6ET5

Reaction centre light harvesting complex 1 from Blc. virids

PDB DOI: https://doi.org/10.2210/pdb6ET5/pdb
EM Map EMD-3951: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2017-10-25 Released: 2018-04-11
Deposition Author(s): Qian, P., Siebert, C.A., Canniffe, D.P., Wang, P., Hunter, C.N.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 angstrom.

Qian, P., Siebert, C.A., Wang, P., Canniffe, D.P., Hunter, C.N.

(2018) Nature 556: 203-208

PubMed: 29618818 Search on PubMed
DOI: https://doi.org/10.1038/s41586-018-0014-5
Primary Citation of Related Structures:
6ET5

PubMed 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 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 _P, which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc ₁ complex.

Organizational Affiliation

Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.

Macromolecule Content

Total Structure Weight: 454.55 kDa
Atom Count: 31,994
Modelled Residue Count: 3,492
Deposited Residue Count: 3,527
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	333	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07173
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	274	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06009
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06010
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	D [auth H]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06008
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-1015 alpha chain	E [auth z] H [auth F] I [auth K] J [auth P] K [auth S] E [auth z], H [auth F], I [auth K], J [auth P], K [auth S], L [auth V], M [auth Y], N [auth b], O [auth e], P [auth h], Q [auth k], R [auth n], S [auth q], T [auth t], U [auth w], V [auth 3], W [auth 6]	59	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04123 (Blastochloris viridis) Explore P04123 Go to UniProtKB: P04123
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04123
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-1015 beta chain	AA [auth T] BA [auth W] CA [auth Z] DA [auth c] EA [auth f] AA [auth T], BA [auth W], CA [auth Z], DA [auth c], EA [auth f], F [auth 1], FA [auth i], GA [auth l], HA [auth o], IA [auth r], JA [auth u], KA [auth x], LA [auth 4], MA [auth 7], X [auth G], Y [auth N], Z [auth Q]	56	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04124 (Blastochloris viridis) Explore P04124 Go to UniProtKB: P04124
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04124
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-1015 gamma chain	AB [auth y] BB [auth 5] G [auth 2] NA [auth I] OA [auth O] AB [auth y], BB [auth 5], G [auth 2], NA [auth I], OA [auth O], PA [auth R], QA [auth U], RA [auth X], SA [auth a], TA [auth d], UA [auth g], VA [auth j], WA [auth m], XA [auth p], YA [auth s], ZA [auth v]	24	Blastochloris viridis	Mutation(s): 0
UniProt
Find proteins for P04126 (Blastochloris viridis) Explore P04126 Go to UniProtKB: P04126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04126
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Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download Ideal Coordinates CCD File SDF format, chain AC [auth 1] SDF format, chain BD [auth W] SDF format, chain CC [auth F] SDF format, chain DC [auth K] SDF format, chain DD [auth Z] SDF format, chain EC [auth P] SDF format, chain FC [auth S] SDF format, chain FD [auth c] SDF format, chain GB [auth L] SDF format, chain GC [auth V] SDF format, chain HB [auth L] SDF format, chain HC [auth Y] SDF format, chain HD [auth f] SDF format, chain IC [auth b] SDF format, chain JC [auth e] SDF format, chain JD [auth i] SDF format, chain KC [auth h] SDF format, chain LC [auth k] SDF format, chain LD [auth l] SDF format, chain MC [auth n] SDF format, chain NC [auth q] SDF format, chain ND [auth o] SDF format, chain OC [auth t] SDF format, chain PB [auth M] SDF format, chain PC [auth w] SDF format, chain PD [auth r] SDF format, chain QB [auth M] SDF format, chain QC [auth 3] SDF format, chain RD [auth u] SDF format, chain SC [auth 6] SDF format, chain TC [auth G] SDF format, chain TD [auth x] SDF format, chain VC [auth N] SDF format, chain VD [auth 4] SDF format, chain XC [auth Q] SDF format, chain XD [auth 7] SDF format, chain ZB [auth z] SDF format, chain ZC [auth T] MOL2 format, chain AC [auth 1] MOL2 format, chain BD [auth W] MOL2 format, chain CC [auth F] MOL2 format, chain DC [auth K] MOL2 format, chain DD [auth Z] MOL2 format, chain EC [auth P] MOL2 format, chain FC [auth S] MOL2 format, chain FD [auth c] MOL2 format, chain GB [auth L] MOL2 format, chain GC [auth V] MOL2 format, chain HB [auth L] MOL2 format, chain HC [auth Y] MOL2 format, chain HD [auth f] MOL2 format, chain IC [auth b] MOL2 format, chain JC [auth e] MOL2 format, chain JD [auth i] MOL2 format, chain KC [auth h] MOL2 format, chain LC [auth k] MOL2 format, chain LD [auth l] MOL2 format, chain MC [auth n] MOL2 format, chain NC [auth q] MOL2 format, chain ND [auth o] MOL2 format, chain OC [auth t] MOL2 format, chain PB [auth M] MOL2 format, chain PC [auth w] MOL2 format, chain PD [auth r] MOL2 format, chain QB [auth M] MOL2 format, chain QC [auth 3] MOL2 format, chain RD [auth u] MOL2 format, chain SC [auth 6] MOL2 format, chain TC [auth G] MOL2 format, chain TD [auth x] MOL2 format, chain VC [auth N] MOL2 format, chain VD [auth 4] MOL2 format, chain XC [auth Q] MOL2 format, chain XD [auth 7] MOL2 format, chain ZB [auth z] MOL2 format, chain ZC [auth T]	AC [auth 1] BD [auth W] CC [auth F] DC [auth K] DD [auth Z] AC [auth 1], BD [auth W], CC [auth F], DC [auth K], DD [auth Z], EC [auth P], FC [auth S], FD [auth c], GB [auth L], GC [auth V], HB [auth L], HC [auth Y], HD [auth f], IC [auth b], JC [auth e], JD [auth i], KC [auth h], LC [auth k], LD [auth l], MC [auth n], NC [auth q], ND [auth o], OC [auth t], PB [auth M], PC [auth w], PD [auth r], QB [auth M], QC [auth 3], RD [auth u], SC [auth 6], TC [auth G], TD [auth x], VC [auth N], VD [auth 4], XC [auth Q], XD [auth 7], ZB [auth z], ZC [auth T]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain AC [auth 1] Focus chain BD [auth W] Focus chain CC [auth F] Focus chain DC [auth K] Focus chain DD [auth Z] Focus chain EC [auth P] Focus chain FC [auth S] Focus chain FD [auth c] Focus chain GB [auth L] Focus chain GC [auth V] Focus chain HB [auth L] Focus chain HC [auth Y] Focus chain HD [auth f] Focus chain IC [auth b] Focus chain JC [auth e] Focus chain JD [auth i] Focus chain KC [auth h] Focus chain LC [auth k] Focus chain LD [auth l] Focus chain MC [auth n] Focus chain NC [auth q] Focus chain ND [auth o] Focus chain OC [auth t] Focus chain PB [auth M] Focus chain PC [auth w] Focus chain PD [auth r] Focus chain QB [auth M] Focus chain QC [auth 3] Focus chain RD [auth u] Focus chain SC [auth 6] Focus chain TC [auth G] Focus chain TD [auth x] Focus chain VC [auth N] Focus chain VD [auth 4] Focus chain XC [auth Q] Focus chain XD [auth 7] Focus chain ZB [auth z] Focus chain ZC [auth T] Interactions & Density Focus chain AC [auth 1] Focus chain BD [auth W] Focus chain CC [auth F] Focus chain DC [auth K] Focus chain DD [auth Z] Focus chain EC [auth P] Focus chain FC [auth S] Focus chain FD [auth c] Focus chain GB [auth L] Focus chain GC [auth V] Focus chain HB [auth L] Focus chain HC [auth Y] Focus chain HD [auth f] Focus chain IC [auth b] Focus chain JC [auth e] Focus chain JD [auth i] Focus chain KC [auth h] Focus chain LC [auth k] Focus chain LD [auth l] Focus chain MC [auth n] Focus chain NC [auth q] Focus chain ND [auth o] Focus chain OC [auth t] Focus chain PB [auth M] Focus chain PC [auth w] Focus chain PD [auth r] Focus chain QB [auth M] Focus chain QC [auth 3] Focus chain RD [auth u] Focus chain SC [auth 6] Focus chain TC [auth G] Focus chain TD [auth x] Focus chain VC [auth N] Focus chain VD [auth 4] Focus chain XC [auth Q] Focus chain XD [auth 7] Focus chain ZB [auth z] Focus chain ZC [auth T]
BPB Query on BPB Download Ideal Coordinates CCD File SDF format, chain IB [auth L] SDF format, chain RB [auth M] MOL2 format, chain IB [auth L] MOL2 format, chain RB [auth M]	IB [auth L], RB [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain IB [auth L] Focus chain RB [auth M] Interactions & Density Focus chain IB [auth L] Focus chain RB [auth M]
UQ9 Query on UQ9 Download Ideal Coordinates CCD File SDF format, chain JB [auth L] SDF format, chain RC [auth 6] MOL2 format, chain JB [auth L] MOL2 format, chain RC [auth 6]	JB [auth L], RC [auth 6]	Ubiquinone-9 C₅₄ H₈₂ O₄ UUGXJSBPSRROMU-YJKFELPISA-N		Interactions Focus chain JB [auth L] Focus chain RC [auth 6] Interactions & Density Focus chain JB [auth L] Focus chain RC [auth 6]
MQ9 Query on MQ9 Download Ideal Coordinates CCD File SDF format, chain TB [auth M] MOL2 format, chain TB [auth M]	TB [auth M]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain TB [auth M] Interactions & Density Focus chain TB [auth M]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C]	CB [auth C], DB [auth C], EB [auth C], FB [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C]
NS0 Query on NS0 Download Ideal Coordinates CCD File SDF format, chain AD [auth T] SDF format, chain BC [auth 1] SDF format, chain CD [auth W] SDF format, chain ED [auth Z] SDF format, chain GD [auth c] SDF format, chain ID [auth f] SDF format, chain KD [auth i] SDF format, chain MD [auth l] SDF format, chain OD [auth o] SDF format, chain QD [auth r] SDF format, chain SD [auth u] SDF format, chain UC [auth G] SDF format, chain UD [auth x] SDF format, chain WC [auth N] SDF format, chain WD [auth 4] SDF format, chain YC [auth Q] SDF format, chain YD [auth 7] MOL2 format, chain AD [auth T] MOL2 format, chain BC [auth 1] MOL2 format, chain CD [auth W] MOL2 format, chain ED [auth Z] MOL2 format, chain GD [auth c] MOL2 format, chain ID [auth f] MOL2 format, chain KD [auth i] MOL2 format, chain MD [auth l] MOL2 format, chain OD [auth o] MOL2 format, chain QD [auth r] MOL2 format, chain SD [auth u] MOL2 format, chain UC [auth G] MOL2 format, chain UD [auth x] MOL2 format, chain WC [auth N] MOL2 format, chain WD [auth 4] MOL2 format, chain YC [auth Q] MOL2 format, chain YD [auth 7]	AD [auth T] BC [auth 1] CD [auth W] ED [auth Z] GD [auth c] AD [auth T], BC [auth 1], CD [auth W], ED [auth Z], GD [auth c], ID [auth f], KD [auth i], MD [auth l], OD [auth o], QD [auth r], SD [auth u], UC [auth G], UD [auth x], WC [auth N], WD [auth 4], YC [auth Q], YD [auth 7]	all-trans-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-XILUKMICSA-N		Interactions Focus chain AD [auth T] Focus chain BC [auth 1] Focus chain CD [auth W] Focus chain ED [auth Z] Focus chain GD [auth c] Focus chain ID [auth f] Focus chain KD [auth i] Focus chain MD [auth l] Focus chain OD [auth o] Focus chain QD [auth r] Focus chain SD [auth u] Focus chain UC [auth G] Focus chain UD [auth x] Focus chain WC [auth N] Focus chain WD [auth 4] Focus chain YC [auth Q] Focus chain YD [auth 7] Interactions & Density Focus chain AD [auth T] Focus chain BC [auth 1] Focus chain CD [auth W] Focus chain ED [auth Z] Focus chain GD [auth c] Focus chain ID [auth f] Focus chain KD [auth i] Focus chain MD [auth l] Focus chain OD [auth o] Focus chain QD [auth r] Focus chain SD [auth u] Focus chain UC [auth G] Focus chain UD [auth x] Focus chain WC [auth N] Focus chain WD [auth 4] Focus chain YC [auth Q] Focus chain YD [auth 7]
NS5 Query on NS5 Download Ideal Coordinates CCD File SDF format, chain UB [auth M] MOL2 format, chain UB [auth M]	UB [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain UB [auth M] Interactions & Density Focus chain UB [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain SB [auth M] SDF format, chain VB [auth H] MOL2 format, chain SB [auth M] MOL2 format, chain VB [auth H]	SB [auth M], VB [auth H]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain SB [auth M] Focus chain VB [auth H] Interactions & Density Focus chain SB [auth M] Focus chain VB [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain LB [auth M] SDF format, chain MB [auth M] SDF format, chain NB [auth M] SDF format, chain OB [auth M] SDF format, chain WB [auth H] SDF format, chain XB [auth H] SDF format, chain YB [auth H] MOL2 format, chain LB [auth M] MOL2 format, chain MB [auth M] MOL2 format, chain NB [auth M] MOL2 format, chain OB [auth M] MOL2 format, chain WB [auth H] MOL2 format, chain XB [auth H] MOL2 format, chain YB [auth H]	LB [auth M] MB [auth M] NB [auth M] OB [auth M] WB [auth H] LB [auth M], MB [auth M], NB [auth M], OB [auth M], WB [auth H], XB [auth H], YB [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain LB [auth M] Focus chain MB [auth M] Focus chain NB [auth M] Focus chain OB [auth M] Focus chain WB [auth H] Focus chain XB [auth H] Focus chain YB [auth H] Interactions & Density Focus chain LB [auth M] Focus chain MB [auth M] Focus chain NB [auth M] Focus chain OB [auth M] Focus chain WB [auth H] Focus chain XB [auth H] Focus chain YB [auth H]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain KB [auth L] MOL2 format, chain KB [auth L]	KB [auth L]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain KB [auth L] Interactions & Density Focus chain KB [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	D [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	REFMAC	5.7

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council		--

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 1.2: 2018-05-30
Changes: Data collection, Structure summary
Version 1.3: 2018-10-10
Changes: Data collection, Refinement description, Structure summary
Version 1.4: 2018-10-24
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.5: 2019-10-23
Changes: Data collection, Other

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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6ET5

Reaction centre light harvesting complex 1 from Blc. virids

Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 angstrom.

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Experimental Data

Structure Validation

Deposition Data

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