7EQD | pdb_00007eqd

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM

PDB DOI: https://doi.org/10.2210/pdb7EQD/pdb
EM Map EMD-31258: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Rhodospirillum rubrum, Rhodospirillum rubrum ATCC 11170
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2021-05-01 Released: 2021-08-18
Deposition Author(s): Tani, K., Kanno, R., Ji, X.-C., Yu, L.-J., Hall, M., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum .

Tani, K., Kanno, R., Ji, X.C., Hall, M., Yu, L.J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.Y.

(2021) Biochemistry

PubMed: 34323477 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.1c00360
Primary Citation Related Structures:
7EQD

PubMed Abstract:
Rhodospirillum ( Rsp. ) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl a _G) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the Q _A site in the RC. The geranylgeraniol side chains of BChl a _G coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls a _G. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.

Organizational Affiliation

Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan.

Macromolecule Content

Total Structure Weight: 374.83 kDa
Atom Count: 23,122
Modeled Residue Count: 2,302
Deposited Residue Count: 2,708
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A [auth L]	275	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10717 (Rhodospirillum rubrum) Explore P10717 Go to UniProtKB: P10717
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10717
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B [auth M]	305	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ26 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ26 Go to UniProtKB: Q2RQ26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2RQ26
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoreaction center protein H	C [auth H]	256	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q7M149 (Rhodospirillum rubrum) Explore Q7M149 Go to UniProtKB: Q7M149
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7M149
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-870 alpha chain	BA [auth 3] D [auth A] DA [auth 5] F [auth D] FA [auth 7] BA [auth 3], D [auth A], DA [auth 5], F [auth D], FA [auth 7], H [auth F], HA [auth 9], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth U], V [auth W], X [auth Y], Z [auth 1]	62	Rhodospirillum rubrum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02947 (Rhodospirillum rubrum) Explore P02947 Go to UniProtKB: P02947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-870 beta chain	AA [auth 2] CA [auth 4] E [auth B] EA [auth 6] G [auth E] AA [auth 2], CA [auth 4], E [auth B], EA [auth 6], G [auth E], GA [auth 8], I [auth G], IA [auth 0], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth V], W [auth X], Y [auth Z]	55	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ23 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ23 Go to UniProtKB: Q2RQ23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2RQ23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain YA [auth M] SDF format, chain XA [auth M] SDF format, chain EB [auth H] SDF format, chain DB [auth H] SDF format, chain BB [auth H] MOL2 format, chain YA [auth M] MOL2 format, chain XA [auth M] MOL2 format, chain EB [auth H] MOL2 format, chain DB [auth H] MOL2 format, chain BB [auth H] mmCIF format, chain YA [auth M] mmCIF format, chain XA [auth M] mmCIF format, chain EB [auth H] mmCIF format, chain DB [auth H] mmCIF format, chain BB [auth H]	BB [auth H], DB [auth H], EB [auth H], XA [auth M], YA [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth H] Focus chain DB [auth H] Focus chain EB [auth H] Focus chain XA [auth M] Focus chain YA [auth M] Interactions & Density Focus chain BB [auth H] Focus chain DB [auth H] Focus chain EB [auth H] Focus chain XA [auth M] Focus chain YA [auth M]
07D Query on 07D Download:Ideal Coordinates CCD File SDF format, chain ZC [auth Z] SDF format, chain XC [auth Y] SDF format, chain XB [auth K] SDF format, chain VD [auth 0] SDF format, chain VC [auth X] SDF format, chain VB [auth J] SDF format, chain TD [auth 9] SDF format, chain TC [auth W] SDF format, chain TB [auth I] SDF format, chain TA [auth M] SDF format, chain SA [auth M] SDF format, chain RD [auth 8] SDF format, chain RC [auth V] SDF format, chain RB [auth G] SDF format, chain PD [auth 7] SDF format, chain PC [auth U] SDF format, chain PB [auth F] SDF format, chain PA [auth L] SDF format, chain ND [auth 6] SDF format, chain NC [auth T] SDF format, chain NB [auth E] SDF format, chain LC [auth S] SDF format, chain LB [auth D] SDF format, chain KD [auth 5] SDF format, chain JB [auth B] SDF format, chain JA [auth L] SDF format, chain IC [auth Q] SDF format, chain HD [auth 4] SDF format, chain HC [auth Q] SDF format, chain HB [auth A] SDF format, chain FD [auth 3] SDF format, chain FC [auth P] SDF format, chain DD [auth 2] SDF format, chain DC [auth O] SDF format, chain BD [auth 1] SDF format, chain BC [auth N] MOL2 format, chain ZC [auth Z] MOL2 format, chain XC [auth Y] MOL2 format, chain XB [auth K] MOL2 format, chain VD [auth 0] MOL2 format, chain VC [auth X] MOL2 format, chain VB [auth J] MOL2 format, chain TD [auth 9] MOL2 format, chain TC [auth W] MOL2 format, chain TB [auth I] MOL2 format, chain TA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain RD [auth 8] MOL2 format, chain RC [auth V] MOL2 format, chain RB [auth G] MOL2 format, chain PD [auth 7] MOL2 format, chain PC [auth U] MOL2 format, chain PB [auth F] MOL2 format, chain PA [auth L] MOL2 format, chain ND [auth 6] MOL2 format, chain NC [auth T] MOL2 format, chain NB [auth E] MOL2 format, chain LC [auth S] MOL2 format, chain LB [auth D] MOL2 format, chain KD [auth 5] MOL2 format, chain JB [auth B] MOL2 format, chain JA [auth L] MOL2 format, chain IC [auth Q] MOL2 format, chain HD [auth 4] MOL2 format, chain HC [auth Q] MOL2 format, chain HB [auth A] MOL2 format, chain FD [auth 3] MOL2 format, chain FC [auth P] MOL2 format, chain DD [auth 2] MOL2 format, chain DC [auth O] MOL2 format, chain BD [auth 1] MOL2 format, chain BC [auth N] mmCIF format, chain ZC [auth Z] mmCIF format, chain XC [auth Y] mmCIF format, chain XB [auth K] mmCIF format, chain VD [auth 0] mmCIF format, chain VC [auth X] mmCIF format, chain VB [auth J] mmCIF format, chain TD [auth 9] mmCIF format, chain TC [auth W] mmCIF format, chain TB [auth I] mmCIF format, chain TA [auth M] mmCIF format, chain SA [auth M] mmCIF format, chain RD [auth 8] mmCIF format, chain RC [auth V] mmCIF format, chain RB [auth G] mmCIF format, chain PD [auth 7] mmCIF format, chain PC [auth U] mmCIF format, chain PB [auth F] mmCIF format, chain PA [auth L] mmCIF format, chain ND [auth 6] mmCIF format, chain NC [auth T] mmCIF format, chain NB [auth E] mmCIF format, chain LC [auth S] mmCIF format, chain LB [auth D] mmCIF format, chain KD [auth 5] mmCIF format, chain JB [auth B] mmCIF format, chain JA [auth L] mmCIF format, chain IC [auth Q] mmCIF format, chain HD [auth 4] mmCIF format, chain HC [auth Q] mmCIF format, chain HB [auth A] mmCIF format, chain FD [auth 3] mmCIF format, chain FC [auth P] mmCIF format, chain DD [auth 2] mmCIF format, chain DC [auth O] mmCIF format, chain BD [auth 1] mmCIF format, chain BC [auth N]	BC [auth N] BD [auth 1] DC [auth O] DD [auth 2] FC [auth P] BC [auth N], BD [auth 1], DC [auth O], DD [auth 2], FC [auth P], FD [auth 3], HB [auth A], HC [auth Q], HD [auth 4], IC [auth Q], JA [auth L], JB [auth B], KD [auth 5], LB [auth D], LC [auth S], NB [auth E], NC [auth T], ND [auth 6], PA [auth L], PB [auth F], PC [auth U], PD [auth 7], RB [auth G], RC [auth V], RD [auth 8], SA [auth M], TA [auth M], TB [auth I], TC [auth W], TD [auth 9], VB [auth J], VC [auth X], VD [auth 0], XB [auth K], XC [auth Y], ZC [auth Z]	Trans-Geranyl BACTERIOCHLOROPHYLL A C₅₅ H₆₄ Mg N₄ O₆ ZBSZXIUSELHDGQ-POZHEDQMSA-M		Interactions Focus chain BC [auth N] Focus chain BD [auth 1] Focus chain DC [auth O] Focus chain DD [auth 2] Focus chain FC [auth P] Focus chain FD [auth 3] Focus chain HB [auth A] Focus chain HC [auth Q] Focus chain HD [auth 4] Focus chain IC [auth Q] Focus chain JA [auth L] Focus chain JB [auth B] Focus chain KD [auth 5] Focus chain LB [auth D] Focus chain LC [auth S] Focus chain NB [auth E] Focus chain NC [auth T] Focus chain ND [auth 6] Focus chain PA [auth L] Focus chain PB [auth F] Focus chain PC [auth U] Focus chain PD [auth 7] Focus chain RB [auth G] Focus chain RC [auth V] Focus chain RD [auth 8] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain TB [auth I] Focus chain TC [auth W] Focus chain TD [auth 9] Focus chain VB [auth J] Focus chain VC [auth X] Focus chain VD [auth 0] Focus chain XB [auth K] Focus chain XC [auth Y] Focus chain ZC [auth Z] Interactions & Density Focus chain BC [auth N] Focus chain BD [auth 1] Focus chain DC [auth O] Focus chain DD [auth 2] Focus chain FC [auth P] Focus chain FD [auth 3] Focus chain HB [auth A] Focus chain HC [auth Q] Focus chain HD [auth 4] Focus chain IC [auth Q] Focus chain JA [auth L] Focus chain JB [auth B] Focus chain KD [auth 5] Focus chain LB [auth D] Focus chain LC [auth S] Focus chain NB [auth E] Focus chain NC [auth T] Focus chain ND [auth 6] Focus chain PA [auth L] Focus chain PB [auth F] Focus chain PC [auth U] Focus chain PD [auth 7] Focus chain RB [auth G] Focus chain RC [auth V] Focus chain RD [auth 8] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain TB [auth I] Focus chain TC [auth W] Focus chain TD [auth 9] Focus chain VB [auth J] Focus chain VC [auth X] Focus chain VD [auth 0] Focus chain XB [auth K] Focus chain XC [auth Y] Focus chain ZC [auth Z]
08I Query on 08I Download:Ideal Coordinates CCD File SDF format, chain UA [auth M] SDF format, chain KA [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain KA [auth L] mmCIF format, chain UA [auth M] mmCIF format, chain KA [auth L]	KA [auth L], UA [auth M]	Trans-Geranyl BACTERIOPHEOPHYTIN A C₅₅ H₆₆ N₄ O₆ HZSDVJXREXKBMW-FAWFAMGLSA-N		Interactions Focus chain KA [auth L] Focus chain UA [auth M] Interactions & Density Focus chain KA [auth L] Focus chain UA [auth M]
U10 Query on U10 Download:Ideal Coordinates CCD File SDF format, chain QA [auth M] SDF format, chain LA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain LA [auth L] mmCIF format, chain QA [auth M] mmCIF format, chain LA [auth L]	LA [auth L], QA [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain LA [auth L] Focus chain QA [auth M] Interactions & Density Focus chain LA [auth L] Focus chain QA [auth M]
RQ0 (Subject of Investigation/LOI) Query on RQ0 Download:Ideal Coordinates CCD File SDF format, chain VA [auth M] MOL2 format, chain VA [auth M] mmCIF format, chain VA [auth M]	VA [auth M]	2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione C₅₈ H₈₅ N O₃ WXESXKLCRFKYIR-NBYUNPNPSA-N		Interactions Focus chain VA [auth M] Interactions & Density Focus chain VA [auth M]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain MA [auth L] SDF format, chain CB [auth H] MOL2 format, chain MA [auth L] MOL2 format, chain CB [auth H] mmCIF format, chain MA [auth L] mmCIF format, chain CB [auth H]	CB [auth H], MA [auth L]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain CB [auth H] Focus chain MA [auth L] Interactions & Density Focus chain CB [auth H] Focus chain MA [auth L]
PEF Query on PEF Download:Ideal Coordinates CCD File SDF format, chain ZB [auth K] SDF format, chain YB [auth K] SDF format, chain FB [auth H] MOL2 format, chain ZB [auth K] MOL2 format, chain YB [auth K] MOL2 format, chain FB [auth H] mmCIF format, chain ZB [auth K] mmCIF format, chain YB [auth K] mmCIF format, chain FB [auth H]	FB [auth H], YB [auth K], ZB [auth K]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain FB [auth H] Focus chain YB [auth K] Focus chain ZB [auth K] Interactions & Density Focus chain FB [auth H] Focus chain YB [auth K] Focus chain ZB [auth K]
CRT Query on CRT Download:Ideal Coordinates CCD File SDF format, chain YC [auth Z] SDF format, chain WA [auth M] SDF format, chain UD [auth 0] SDF format, chain UC [auth X] SDF format, chain UB [auth J] SDF format, chain QD [auth 8] SDF format, chain QC [auth V] SDF format, chain QB [auth G] SDF format, chain MD [auth 6] SDF format, chain MC [auth T] SDF format, chain MB [auth E] SDF format, chain JC [auth R] SDF format, chain IB [auth A] SDF format, chain GD [auth 4] SDF format, chain EC [auth P] SDF format, chain CD [auth 2] SDF format, chain AC [auth N] MOL2 format, chain YC [auth Z] MOL2 format, chain WA [auth M] MOL2 format, chain UD [auth 0] MOL2 format, chain UC [auth X] MOL2 format, chain UB [auth J] MOL2 format, chain QD [auth 8] MOL2 format, chain QC [auth V] MOL2 format, chain QB [auth G] MOL2 format, chain MD [auth 6] MOL2 format, chain MC [auth T] MOL2 format, chain MB [auth E] MOL2 format, chain JC [auth R] MOL2 format, chain IB [auth A] MOL2 format, chain GD [auth 4] MOL2 format, chain EC [auth P] MOL2 format, chain CD [auth 2] MOL2 format, chain AC [auth N] mmCIF format, chain YC [auth Z] mmCIF format, chain WA [auth M] mmCIF format, chain UD [auth 0] mmCIF format, chain UC [auth X] mmCIF format, chain UB [auth J] mmCIF format, chain QD [auth 8] mmCIF format, chain QC [auth V] mmCIF format, chain QB [auth G] mmCIF format, chain MD [auth 6] mmCIF format, chain MC [auth T] mmCIF format, chain MB [auth E] mmCIF format, chain JC [auth R] mmCIF format, chain IB [auth A] mmCIF format, chain GD [auth 4] mmCIF format, chain EC [auth P] mmCIF format, chain CD [auth 2] mmCIF format, chain AC [auth N]	AC [auth N] CD [auth 2] EC [auth P] GD [auth 4] IB [auth A] AC [auth N], CD [auth 2], EC [auth P], GD [auth 4], IB [auth A], JC [auth R], MB [auth E], MC [auth T], MD [auth 6], QB [auth G], QC [auth V], QD [auth 8], UB [auth J], UC [auth X], UD [auth 0], WA [auth M], YC [auth Z]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain AC [auth N] Focus chain CD [auth 2] Focus chain EC [auth P] Focus chain GD [auth 4] Focus chain IB [auth A] Focus chain JC [auth R] Focus chain MB [auth E] Focus chain MC [auth T] Focus chain MD [auth 6] Focus chain QB [auth G] Focus chain QC [auth V] Focus chain QD [auth 8] Focus chain UB [auth J] Focus chain UC [auth X] Focus chain UD [auth 0] Focus chain WA [auth M] Focus chain YC [auth Z] Interactions & Density Focus chain AC [auth N] Focus chain CD [auth 2] Focus chain EC [auth P] Focus chain GD [auth 4] Focus chain IB [auth A] Focus chain JC [auth R] Focus chain MB [auth E] Focus chain MC [auth T] Focus chain MD [auth 6] Focus chain QB [auth G] Focus chain QC [auth V] Focus chain QD [auth 8] Focus chain UB [auth J] Focus chain UC [auth X] Focus chain UD [auth 0] Focus chain WA [auth M] Focus chain YC [auth Z]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain ZA [auth M] SDF format, chain WD [auth 0] SDF format, chain WC [auth X] SDF format, chain WB [auth J] SDF format, chain SD [auth 8] SDF format, chain SC [auth V] SDF format, chain SB [auth G] SDF format, chain OD [auth 6] SDF format, chain OC [auth T] SDF format, chain OB [auth E] SDF format, chain OA [auth L] SDF format, chain NA [auth L] SDF format, chain LD [auth 5] SDF format, chain KC [auth R] SDF format, chain KB [auth B] SDF format, chain JD [auth 5] SDF format, chain ID [auth 4] SDF format, chain GC [auth P] SDF format, chain GB [auth H] SDF format, chain ED [auth 2] SDF format, chain CC [auth N] SDF format, chain AD [auth Z] SDF format, chain AB [auth M] MOL2 format, chain ZA [auth M] MOL2 format, chain WD [auth 0] MOL2 format, chain WC [auth X] MOL2 format, chain WB [auth J] MOL2 format, chain SD [auth 8] MOL2 format, chain SC [auth V] MOL2 format, chain SB [auth G] MOL2 format, chain OD [auth 6] MOL2 format, chain OC [auth T] MOL2 format, chain OB [auth E] MOL2 format, chain OA [auth L] MOL2 format, chain NA [auth L] MOL2 format, chain LD [auth 5] MOL2 format, chain KC [auth R] MOL2 format, chain KB [auth B] MOL2 format, chain JD [auth 5] MOL2 format, chain ID [auth 4] MOL2 format, chain GC [auth P] MOL2 format, chain GB [auth H] MOL2 format, chain ED [auth 2] MOL2 format, chain CC [auth N] MOL2 format, chain AD [auth Z] MOL2 format, chain AB [auth M] mmCIF format, chain ZA [auth M] mmCIF format, chain WD [auth 0] mmCIF format, chain WC [auth X] mmCIF format, chain WB [auth J] mmCIF format, chain SD [auth 8] mmCIF format, chain SC [auth V] mmCIF format, chain SB [auth G] mmCIF format, chain OD [auth 6] mmCIF format, chain OC [auth T] mmCIF format, chain OB [auth E] mmCIF format, chain OA [auth L] mmCIF format, chain NA [auth L] mmCIF format, chain LD [auth 5] mmCIF format, chain KC [auth R] mmCIF format, chain KB [auth B] mmCIF format, chain JD [auth 5] mmCIF format, chain ID [auth 4] mmCIF format, chain GC [auth P] mmCIF format, chain GB [auth H] mmCIF format, chain ED [auth 2] mmCIF format, chain CC [auth N] mmCIF format, chain AD [auth Z] mmCIF format, chain AB [auth M]	AB [auth M] AD [auth Z] CC [auth N] ED [auth 2] GB [auth H] AB [auth M], AD [auth Z], CC [auth N], ED [auth 2], GB [auth H], GC [auth P], ID [auth 4], JD [auth 5], KB [auth B], KC [auth R], LD [auth 5], NA [auth L], OA [auth L], OB [auth E], OC [auth T], OD [auth 6], SB [auth G], SC [auth V], SD [auth 8], WB [auth J], WC [auth X], WD [auth 0], ZA [auth M]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AB [auth M] Focus chain AD [auth Z] Focus chain CC [auth N] Focus chain ED [auth 2] Focus chain GB [auth H] Focus chain GC [auth P] Focus chain ID [auth 4] Focus chain JD [auth 5] Focus chain KB [auth B] Focus chain KC [auth R] Focus chain LD [auth 5] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain OB [auth E] Focus chain OC [auth T] Focus chain OD [auth 6] Focus chain SB [auth G] Focus chain SC [auth V] Focus chain SD [auth 8] Focus chain WB [auth J] Focus chain WC [auth X] Focus chain WD [auth 0] Focus chain ZA [auth M] Interactions & Density Focus chain AB [auth M] Focus chain AD [auth Z] Focus chain CC [auth N] Focus chain ED [auth 2] Focus chain GB [auth H] Focus chain GC [auth P] Focus chain ID [auth 4] Focus chain JD [auth 5] Focus chain KB [auth B] Focus chain KC [auth R] Focus chain LD [auth 5] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain OB [auth E] Focus chain OC [auth T] Focus chain OD [auth 6] Focus chain SB [auth G] Focus chain SC [auth V] Focus chain SD [auth 8] Focus chain WB [auth J] Focus chain WC [auth X] Focus chain WD [auth 0] Focus chain ZA [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain RA [auth M] MOL2 format, chain RA [auth M] mmCIF format, chain RA [auth M]	RA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain RA [auth M] Interactions & Density Focus chain RA [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	BA [auth 3] D [auth A] DA [auth 5] F [auth D] FA [auth 7] BA [auth 3], D [auth A], DA [auth 5], F [auth D], FA [auth 7], H [auth F], HA [auth 9], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth U], V [auth W], X [auth Y], Z [auth 1]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101116
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04174
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05153
Japan Society for the Promotion of Science (JSPS)	Japan	20H05086
Japan Society for the Promotion of Science (JSPS)	Japan	20H02856