5YQ7 | pdb_00005yq7

Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii

PDB DOI: https://doi.org/10.2210/pdb5YQ7/pdb
EM Map EMD-6828: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Roseiflexus castenholzii
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2017-11-05 Released: 2018-05-02
Deposition Author(s): Shi, Y., Xin, Y.Y., Niu, T.X., Wang, Q.Q., Niu, W.Q., Huang, X.J., Ding, W., Blankenship, R.E., Xu, X.L., Sun, F.
Funding Organization(s): Chinese Academy of Sciences, Ministry of Science and Technology of China

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.

Xin, Y.Y., Shi, Y., Niu, T.X., Wang, Q.Q., Niu, W.Q., Huang, X.J., Ding, W., Yang, L., Blankenship, R.E., Xu, X.L., Sun, F.

(2018) Nat Commun 9: 1568-1568

PubMed: 29674684 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-018-03881-x
Primary Citation Related Structures:
5YQ7

PubMed Abstract:
Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC-LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.

Organizational Affiliation

Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China.

Macromolecule Content

Total Structure Weight: 334.27 kDa
Atom Count: 20,009
Modeled Residue Count: 2,155
Deposited Residue Count: 2,439
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta subunit of light-harvesting 1	A [auth E] B C [auth 0] E [auth 8] F [auth 6] A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	55	Roseiflexus castenholzii	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q83XD2 (Roseiflexus castenholzii) Explore Q83XD2 Go to UniProtKB: Q83XD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83XD2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Precursor for L subunits of photosynthetic reaction center	D [auth L]	310	Roseiflexus castenholzii	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q83XD0 (Roseiflexus castenholzii) Explore Q83XD0 Go to UniProtKB: Q83XD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83XD0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome subunit of photosynthetic reaction center	J [auth C]	320	Roseiflexus castenholzii	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q83XC9 (Roseiflexus castenholzii) Explore Q83XC9 Go to UniProtKB: Q83XC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83XC9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit of light-harvesting 1	AA [auth A] BA [auth 9] CA [auth 7] DA [auth 5] EA [auth 3] AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], FA [auth 1], O [auth T], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	42	Roseiflexus castenholzii	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q83XD1 (Roseiflexus castenholzii) Explore Q83XD1 Go to UniProtKB: Q83XD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83XD1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Precursor for L and M subunits of photosynthetic reaction center	GA [auth Y]	25	Roseiflexus castenholzii	Mutation(s): 0

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit X	HA [auth X]	23	Roseiflexus castenholzii	Mutation(s): 0

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Precursor for M subunits of photosynthetic reaction center	IA [auth M]	306	Roseiflexus castenholzii	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q83XD0 (Roseiflexus castenholzii) Explore Q83XD0 Go to UniProtKB: Q83XD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83XD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MQE Query on MQE Download:Ideal Coordinates CCD File SDF format, chain SA [auth L] SDF format, chain ZC [auth M] MOL2 format, chain SA [auth L] MOL2 format, chain ZC [auth M] mmCIF format, chain SA [auth L] mmCIF format, chain ZC [auth M]	SA [auth L], ZC [auth M]	2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione C₆₆ H₉₆ O₂ YYDMANIEKFAEJC-RYZSZPJESA-N		Interactions Focus chain SA [auth L] Focus chain ZC [auth M] Interactions & Density Focus chain SA [auth L] Focus chain ZC [auth M]
BCL Query on BCL Download:Ideal Coordinates CCD File SDF format, chain AB [auth 2] SDF format, chain AC [auth R] SDF format, chain AD [auth M] SDF format, chain BB [auth K] SDF format, chain BC [auth P] SDF format, chain CB [auth K] SDF format, chain EC [auth N] SDF format, chain GC [auth J] SDF format, chain HB [auth I] SDF format, chain HC [auth H] SDF format, chain IB [auth I] SDF format, chain JA [auth E] SDF format, chain JB [auth G] SDF format, chain KA [auth E] SDF format, chain KB [auth G] SDF format, chain KC [auth F] SDF format, chain LA [auth B] SDF format, chain LB [auth W] SDF format, chain LC [auth D] SDF format, chain MA [auth B] SDF format, chain MB [auth W] SDF format, chain NA [auth 0] SDF format, chain NB [auth U] SDF format, chain NC [auth A] SDF format, chain OA [auth 0] SDF format, chain OB [auth U] SDF format, chain PA [auth L] SDF format, chain QA [auth L] SDF format, chain QC [auth 9] SDF format, chain RB [auth T] SDF format, chain RC [auth 7] SDF format, chain SB [auth S] SDF format, chain TA [auth 8] SDF format, chain TB [auth S] SDF format, chain TC [auth 5] SDF format, chain UA [auth 8] SDF format, chain UB [auth Q] SDF format, chain VA [auth 6] SDF format, chain VB [auth Q] SDF format, chain VC [auth 3] SDF format, chain WA [auth 6] SDF format, chain WB [auth O] SDF format, chain XA [auth 4] SDF format, chain XB [auth O] SDF format, chain XC [auth 1] SDF format, chain YA [auth 4] SDF format, chain YB [auth V] SDF format, chain ZA [auth 2] MOL2 format, chain AB [auth 2] MOL2 format, chain AC [auth R] MOL2 format, chain AD [auth M] MOL2 format, chain BB [auth K] MOL2 format, chain BC [auth P] MOL2 format, chain CB [auth K] MOL2 format, chain EC [auth N] MOL2 format, chain GC [auth J] MOL2 format, chain HB [auth I] MOL2 format, chain HC [auth H] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth G] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth G] MOL2 format, chain KC [auth F] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth W] MOL2 format, chain LC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth W] MOL2 format, chain NA [auth 0] MOL2 format, chain NB [auth U] MOL2 format, chain NC [auth A] MOL2 format, chain OA [auth 0] MOL2 format, chain OB [auth U] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain QC [auth 9] MOL2 format, chain RB [auth T] MOL2 format, chain RC [auth 7] MOL2 format, chain SB [auth S] MOL2 format, chain TA [auth 8] MOL2 format, chain TB [auth S] MOL2 format, chain TC [auth 5] MOL2 format, chain UA [auth 8] MOL2 format, chain UB [auth Q] MOL2 format, chain VA [auth 6] MOL2 format, chain VB [auth Q] MOL2 format, chain VC [auth 3] MOL2 format, chain WA [auth 6] MOL2 format, chain WB [auth O] MOL2 format, chain XA [auth 4] MOL2 format, chain XB [auth O] MOL2 format, chain XC [auth 1] MOL2 format, chain YA [auth 4] MOL2 format, chain YB [auth V] MOL2 format, chain ZA [auth 2] mmCIF format, chain AB [auth 2] mmCIF format, chain AC [auth R] mmCIF format, chain AD [auth M] mmCIF format, chain BB [auth K] mmCIF format, chain BC [auth P] mmCIF format, chain CB [auth K] mmCIF format, chain EC [auth N] mmCIF format, chain GC [auth J] mmCIF format, chain HB [auth I] mmCIF format, chain HC [auth H] mmCIF format, chain IB [auth I] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth G] mmCIF format, chain KA [auth E] mmCIF format, chain KB [auth G] mmCIF format, chain KC [auth F] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth W] mmCIF format, chain LC [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth W] mmCIF format, chain NA [auth 0] mmCIF format, chain NB [auth U] mmCIF format, chain NC [auth A] mmCIF format, chain OA [auth 0] mmCIF format, chain OB [auth U] mmCIF format, chain PA [auth L] mmCIF format, chain QA [auth L] mmCIF format, chain QC [auth 9] mmCIF format, chain RB [auth T] mmCIF format, chain RC [auth 7] mmCIF format, chain SB [auth S] mmCIF format, chain TA [auth 8] mmCIF format, chain TB [auth S] mmCIF format, chain TC [auth 5] mmCIF format, chain UA [auth 8] mmCIF format, chain UB [auth Q] mmCIF format, chain VA [auth 6] mmCIF format, chain VB [auth Q] mmCIF format, chain VC [auth 3] mmCIF format, chain WA [auth 6] mmCIF format, chain WB [auth O] mmCIF format, chain XA [auth 4] mmCIF format, chain XB [auth O] mmCIF format, chain XC [auth 1] mmCIF format, chain YA [auth 4] mmCIF format, chain YB [auth V] mmCIF format, chain ZA [auth 2]	AB [auth 2] AC [auth R] AD [auth M] BB [auth K] BC [auth P] AB [auth 2], AC [auth R], AD [auth M], BB [auth K], BC [auth P], CB [auth K], EC [auth N], GC [auth J], HB [auth I], HC [auth H], IB [auth I], JA [auth E], JB [auth G], KA [auth E], KB [auth G], KC [auth F], LA [auth B], LB [auth W], LC [auth D], MA [auth B], MB [auth W], NA [auth 0], NB [auth U], NC [auth A], OA [auth 0], OB [auth U], PA [auth L], QA [auth L], QC [auth 9], RB [auth T], RC [auth 7], SB [auth S], TA [auth 8], TB [auth S], TC [auth 5], UA [auth 8], UB [auth Q], VA [auth 6], VB [auth Q], VC [auth 3], WA [auth 6], WB [auth O], XA [auth 4], XB [auth O], XC [auth 1], YA [auth 4], YB [auth V], ZA [auth 2]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth 2] Focus chain AC [auth R] Focus chain AD [auth M] Focus chain BB [auth K] Focus chain BC [auth P] Focus chain CB [auth K] Focus chain EC [auth N] Focus chain GC [auth J] Focus chain HB [auth I] Focus chain HC [auth H] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth G] Focus chain KA [auth E] Focus chain KB [auth G] Focus chain KC [auth F] Focus chain LA [auth B] Focus chain LB [auth W] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MB [auth W] Focus chain NA [auth 0] Focus chain NB [auth U] Focus chain NC [auth A] Focus chain OA [auth 0] Focus chain OB [auth U] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain QC [auth 9] Focus chain RB [auth T] Focus chain RC [auth 7] Focus chain SB [auth S] Focus chain TA [auth 8] Focus chain TB [auth S] Focus chain TC [auth 5] Focus chain UA [auth 8] Focus chain UB [auth Q] Focus chain VA [auth 6] Focus chain VB [auth Q] Focus chain VC [auth 3] Focus chain WA [auth 6] Focus chain WB [auth O] Focus chain XA [auth 4] Focus chain XB [auth O] Focus chain XC [auth 1] Focus chain YA [auth 4] Focus chain YB [auth V] Focus chain ZA [auth 2] Interactions & Density Focus chain AB [auth 2] Focus chain AC [auth R] Focus chain AD [auth M] Focus chain BB [auth K] Focus chain BC [auth P] Focus chain CB [auth K] Focus chain EC [auth N] Focus chain GC [auth J] Focus chain HB [auth I] Focus chain HC [auth H] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth G] Focus chain KA [auth E] Focus chain KB [auth G] Focus chain KC [auth F] Focus chain LA [auth B] Focus chain LB [auth W] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MB [auth W] Focus chain NA [auth 0] Focus chain NB [auth U] Focus chain NC [auth A] Focus chain OA [auth 0] Focus chain OB [auth U] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain QC [auth 9] Focus chain RB [auth T] Focus chain RC [auth 7] Focus chain SB [auth S] Focus chain TA [auth 8] Focus chain TB [auth S] Focus chain TC [auth 5] Focus chain UA [auth 8] Focus chain UB [auth Q] Focus chain VA [auth 6] Focus chain VB [auth Q] Focus chain VC [auth 3] Focus chain WA [auth 6] Focus chain WB [auth O] Focus chain XA [auth 4] Focus chain XB [auth O] Focus chain XC [auth 1] Focus chain YA [auth 4] Focus chain YB [auth V] Focus chain ZA [auth 2]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain BD [auth M] SDF format, chain CD [auth M] SDF format, chain RA [auth L] MOL2 format, chain BD [auth M] MOL2 format, chain CD [auth M] MOL2 format, chain RA [auth L] mmCIF format, chain BD [auth M] mmCIF format, chain CD [auth M] mmCIF format, chain RA [auth L]	BD [auth M], CD [auth M], RA [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain BD [auth M] Focus chain CD [auth M] Focus chain RA [auth L] Interactions & Density Focus chain BD [auth M] Focus chain CD [auth M] Focus chain RA [auth L]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C]	DB [auth C], EB [auth C], FB [auth C], GB [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Interactions & Density Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C]
KGD Query on KGD Download:Ideal Coordinates CCD File SDF format, chain CC [auth N] SDF format, chain DC [auth N] SDF format, chain FC [auth J] SDF format, chain IC [auth H] SDF format, chain JC [auth F] SDF format, chain MC [auth A] SDF format, chain OC [auth 9] SDF format, chain PB [auth T] SDF format, chain PC [auth 9] SDF format, chain QB [auth T] SDF format, chain SC [auth 5] SDF format, chain UC [auth 3] SDF format, chain WC [auth 3] SDF format, chain ZB [auth R] MOL2 format, chain CC [auth N] MOL2 format, chain DC [auth N] MOL2 format, chain FC [auth J] MOL2 format, chain IC [auth H] MOL2 format, chain JC [auth F] MOL2 format, chain MC [auth A] MOL2 format, chain OC [auth 9] MOL2 format, chain PB [auth T] MOL2 format, chain PC [auth 9] MOL2 format, chain QB [auth T] MOL2 format, chain SC [auth 5] MOL2 format, chain UC [auth 3] MOL2 format, chain WC [auth 3] MOL2 format, chain ZB [auth R] mmCIF format, chain CC [auth N] mmCIF format, chain DC [auth N] mmCIF format, chain FC [auth J] mmCIF format, chain IC [auth H] mmCIF format, chain JC [auth F] mmCIF format, chain MC [auth A] mmCIF format, chain OC [auth 9] mmCIF format, chain PB [auth T] mmCIF format, chain PC [auth 9] mmCIF format, chain QB [auth T] mmCIF format, chain SC [auth 5] mmCIF format, chain UC [auth 3] mmCIF format, chain WC [auth 3] mmCIF format, chain ZB [auth R]	CC [auth N] DC [auth N] FC [auth J] IC [auth H] JC [auth F] CC [auth N], DC [auth N], FC [auth J], IC [auth H], JC [auth F], MC [auth A], OC [auth 9], PB [auth T], PC [auth 9], QB [auth T], SC [auth 5], UC [auth 3], WC [auth 3], ZB [auth R]	beta,psi-caroten-4-one C₄₀ H₅₄ O BRKQDNOGSHYATK-HNNISBQLSA-N		Interactions Focus chain CC [auth N] Focus chain DC [auth N] Focus chain FC [auth J] Focus chain IC [auth H] Focus chain JC [auth F] Focus chain MC [auth A] Focus chain OC [auth 9] Focus chain PB [auth T] Focus chain PC [auth 9] Focus chain QB [auth T] Focus chain SC [auth 5] Focus chain UC [auth 3] Focus chain WC [auth 3] Focus chain ZB [auth R] Interactions & Density Focus chain CC [auth N] Focus chain DC [auth N] Focus chain FC [auth J] Focus chain IC [auth H] Focus chain JC [auth F] Focus chain MC [auth A] Focus chain OC [auth 9] Focus chain PB [auth T] Focus chain PC [auth 9] Focus chain QB [auth T] Focus chain SC [auth 5] Focus chain UC [auth 3] Focus chain WC [auth 3] Focus chain ZB [auth R]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain YC [auth M] MOL2 format, chain YC [auth M] mmCIF format, chain YC [auth M]	YC [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain YC [auth M] Interactions & Density Focus chain YC [auth M]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB08030202
Ministry of Science and Technology of China	China	2014CB910700

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 2.0: 2025-06-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary