGTQP PVAPPAAPTA TAAPDLAVQD STKADSTAVA DTLMDLSMVM AAEAAAATV TTAPVAVAPT AWPVDPTTGQ TLINGRPVVG RVFIMRKTDG TVKYPNVADV VAHEALAPLP PVVGSSYQQA P ITNQRRMR ...String: MPASPSPLPR SSRVRNAAVV VALVAVGLAA RGRDAQGTQP PVAPPAAPTA TAAPDLAVQD STKADSTAVA DTLMDLSMVM AAEAAAATV TTAPVAVAPT AWPVDPTTGQ TLINGRPVVG RVFIMRKTDG TVKYPNVADV VAHEALAPLP PVVGSSYQQA P ITNQRRMR GIMIQSTLWD MDRKRSATRQ RYYPASTPAN QLGQ

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Macromolecule #5: RC-U

Macromolecule	Name: RC-U / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 13.656403 KDa
Sequence	String: MNMHSSDATV SIPDDIDLIL VDSVPVNDGI WAWYGIDDDR PMAAWSRFHA TRCVEQLAIN RARVGAAEWA LADVQARGIV PCIAKAAAH LARARAELAD WEAQGHRLEA ARKVTPGAWT TPVIES

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Macromolecule #6: PRCH domain-containing protein

Macromolecule	Name: PRCH domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 7.854894 KDa
Sequence	String: (FME)MEYIDGAQI ALYAFWLFFF GLIIYLRRED KREGYPLESP QGPRDGWPKG APKKTYVHRD HGGEGTH

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Macromolecule #7: RC-Hc

Macromolecule	Name: RC-Hc / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 20.022566 KDa
Sequence	String: MSDVKFVPAD NYNGSPIIPT GNPMIDGVGP ASWAEDRRDE PDLTYHGSHK IVPMRLDPTF SIAKGDPDPR GLPVIAADKQ VAGTVVELW VNRSEPQVSY YEVQLASGER RVLLPTGYVQ WPNFGLWGND KLLVKSITAA QFANVPATKR DDQITLLEED K ICAYYAGG HMYAFAERSQ PII

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Macromolecule #8: Photosynthetic reaction center L subunit

Macromolecule	Name: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 30.581662 KDa
Sequence	String: MAMLSFEKKY RVRGGTLIGG DLFDFWFGPF YVGFFGVTTI FFVTLGTLLC VWGAAMGPTW NLWQINIAPP DLKYGLGLAP LREGGLWQI ITLCALGAFG SWALRQAEIA RKLGMGMHIP WAYGGAILAY TTLVVIRPFL LGAWGHGFPY GIFSHLDWVS N VGYQYLHF ...String: MAMLSFEKKY RVRGGTLIGG DLFDFWFGPF YVGFFGVTTI FFVTLGTLLC VWGAAMGPTW NLWQINIAPP DLKYGLGLAP LREGGLWQI ITLCALGAFG SWALRQAEIA RKLGMGMHIP WAYGGAILAY TTLVVIRPFL LGAWGHGFPY GIFSHLDWVS N VGYQYLHF HYNPAHMIAV TFFFTNCLAL AMHGSLILSV TNPPKGTPTG TSEQENVFFR DLLGYSIGAI GIHRLGLFLA VG AAVWSAI CIVISGPFWT QGWPEWWNWW LNLPIWK

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Macromolecule #9: RC-M

Macromolecule	Name: RC-M / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 41.154074 KDa
Sequence	String: MLEYQNLFTR VQVRTVPEPG IPIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFIAIEI IGLNMWASVG WDPVEFIRQ LPWLALEPPP PQYGLRVPPL NQGGWYLMAG FFLTVSIILW WIRIYRRARA LQMGSHLPWA FASAIFLYST F FFQPLLVG ...String: MLEYQNLFTR VQVRTVPEPG IPIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFIAIEI IGLNMWASVG WDPVEFIRQ LPWLALEPPP PQYGLRVPPL NQGGWYLMAG FFLTVSIILW WIRIYRRARA LQMGSHLPWA FASAIFLYST F FFQPLLVG SWSEMVPFGI FPHLDWTSAF SIRYGNLYYN PFHALSIAFL YGSAVLFAMH GATILAVARM GGEREIEQIT DR GTAAERS MLFWRWCMGF NATMESIHRW AWWFAVLTTF TGGIGILLTG TVVDNWYLWG VKHGLVAPYP AQNQLTPEQQ DLL RGRYQG TAPDSFPSYV VPQNATMPDT AAAPIVTDSI TTDSTKTGGT Q

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Macromolecule #10: LHC domain-containing protein

Macromolecule	Name: LHC domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 7.695042 KDa
Sequence	String: MHRIWLMYDP RRVMVALVGF LAVLALVIHF VLLSSQRYSW IENGTLGADQ APVGASAPAA AAEMSPLPPG R

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Macromolecule #11: LHC domain-containing protein

Macromolecule	Name: LHC domain-containing protein / type: protein_or_peptide / ID: 11 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)	Organism: Gemmatimonas phototrophica (bacteria)
Molecular weight	Theoretical: 7.723052 KDa
Sequence	String: (FME)HRIWLMYDP RRVMVALVGF LAVLALVIHF VLLSSQRYSW IENGTLGADQ APVGASAPAA AAEMSPLPPG R

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Macromolecule #13: BACTERIOCHLOROPHYLL A

Macromolecule	Name: BACTERIOCHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 108 / Formula: BCL
Molecular weight	Theoretical: 911.504 Da
Chemical component information	ChemComp-BCL: BACTERIOCHLOROPHYLL A

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Macromolecule #14: DODECYL-BETA-D-MALTOSIDE

Macromolecule	Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 14 / Number of copies: 119 / Formula: LMT
Molecular weight	Theoretical: 510.615 Da
Chemical component information	ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #15: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

Macromolecule	Name: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid type: ligand / ID: 15 / Number of copies: 40 / Formula: V7N
Molecular weight	Theoretical: 610.865 Da
Chemical component information	ChemComp-V7N: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid

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Macromolecule #16: HEME C

Macromolecule	Name: HEME C / type: ligand / ID: 16 / Number of copies: 4 / Formula: HEC
Molecular weight	Theoretical: 618.503 Da
Chemical component information	ChemComp-HEC: HEME C

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Macromolecule #17: 2-acetamido-2-deoxy-alpha-D-glucopyranose

Macromolecule	Name: 2-acetamido-2-deoxy-alpha-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 2 / Formula: NDG
Molecular weight	Theoretical: 221.208 Da
Chemical component information	ChemComp-NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose

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Macromolecule #18: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carb...

Macromolecule	Name: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid type: ligand / ID: 18 / Number of copies: 2 / Formula: V75
Molecular weight	Theoretical: 262.213 Da
Chemical component information	ChemComp-V75: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid

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Macromolecule #19: (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: 19 / Number of copies: 1 / Formula: PGW
Molecular weight	Theoretical: 749.007 Da

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Macromolecule #20: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...

Macromolecule	Name: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate type: ligand / ID: 20 / Number of copies: 20 / Formula: 0V9
Molecular weight	Theoretical: 689.943 Da
Chemical component information	ChemComp-0V9: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate

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Macromolecule #21: (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: 21 / Number of copies: 6 / 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 #22: BACTERIOPHEOPHYTIN A

Macromolecule	Name: BACTERIOPHEOPHYTIN A / type: ligand / ID: 22 / Number of copies: 2 / Formula: BPH
Molecular weight	Theoretical: 889.215 Da
Chemical component information	ChemComp-BPH: BACTERIOPHEOPHYTIN A

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Macromolecule #23: MENAQUINONE 8

Macromolecule	Name: MENAQUINONE 8 / type: ligand / ID: 23 / Number of copies: 3 / Formula: MQ8
Molecular weight	Theoretical: 717.116 Da
Chemical component information	ChemComp-MQ8: MENAQUINONE 8

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Macromolecule #24: FE (III) ION

Macromolecule	Name: FE (III) ION / type: ligand / ID: 24 / Number of copies: 1 / Formula: FE
Molecular weight	Theoretical: 55.845 Da

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Macromolecule #25: SPIRILLOXANTHIN

Macromolecule	Name: SPIRILLOXANTHIN / type: ligand / ID: 25 / Number of copies: 1 / Formula: CRT
Molecular weight	Theoretical: 596.925 Da
Chemical component information	ChemComp-CRT: SPIRILLOXANTHIN

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Macromolecule #26: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[...

Macromolecule	Name: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12- ...Name: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate type: ligand / ID: 26 / Number of copies: 2 / Formula: V7B
Molecular weight	Theoretical: 837.086 Da
Chemical component information	ChemComp-V7B: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate

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Macromolecule #27: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4...

Macromolecule	Name: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate type: ligand / ID: 27 / Number of copies: 1 / Formula: UYH
Molecular weight	Theoretical: 787.158 Da
Chemical component information	ChemComp-UYH: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate

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Macromolecule #28: water

Macromolecule	Name: water / type: ligand / ID: 28 / Number of copies: 521 / 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

6.5 mg/mL

Buffer

pH: 8 / Component:

Concentration	Name
20.0 mM	Tris.Cl
0.02 %	DDM

Details: The final purified complex is in 20mM Tris.Cl, 0.025 DDM, PH 8.0 buffer.

Grid

Model: Homemade / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER

Vitrification

Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Talmon type.

Details

The protein complex was isolated from photosynthetic membrane using detergent beta-DDM. After purification, concentrated protein sample solution was stored in LN before using.

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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: 19865 / Average exposure time: 1.2 sec. / Average electron dose: 24.8 e/Å² Details: All movies were recorded from a HexAuFoil grid with a special EPU version, which can recognise 300 nm holes on the grid.
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 defocus max: -2.4 µm / Nominal defocus min: -0.8 µm / 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

Particle selection	Number selected: 1517482
CTF correction	Software - Name: CTFFIND (ver. 4)
Startup model	Type of model: INSILICO MODEL In silico model: 2D classes obtained form RELION calculation were used to built up a initial 3D model using EMAN2
Final reconstruction	Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 73853
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
Final 3D classification	Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	(PDB ID: 1lgh , 5y5s , 6et5 )
Details	ISOLDE incorporated in ChimeraX was used.
Refinement	Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 30
Output model	PDB-7o0x: Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A

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-Supplemental data

-Sample components

+Entire : RC-dLH model_2b

+Supramolecule #1: RC-dLH model_2b

+Macromolecule #1: LHh-alpha

+Macromolecule #2: Light-harvesting protein B:885 subunit beta

+Macromolecule #3: MULTIHEME_CYTC domain-containing protein

+Macromolecule #4: RC-S

+Macromolecule #5: RC-U

+Macromolecule #6: PRCH domain-containing protein

+Macromolecule #7: RC-Hc

+Macromolecule #8: Photosynthetic reaction center L subunit

+Macromolecule #9: RC-M

+Macromolecule #10: LHC domain-containing protein

+Macromolecule #11: LHC domain-containing protein

+Macromolecule #13: BACTERIOCHLOROPHYLL A

+Macromolecule #14: DODECYL-BETA-D-MALTOSIDE

+Macromolecule #15: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

+Macromolecule #16: HEME C

+Macromolecule #17: 2-acetamido-2-deoxy-alpha-D-glucopyranose

+Macromolecule #18: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carb...

+Macromolecule #19: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

+Macromolecule #20: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...

+Macromolecule #21: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

+Macromolecule #22: BACTERIOPHEOPHYTIN A

+Macromolecule #23: MENAQUINONE 8

+Macromolecule #24: FE (III) ION

+Macromolecule #25: SPIRILLOXANTHIN

+Macromolecule #26: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[...

+Macromolecule #27: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4...

+Macromolecule #28: water

-Experimental details

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-Sample preparation

-Electron microscopy

+Image processing

-Atomic model buiding 1

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