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- PDB-6et5: Reaction centre light harvesting complex 1 from Blc. virids -

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Basic information

Entry
Database: PDB / ID: 6et5
TitleReaction centre light harvesting complex 1 from Blc. virids
Components
  • (Light-harvesting protein B-1015 ...) x 3
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / Reaction centre light harvesting complex 1 Blc. viridis Cryo-EM RC-LH1 Photosynthesis
Function / homology
Function and homology information


light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis ...light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Light-harvesting complex / Light-harvesting Protein / Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / 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 ...Light-harvesting complex / Light-harvesting Protein / Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / 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. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / all-trans-1,2-dihydroneurosporene / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 / Light-harvesting protein B-1015 alpha chain / Light-harvesting protein B-1015 beta chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / all-trans-1,2-dihydroneurosporene / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 / Light-harvesting protein B-1015 alpha chain / Light-harvesting protein B-1015 beta chain / Light-harvesting protein B-1015 gamma chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsQian, P. / Siebert, C.A. / Canniffe, D.P. / Wang, P. / Hunter, C.N.
Funding support1items
OrganizationGrant numberCountry
European Research Council
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å.
Authors: Pu Qian / C Alistair Siebert / Peiyi Wang / Daniel P Canniffe / C Neil Hunter /
Abstract: The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the ...The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the bacteriochlorophyll b-based LH1-RC complex from Blastochloris viridis that reveals the structural basis for absorption of infrared light and the molecular mechanism of quinone migration across the LH1 complex. The triple-ring LH1 complex comprises a circular array of 17 β-polypeptides sandwiched between 17 α- and 16 γ-polypeptides. Tight packing of the γ-apoproteins between β-polypeptides collectively interlocks and stabilizes the LH1 structure; this, together with the short Mg-Mg distances of bacteriochlorophyll b pairs, contributes to the large redshift of bacteriochlorophyll b absorption. The 'missing' 17th γ-polypeptide creates a pore in the LH1 ring, and an adjacent binding pocket provides a folding template for a quinone, Q , which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc complex.
History
DepositionOct 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 10, 2018Group: Data collection / Refinement description / Structure summary
Category: computing / entity / refine / Item: _entity.formula_weight
Revision 1.4Oct 24, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_software / entity ...em_software / entity / pdbx_validate_close_contact / struct_conn
Item: _em_software.name / _em_software.version / _entity.formula_weight
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
z: Light-harvesting protein B-1015 alpha chain
1: Light-harvesting protein B-1015 beta chain
2: Light-harvesting protein B-1015 gamma chain
F: Light-harvesting protein B-1015 alpha chain
K: Light-harvesting protein B-1015 alpha chain
P: Light-harvesting protein B-1015 alpha chain
S: Light-harvesting protein B-1015 alpha chain
V: Light-harvesting protein B-1015 alpha chain
Y: Light-harvesting protein B-1015 alpha chain
b: Light-harvesting protein B-1015 alpha chain
e: Light-harvesting protein B-1015 alpha chain
h: Light-harvesting protein B-1015 alpha chain
k: Light-harvesting protein B-1015 alpha chain
n: Light-harvesting protein B-1015 alpha chain
q: Light-harvesting protein B-1015 alpha chain
t: Light-harvesting protein B-1015 alpha chain
w: Light-harvesting protein B-1015 alpha chain
3: Light-harvesting protein B-1015 alpha chain
6: Light-harvesting protein B-1015 alpha chain
G: Light-harvesting protein B-1015 beta chain
N: Light-harvesting protein B-1015 beta chain
Q: Light-harvesting protein B-1015 beta chain
T: Light-harvesting protein B-1015 beta chain
W: Light-harvesting protein B-1015 beta chain
Z: Light-harvesting protein B-1015 beta chain
c: Light-harvesting protein B-1015 beta chain
f: Light-harvesting protein B-1015 beta chain
i: Light-harvesting protein B-1015 beta chain
l: Light-harvesting protein B-1015 beta chain
o: Light-harvesting protein B-1015 beta chain
r: Light-harvesting protein B-1015 beta chain
u: Light-harvesting protein B-1015 beta chain
x: Light-harvesting protein B-1015 beta chain
4: Light-harvesting protein B-1015 beta chain
7: Light-harvesting protein B-1015 beta chain
I: Light-harvesting protein B-1015 gamma chain
O: Light-harvesting protein B-1015 gamma chain
R: Light-harvesting protein B-1015 gamma chain
U: Light-harvesting protein B-1015 gamma chain
X: Light-harvesting protein B-1015 gamma chain
a: Light-harvesting protein B-1015 gamma chain
d: Light-harvesting protein B-1015 gamma chain
g: Light-harvesting protein B-1015 gamma chain
j: Light-harvesting protein B-1015 gamma chain
m: Light-harvesting protein B-1015 gamma chain
p: Light-harvesting protein B-1015 gamma chain
s: Light-harvesting protein B-1015 gamma chain
v: Light-harvesting protein B-1015 gamma chain
y: Light-harvesting protein B-1015 gamma chain
5: Light-harvesting protein B-1015 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,554129
Polymers402,45454
Non-polymers52,10075
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area246370 Å2
ΔGint-1984 kcal/mol
Surface area136420 Å2
MethodPISA

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Photosynthetic reaction center cytochrome c subunit / Cytochrome c558/c559


Mass: 37179.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: reaction centre cytochrome subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173

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Reaction center protein ... , 3 types, 3 molecules LMH

#2: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: reaction centre L subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#3: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Teaction centre M subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010
#4: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Reaction centre H subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008

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Light-harvesting protein B-1015 ... , 3 types, 50 molecules zFKPSVYbehknqtw361GNQTWZcfilor...

#5: Protein
Light-harvesting protein B-1015 alpha chain / Antenna pigment protein alpha chain


Mass: 6984.262 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Details: Light harvesting complex 1 alpha subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P04123
#6: Protein
Light-harvesting protein B-1015 beta chain / Antenna pigment protein beta chain


Mass: 6274.327 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Details: Light harvesting complex 1 beta subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P04124
#7: Protein/peptide
Light-harvesting protein B-1015 gamma chain


Mass: 2799.292 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Details: Light harvesting complex 1 gamma subunit / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P04126

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Non-polymers , 10 types, 75 molecules

#8: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical...
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


Mass: 909.488 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#10: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#11: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H82O4
#12: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#14: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#15: Chemical ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#16: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#17: Chemical
ChemComp-NS0 / all-trans-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C40H60

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Reaction centre-Light harvesting complex 1 (RC-LH1) / Type: COMPLEX
Details: The protein was isolated from a photosynthetic bacterium Blc. viridis.
Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.414 MDa / Experimental value: YES
Source (natural)Organism: Blastochloris viridis (bacteria)
Buffer solutionpH: 7.8 / Details: 20 mMol HEPES, pH 7.8, 100 mM NaCl
Buffer componentConc.: 20 mMol / Name: HEPES
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Protein was solubilised by the use detergent of beta-DDM. The protein particle therefore contains a detergent belt in its hydrophobic region.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temp: 277 K / Humidity: 99 % / Chamber temperature: 278 K
Details: Blot for 3.5 seconds. Humidity: 99% Temperature:4C.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 130000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 77 K
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 2.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6472
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.8.7model fitting
9EMAN2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13REFMAC5.7model refinement
Image processingDetails: Dose fractioned
CTF correctionDetails: gctf was used for CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 267726 / Details: Protein was checked using negatively stained EM.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267726 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
RefinementResolution: 3→243.8 Å / Cor.coef. Fo:Fc: 0.875 / SU B: 12.39 / SU ML: 0.188 / ESU R: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.35197 --
obs0.35197 1123681 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 153.894 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20.28 Å2-1.86 Å2
2--1.48 Å20.31 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Total: 31896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.0233154
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg3.4682.07645896
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.64953436
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.14321.7761143
ELECTRON MICROSCOPYr_dihedral_angle_3_deg22.411154409
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.04215182
ELECTRON MICROSCOPYr_chiral_restr0.3320.24928
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.02125349
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it13.314.96213910
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it21.45922.28617292
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it16.67915.08619244
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined39.469109171
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.88 83248 -
Rfree-0 -
obs--100 %

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