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

2024-10-23 REL PDBe PDBe PDBe 2021-03-27 2022-03-02 2022-03-02 2024-10-23 Czech Science Foundation 19-28778X,19-28323X Czech Republic Biotechnology and Biological Sciences Research Council (BBSRC) BB/M000265/1 United Kingdom European Research Council (ERC) 854126 European Union European Regional Development Fund CZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic Wellcome Trust Wellcome Trust United Kingdom Medical Research Council (MRC, United Kingdom) MC UP 120117 United Kingdom Royal Society UF160039 United Kingdom Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A Qian P Koblizek M Photosynthesis, reaction centre light harvesting complex, RC-dLH, RC-LH1, carotenoid, quinone, bacteriochlorophyll a, Gemmatimonas phototrophica, MEMBRANE PROTEIN Qian P Gardiner AT Simova I Naydenova K Croll TI Jackson PJ Kloz M Cubakova P Kuzma M Zeng Y Castro-Hartmann P van Knippenberg B Goldie KN Kaftan D Hrouzek P Hajek J Agirre J Siebert CA Bina D Sader K Stahlberg H Sobotka R Russo CJ Polivka T Hunter CN Koblizek M 2.4- angstrom structure of the double-ring Gemmatimonas phototrophica photosystem. Sci Adv US 8 eabk3139 eabk3139 2022 35171663 doi:10.1126/sciadv.abk3139 2375-2548 7o0u FULLOVERLAP RC-dLH model_1a RC-dLH model_1a 0 1 2 3 4 5 6 7 8 9

Reaction centre light harvesting complex model_1a from Gemmatimonas phototrophic AP64

Gemmatimonas phototrophica AP64 0.800 LHh-alpha Gemmatimonas phototrophica AP64 0.006061153 24 LEVO (FME)HRIWMGTDPHIIMSALGSFLVGAVLVMHIWAYGQFNWPATLKAKYATPPAATR Light-harvesting protein B:885 subunit beta Gemmatimonas phototrophica 0.005084809 40 LEVO MSEKGGMTEEEARRFHGYMVTGTLGYVVVASVAHFLAWSWRPWF A0A143BHS8 MULTIHEME_CYTC domain-containing protein Gemmatimonas phototrophica 0.038457609 1 LEVO MVPVSLLTLGACGDAATDTVQVGYRGTAMEQNYDHGDLKTKFAQVKLPQSPPPAGESPPGPLPWKNVQVLNDISIAEFNR TMIAMSTWVAGTGNCAYCHNVAAFQDDTLPNGKPLYTKIVARRMLQMTRNINGNYSQHVKNTGVTCYTCHMGKPLPNGLW FYSSQTDYLRHYLDRDGARVITQGVAPSNANRSSTKQAEWTYALMISQSRSLGVNCTYCHNTRQFASWREAPPARVTAYH GILMLRDVNQNYLAPLQPVYPAVRLGAMGDAPKAQCVTCHNGAYKPLYGAQMAKDFPAMWGRADWNGVPFPGIMRVAADS TKTDSTVVAAPAAAPAQRTSARPGSVTTPVGGVN A0A143BHR6 RC-S Gemmatimonas phototrophica AP64 0.021079074 1 LEVO MPASPSPLPRSSRVRNAAVVVALVAVGLAARGRDAQGTQPPVAPPAAPTATAAPDLAVQDSTKADSTAVADTLMDLSMVM AAEAAAATVTTAPVAVAPTAWPVDPTTGQTLINGRPVVGRVFIMRKTDGTVKYPNVADVVAHEALAPLPPVVGSSYQQAP ITNQRRMRGIMIQSTLWDMDRKRSATRQRYYPASTPANQLGQ PRCH domain-containing protein Gemmatimonas phototrophica 0.007854894 1 LEVO (FME)MEYIDGAQIALYAFWLFFFGLIIYLRREDKREGYPLESPQGPRDGWPKGAPKKTYVHRDHGGEGTH A0A143BJ28 RC-Hc Gemmatimonas phototrophica AP64 0.020022566 1 LEVO MSDVKFVPADNYNGSPIIPTGNPMIDGVGPASWAEDRRDEPDLTYHGSHKIVPMRLDPTFSIAKGDPDPRGLPVIAADKQ VAGTVVELWVNRSEPQVSYYEVQLASGERRVLLPTGYVQWPNFGLWGNDKLLVKSITAAQFANVPATKRDDQITLLEEDK ICAYYAGGHMYAFAERSQPII Photosynthetic reaction center L subunit Gemmatimonas phototrophica 0.030581662 1 LEVO MAMLSFEKKYRVRGGTLIGGDLFDFWFGPFYVGFFGVTTIFFVTLGTLLCVWGAAMGPTWNLWQINIAPPDLKYGLGLAP LREGGLWQIITLCALGAFGSWALRQAEIARKLGMGMHIPWAYGGAILAYTTLVVIRPFLLGAWGHGFPYGIFSHLDWVSN VGYQYLHFHYNPAHMIAVTFFFTNCLALAMHGSLILSVTNPPKGTPTGTSEQENVFFRDLLGYSIGAIGIHRLGLFLAVG AAVWSAICIVISGPFWTQGWPEWWNWWLNLPIWK A0A143BHR2 RC-M Gemmatimonas phototrophica AP64 0.041182082 1 LEVO (FME)LEYQNLFTRVQVRTVPEPGIPIDESTGTRYGTGTFSYLAGKFGDAQIGPIYLGWAGVLSLIFGFIAIEIIGLNMW ASVGWDPVEFIRQLPWLALEPPPPQYGLRVPPLNQGGWYLMAGFFLTVSIILWWIRIYRRARALQMGSHLPWAFASAIFL YSTFFFQPLLVGSWSEMVPFGIFPHLDWTSAFSIRYGNLYYNPFHALSIAFLYGSAVLFAMHGATILAVARMGGEREIEQ ITDRGTAAERSMLFWRWCMGFNATMESIHRWAWWFAVLTTFTGGIGILLTGTVVDNWYLWGVKHGLVAPYPAQNQLTPEQ QDLLRGRYQGTAPDSFPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ LHC domain-containing protein Gemmatimonas phototrophica 0.007723051999999999 16 LEVO (FME)HRIWLMYDPRRVMVALVGFLAVLALVIHFVLLSSQRYSWIENGTLGADQAPVGASAPAAAAEMSPLPPGR A0A143BHS7 BACTERIOCHLOROPHYLL A 0.0009115039999999999 108 BCL DODECYL-BETA-D-MALTOSIDE 0.000510615 123 LMT (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 0.0006108649999999999 40 V7N (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate 0.0006899429999999999 20 0V9 HEME C 0.0006185030000000001 4 HEC 2-acetamido-2-deoxy-alpha-D-glucopyranose 0.000221208 2 NDG (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid 0.000262213 2 V75 (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 0.001241633 6 CD4 (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate 0.0007490069999999999 1 PGW MENAQUINONE 8 0.000717116 3 MQ8 BACTERIOPHEOPHYTIN A 0.000889215 2 BPH FE (III) ION 5.5845e-05 1 FE SPIRILLOXANTHIN 0.0005969249999999999 1 CRT [(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 0.000837086 2 V7B [(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 0.0007871579999999999 1 UYH water 1.8015e-05 491 HOH singleParticle particle 6.5 8.0 20.0 Tris.Cl 0.02 DDM

The final purified complex is in 20mM Tris.Cl, 0.025 DDM, PH 8.0 buffer.

Homemade GOLD 400 GOLD HOLEY ARRAY 30.0 PLASMA CLEANING 120 OTHER

plasma chamber (Fischione 1070)

ETHANE 100 277 HOMEMADE PLUNGER

Talmon type.

The protein complex was isolated from photosynthetic membrane using detergent beta-DDM. After purification, concentrated protein sample solution was stored in LN before using.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 -0.8 -2.4 120000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 1 19865 1.2 24.8

All movies were recorded from a HexAuFoil grid with a special EPU version, which can recognise 300 nm holes on the grid.

1 1517482 2D classes obtained form RELION calculation were used to built up a initial 3D model using EMAN2 C1 2.35 FSC 0.143 CUT-OFF RELION 3.1 176531 MAXIMUM LIKELIHOOD EMAN2 MAXIMUM LIKELIHOOD EMAN2 RELION 3.1 emd_12679.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 399.784 399.784 399.784 90.0 90.0 90.0 X Y Z -0.059061177 0.21118456 0.00049854035 0.0041083195 0.99946 0.99946 0.99946 0.0238 AUTHOR ::::EMDATABANK.org::::EMD-12679:::: A reaction centre double light harvesting complex (RC-dLH) from Gem. phototrophic. 1LGH PDB experimental model 5Y5S PDB experimental model 6ET5 PDB experimental model FLEXIBLE FIT

ISOLDE incorporated in ChimeraX was used.

REAL 30.0