Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica

2026-09-23 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.year _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_nonpoly_scheme pdbx_struct_conn_angle pdbx_validate_chiral pdbx_validate_close_contact struct_asym struct_conn _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _struct_asym.entity_id STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight PDBe PDBe 2024-10-10 2025-12-03 2025-12-03 2026-09-23 Czech Academy of Sciences 19-28778X Czech Republic Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica Gardiner AT Jing Y Bina D Mujakic I Gardian Z Kaftan D Joosten M Jakobi A Castro-Hartmann P Qian P Koblizek M photosynthetic bacteria, photosynthesis, reaction cennter light harvesting complex, RC-LH1, RC-dLH, cryo-EM, Gemmatimonas groenlandica Gardiner AT Jin Y Bina D Joosten M Kaftan D Mujakic I Gardian Z Castro-Hartmann P Qian P Koblizek M Two solutions for efficient light-harvesting in phototrophic Gemmatimonadota. Msystems US 11 e0109425 e0109425 2026 41342568 doi:10.1128/msystems.01094-25 2379-5077 9h22 FULLOVERLAP EMDB EMD-51788 associated EM volume

RC-dLH complex model II from Gemmatimonas groenlandica RC-dLH complex model II from Gemmatimonas groenlandica 0 7 9 8 6 4 5 2 3 1

a monomer complex

Gemmatimonas groenlandica 0.65 reaction centre S sub unit Gemmatimonas groenlandica 0.021641564

native protein

1 LEVO MMLRQDRPRVLSRVSTVVGIGALVAVAMAARSQGGQQATPPSAPQPPVAAPSAAPAATDSTMQDSTQRADTTAKADSMLA MPDSMMMQHTAAAPAPQASAMWPVDPVTGQTIINGEPVVGRVFIMQKTDGTVKLGKWQAQYDGEPTAPEAANVGSSYTVP APEHTRRMRGIMIQSTLWSIDGKRSARERRHYRPQTTGAALGQQ A0A6M4IPJ3 Reaction center protein L chain Gemmatimonas groenlandica 0.03054274

native protein

1 LEVO MAMLSFEKKYRVRGGTLIGGDLFDFWFGPFYVGFFGVTTIFFVTLGTLLCVWGAAMGPTWNLWQISIAPPDLKYGLGLAP LREGGLWQIITLCALGAFGSWALRQAEISRKLGMGMHIPWAYGGAVLAYATLVVIRPMLLGAWGHGFPYGIFSHLDWVSN VGYQYLHFHYNPAHMIAVTFFFTNCLALAMHGSLILSVTNPKKGTPVGTSETENVFFRDLLGYSIGAIGIHRLGLFLAVG AAVWSAICIVISGPFWTKGWPEWWNWWLNLPIWR A0A6M4IPC7 Reaction center protein M chain Gemmatimonas groenlandica 0.043396741999999995

native protein

1 LEVO MLEYQNLFTRVQVRTVPEAGIEIDESTGTRYGTGTFSYLAGKFGDAQIGPIYLGWAGVLSLIFGFMAFEIIGLNMWASVG WDPVEFIRQLPWLALEPPPPQYGLRVPPLAQGGWYLMAGFFLTISILLWWVRVYRRARALNMGTHLPWAFASAIFLYSTF FFQPLLVGSWSEMVPFGIFPHLDWTSAFSIRYGNLYYNPFHALSIAFLYGSAVLFAMHGATILAVARLGGEREIEQITDR GTAAERSMLFWRWTMGFNATMESIHRWSWWFAVLTTFSGGIGILLTGTVVDNWYLWGVKHGLVAPYPAQNTLTEEQQQLL RGRYQGTAPDSFPSYVAPQPAMMLDSTAMMAPADSMKADSTKVDSAAAPSAPAAAAPPPAKPPAPSVGGKTP A0A6M4ILR2 reaction centre Ht su unit Gemmatimonas groenlandica 0.007771843

a single helix

1 LEVO MQYIDGAQIALYAFWLFFFGLIIYIRREDKREGYPLESPQGPREGWPAMPEKKTYIHRPTSGEGTH reaction centre Hc sub unit Gemmatimonas groenlandica 0.019669317999999998

native protein

1 LEVO MSDIKAVPADSYNGSALIPTGDPMIDGVGPSSWANRSDTPDMTFHNTAKIVPMRLDPTYSIAKGDPDPRGLPVVAADKQV AGTVIELWVNRAEPQVTYYEVQLTGSERRVMLPAGFVQWPNFGLWGNDKLLVKAITAAQFANVPALKRDDQITLLEEDMV CAYYAGGHLYAMAERSEPII Photosynthetic reaction center cytochrome c subunit Gemmatimonas groenlandica 0.040302758

native protein

1 LEVO MSILRRSIGLVAPLALLSLGACGDTATDSVQVGYRGTGMEQNYDHGDLKKQFAQVKIPTPLPPAGESPPGPLPWQNVQVL NDISVGEFNRTMVAMSTWVAGTGNCAYCHNIANLAADTLPNGKPLYTKLVARRMLQMTRQINGQYSQHVKNTGVTCYTCH MGKPLPNGLWFYSSQTDYLRHYLDRDGARVVTRDVAPSNANRSSVKQTEWTYALMISQSRSLGVNCTYCHNTRQFASWKE APPARVTAYHGILMLRDVNQNYLSPLQPVYPSVRLGTQGDAPKAQCVTCHNGNYKPLYGAQMVKDYPALWGRADWNGVPF QGLSPKADTTSAGAAPAAPAAAAPVPAVKRSSARTVPAPTVIGGAVGSPNTPK A0A6M4ITL7 Light-harvesting protein Gemmatimonas groenlandica 0.006413583

helix

24 LEVO MHRIWQGMDPQIIMSGLGFFLAGLALIIHMWAYSITGWPKYKKAQYNAQTPPTAVR A0A6M4IQ17 Light-harvesting protein Gemmatimonas groenlandica 0.0051839849999999995

helix

40 LEVO MMEKGGMTEDEARRFHGYFVTGTLGYIIVAAVAHFLAWQWRPWF A0A6M4IQ93 Light-harvesting protein Gemmatimonas groenlandica 0.007697122999999999

helix

16 LEVO MHRIWLMFDPRRVMVAMVGFLAVLALVIHFILLSSQRYSWIENGTLSAAQAPVGASAPAAAAEMSPLPPGR A0A6M4INU2 BACTERIOCHLOROPHYLL A 0.0009115039999999999 84 BCL BACTERIOPHEOPHYTIN A 0.000889215 2 BPH DODECYL-BETA-D-MALTOSIDE 0.000510615 48 LMT MENAQUINONE 8 0.000717116 3 MQ8 FE (III) ION 5.5845e-05 1 FE (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 2 CD4 SPIRILLOXANTHIN 0.0005969249999999999 1 CRT 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE 0.0005226319999999999 17 PEX HEME C 0.0006205189999999999 4 HEC (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 water 1.8015e-05 38 HOH singleParticle particle 8.0

10mM Tris-HCl buffer, 20 mM NaCl, pH 8.0

Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 60 AIR ETHANE 100 277 FEI VITROBOT MARK III

blot time, 3 sec blot force, 3.

in buffer solution with detergent beta-DDM. ~4 mg/ml

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.8 2.4 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 88.0 92.0 TFS Selectris X 10 FEI FALCON IV (4k x 4k) 1 23012 5.13 60.0

images were collected in AFIS model

with energy filter slit of 10 eV

935540

cryosparc blob selection first, then model reference selection for final 3d reconstruction

CTFFIND 4.0

CTF collection was performed within cryosparc

PHASE FLIPPING AND AMPLITUDE CORRECTION cryosparc ab-init

a subset of randomly picked-up particles were used for initial model generation.

1 C1 BACK PROJECTION 2.3 FSC 0.143 CUT-OFF cryoSPARC 4.2.1

performed in cryosparc

116858 ANGULAR RECONSTITUTION cryoSPARC 4.2.1

cryosparc Ab-init

ANGULAR RECONSTITUTION cryoSPARC 4.2.1 2 120000.0 cryoSPARC 4.2.1

This complex has two confirmations. 2 classs 3D classification was used for the final separation of the two confirmation.

emd_51788.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 439.19998 439.19998 439.19998 90.0 90.0 90.0 X Y Z -0.22641595 0.54656935 0.0005516693 0.012068127 0.732 0.732 0.732 0.0687 AUTHOR ::::EMDATABANK.org::::EMD-51788:::: AlphaFold in silico model RIGID BODY FIT

Initial model was established with coot. The model was fitted into map using chimera. The refinement was performed y the use of Phenix.

map to model REAL 60.0 emd_51788_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 439.19998 439.19998 439.19998 90.0 90.0 90.0 X Y Z -0.36380237 0.40587184 0.00045777444 0.042502668 0.732 0.732 0.732 AUTHOR ::::EMDATABANK.org::::EMD-51788:::: emd_51788_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 439.19998 439.19998 439.19998 90.0 90.0 90.0 X Y Z -0.37536103 0.45583445 0.00046010895 0.042507205 0.732 0.732 0.732 AUTHOR ::::EMDATABANK.org::::EMD-51788::::