[English] 日本語
Yorodumi
- EMDB-12679: Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12679
TitleCryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A
Map dataA reaction centre double light harvesting complex (RC-dLH) from Gem. phototrophic.
Sample
  • Complex: RC-dLH model_1a
    • Protein or peptide: x 9 types
  • Ligand: x 16 types
KeywordsPhotosynthesis / reaction centre light harvesting complex / RC-dLH / RC-LH1 / carotenoid / quinone / bacteriochlorophyll a / Gemmatimonas phototrophica / MEMBRANE PROTEIN
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 ...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 / 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, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha 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, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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
Reaction center protein L chain / Uncharacterized protein / Antenna complex alpha/beta subunit domain-containing protein / Light-harvesting protein B:885 subunit beta / Photosynthetic reaction centre H subunit N-terminal domain-containing protein
Similarity search - Component
Biological speciesGemmatimonas phototrophica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsQian P / Koblizek M
Funding support Czech Republic, United Kingdom, European Union, 7 items
OrganizationGrant numberCountry
Czech Science Foundation19-28778X,19-28323X Czech Republic
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
European Research Council (ERC)854126European Union
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
Wellcome TrustWellcome Trust United Kingdom
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Royal SocietyUF160039 United Kingdom
CitationJournal: 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 ...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 Castro-Hartmann / Bart van Knippenberg / Kenneth N Goldie / David Kaftan / Pavel Hrouzek / Jan Hájek / Jon Agirre / C Alistair Siebert / David Bína / Kasim Sader / Henning Stahlberg / Roman Sobotka / Christopher J Russo / Tomáš Polívka / C Neil Hunter / Michal Koblížek /
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- ...Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.
History
DepositionMar 27, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0238
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0238
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7o0u
  • Surface level: 0.0238
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12679.png

Downloads & links

-
Map

FileDownload / File: emd_12679.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA reaction centre double light harvesting complex (RC-dLH) from Gem. phototrophic.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (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 sizeX=Y=Z: 0.99946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0238 / Movie #1: 0.0238
Minimum - Maximum-0.059061177 - 0.21118456
Average (Standard dev.)0.00049854035 (±0.0041083195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 399.784 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.999460.999460.99946
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z399.784399.784399.784
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0590.2110.000

-
Supplemental data

-
Sample components

+
Entire : RC-dLH model_1a

EntireName: RC-dLH model_1a
Components
  • Complex: RC-dLH model_1a
    • 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: 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
  • 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: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate
  • 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: (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: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: MENAQUINONE 8
  • Ligand: BACTERIOPHEOPHYTIN A
  • 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

+
Supramolecule #1: RC-dLH model_1a

SupramoleculeName: RC-dLH model_1a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: Reaction centre light harvesting complex model_1a from Gemmatimonas phototrophic AP64
Source (natural)Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weightTheoretical: 800 KDa

+
Macromolecule #1: LHh-alpha

MacromoleculeName: LHh-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weightTheoretical: 6.061153 KDa
SequenceString:
(FME)HRIWMGTDP HIIMSALGSF LVGAVLVMHI WAYGQFNWPA TLKAKYATPP AATR

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

MacromoleculeName: 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 weightTheoretical: 5.084809 KDa
SequenceString:
MSEKGGMTEE EARRFHGYMV TGTLGYVVVA SVAHFLAWSW RPWF

UniProtKB: Light-harvesting protein B:885 subunit beta

+
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: Gemmatimonas phototrophica (bacteria)
Molecular weightTheoretical: 38.457609 KDa
SequenceString: 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

UniProtKB: Uncharacterized protein

+
Macromolecule #4: RC-S

MacromoleculeName: RC-S / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weightTheoretical: 21.079074 KDa
SequenceString: 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

+
Macromolecule #5: PRCH domain-containing protein

MacromoleculeName: PRCH domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria)
Molecular weightTheoretical: 7.854894 KDa
SequenceString:
(FME)MEYIDGAQI ALYAFWLFFF GLIIYLRRED KREGYPLESP QGPRDGWPKG APKKTYVHRD HGGEGTH

UniProtKB: Photosynthetic reaction centre H subunit N-terminal domain-containing protein

+
Macromolecule #6: RC-Hc

MacromoleculeName: RC-Hc / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weightTheoretical: 20.022566 KDa
SequenceString:
MSDVKFVPAD NYNGSPIIPT GNPMIDGVGP ASWAEDRRDE PDLTYHGSHK IVPMRLDPTF SIAKGDPDPR GLPVIAADKQ VAGTVVELW VNRSEPQVSY YEVQLASGER RVLLPTGYVQ WPNFGLWGND KLLVKSITAA QFANVPATKR DDQITLLEED K ICAYYAGG HMYAFAERSQ PII

+
Macromolecule #7: Photosynthetic reaction center L subunit

MacromoleculeName: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria)
Molecular weightTheoretical: 30.581662 KDa
SequenceString: 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

UniProtKB: Reaction center protein L chain

+
Macromolecule #8: RC-M

MacromoleculeName: RC-M / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria) / Strain: AP64
Molecular weightTheoretical: 41.182082 KDa
SequenceString: (FME)LEYQNLFTR VQVRTVPEPG IPIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFIAIEI IGLNMW ASV GWDPVEFIRQ LPWLALEPPP PQYGLRVPPL NQGGWYLMAG FFLTVSIILW WIRIYRRARA LQMGSHLPWA FASAIFL YS TFFFQPLLVG ...String:
(FME)LEYQNLFTR VQVRTVPEPG IPIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFIAIEI IGLNMW ASV GWDPVEFIRQ LPWLALEPPP PQYGLRVPPL NQGGWYLMAG FFLTVSIILW WIRIYRRARA LQMGSHLPWA FASAIFL YS TFFFQPLLVG SWSEMVPFGI FPHLDWTSAF SIRYGNLYYN PFHALSIAFL YGSAVLFAMH GATILAVARM GGEREIEQ I TDRGTAAERS MLFWRWCMGF NATMESIHRW AWWFAVLTTF TGGIGILLTG TVVDNWYLWG VKHGLVAPYP AQNQLTPEQ QDLLRGRYQG TAPDSFPSYV VPQNATMPDT AAAPIVTDSI TTDSTKTGGT Q

+
Macromolecule #9: LHC domain-containing protein

MacromoleculeName: LHC domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas phototrophica (bacteria)
Molecular weightTheoretical: 7.723052 KDa
SequenceString:
(FME)HRIWLMYDP RRVMVALVGF LAVLALVIHF VLLSSQRYSW IENGTLGADQ APVGASAPAA AAEMSPLPPG R

UniProtKB: Antenna complex alpha/beta subunit domain-containing protein

+
Macromolecule #11: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 108 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

+
Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 123 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #13: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

MacromoleculeName: (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: 13 / Number of copies: 40 / Formula: V7N
Molecular weightTheoretical: 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

+
Macromolecule #14: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...

MacromoleculeName: (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: 14 / Number of copies: 20 / Formula: 0V9
Molecular weightTheoretical: 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

+
Macromolecule #15: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 15 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #16: 2-acetamido-2-deoxy-alpha-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-glucopyranose / type: ligand / ID: 16 / Number of copies: 2 / Formula: NDG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NDG:
2-acetamido-2-deoxy-alpha-D-glucopyranose

+
Macromolecule #17: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carb...

MacromoleculeName: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid
type: ligand / ID: 17 / Number of copies: 2 / Formula: V75
Molecular weightTheoretical: 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

+
Macromolecule #18: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

MacromoleculeName: (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: 18 / Number of copies: 6 / Formula: CD4
Molecular weightTheoretical: 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

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

MacromoleculeName: (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 weightTheoretical: 749.007 Da

+
Macromolecule #20: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 20 / Number of copies: 3 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

+
Macromolecule #21: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 21 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

+
Macromolecule #22: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #23: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 23 / Number of copies: 1 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

+
Macromolecule #24: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[...

MacromoleculeName: [(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: 24 / Number of copies: 2 / Formula: V7B
Molecular weightTheoretical: 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

+
Macromolecule #25: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4...

MacromoleculeName: [(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: 25 / Number of copies: 1 / Formula: UYH
Molecular weightTheoretical: 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

+
Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 491 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.5 mg/mL
BufferpH: 8 / Component:
ConcentrationName
20.0 mMTris.Cl
0.02 %DDM

Details: The final purified complex is in 20mM Tris.Cl, 0.025 DDM, PH 8.0 buffer.
GridModel: Homemade / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER / Details: plasma chamber (Fischione 1070)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Talmon type.
DetailsThe protein complex was isolated from photosynthetic membrane using detergent beta-DDM. After purification, concentrated protein sample solution was stored in LN before using.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1517482
Startup modelType 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 176531
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1lgh

source_name: PDB, initial_model_type: experimental model

5y5s

source_name: PDB, initial_model_type: experimental model

6et5

source_name: PDB, initial_model_type: experimental model
DetailsISOLDE incorporated in ChimeraX was used.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 30
Output model

PDB-7o0u:
Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A

+
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