Reaction centre light harvesting complex 1 from Blc. viridis

2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY database_2 em_admin entity _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _entity.formula_weight _entity.pdbx_description EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_software entity pdbx_validate_close_contact struct_conn _em_software.name _em_software.version _entity.formula_weight OTHER atom_sites cell _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][2] _atom_sites.fract_transf_matrix[3][3] _cell.Z_PDB STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond database_2 database_PDB_caveat em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_scheme pdbx_struct_conn_angle pdbx_validate_chiral pdbx_validate_close_contact refine struct_conn struct_site struct_site_gen _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_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _database_PDB_caveat.text _em_admin.last_update _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_validate_close_contact.auth_comp_id_2 _refine.ls_d_res_high _refine.ls_d_res_low _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site_gen.auth_seq_id STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY 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_struct_conn_angle pdbx_validate_chiral pdbx_validate_close_contact struct_conn _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight PDBe PDBe 2017-10-25 2017-12-20 2018-04-11 2026-09-16 European Research Council Reaction centre light harvesting complex 1 from Blc. viridis Qian P Siebert CA Reaction centre light harvesting complex 1 Blc. viridis Cryo-EM RC-LH1 Photosynthesis, PHOTOSYNTHESIS Qian P Siebert CA Wang P Canniffe DP Hunter CN Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 angstrom. Nature UK 556 203 208 2018 29618818 doi:10.1038/s41586-018-0014-5 1476-4687 0006 NATUAS 6et5 FULLOVERLAP EMDB EMD-3951 associated EM volume

Reaction centre light harvesting complex 1 from Blc. viridian

Reaction centre-Light harvesting complex 1 (RC-LH1) Reaction centre-Light harvesting complex 1 (RC-LH1) 0 1 2 3 4 5 6 7

The protein was isolated from a photosynthetic bacterium Blc. viridis.

Blastochloris viridis 0.414 Photosynthetic reaction center cytochrome c subunit Blastochloris viridis 0.037179464999999995

reaction centre cytochrome subunit

1 LEVO CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEW VSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETP THVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSL GTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGAS RLKDYPELGPIKA P07173 Reaction center protein L chain Blastochloris viridis 0.030600298999999997

reaction centre L subunit

1 LEVO MALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAP LLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNN FGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASN IFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS P06009 Reaction center protein M chain Blastochloris viridis 0.035932188

Teaction centre M subunit

1 LEVO ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFD PLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGC IHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRG TAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPG APK P06010 Reaction center protein H chain Blastochloris viridis 0.028557453

Reaction centre H subunit

1 LEVO (FME)YHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTV TVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLP VVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREED KVSAYYAGGLLYATPERAESLL P06008 Light-harvesting protein B-1015 alpha chain Blastochloris viridis 0.006984262

Light harvesting complex 1 alpha subunit

17 LEVO MATEYRTASWKLWLILDPRRVLTALFVYLTVIALLIHFGLLSTDRLNWWEFQRGLPKAA P04123 Light-harvesting protein B-1015 beta chain Blastochloris viridis 0.006274327

Light harvesting complex 1 beta subunit

17 LEVO MADLKPSLTGLTEEEAKEFHGIFVTSTVLYLATAVIVHYLVWTARPWIAPIPKGWV P04124 Light-harvesting protein B-1015 gamma chain Blastochloris viridis 0.0027992919999999997

Light harvesting complex 1 gamma subunit

16 LEVO SDWNLWVPLGILGIPTIWIALTYR P04126 HEME C 0.0006205189999999999 4 HEC BACTERIOCHLOROPHYLL B 0.000909488 38 BCB BACTERIOPHEOPHYTIN B 0.0008871989999999999 2 BPB Ubiquinone-9 0.000795226 2 UQ9 FE (III) ION 5.5845e-05 1 FE SULFATE ION 9.606299999999999e-05 7 SO4 LAURYL DIMETHYLAMINE-N-OXIDE 0.00022940199999999997 2 LDA MENAQUINONE-9 0.0007852329999999999 1 MQ9 15-cis-1,2-dihydroneurosporene 0.0005409039999999999 1 NS5 all-trans-1,2-dihydroneurosporene 0.0005409039999999999 17 NS0 singleParticle cell 4.0 7.8 20.0 HEPES

20 mMol HEPES, pH 7.8, 100 mM NaCl

Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 10.0 GLOW DISCHARGE 30 AIR 0.0002 ETHANE 99 278 LEICA EM GP

Blot for 3.5 seconds. Humidity: 99% Temperature:4C..

Protein was solubilised by the use detergent of beta-DDM. The protein particle therefore contains a detergent belt in its hydrophobic region.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-20 3 6472 0.5 2.25 1

Dose fractioned

267726

Protein was checked using negatively stained EM.

Gctf 1.06

gctf was used for CTF correction

PHASE FLIPPING AND AMPLITUDE CORRECTION EMAN2 was used for initial model creation by the use of 2d classes from relion 2d classification. C1 FOURIER SPACE 2.87 FSC 0.143 CUT-OFF RELION 2.0 267726 COMMON LINE EMAN 2 COMMON LINE RELION 2.0 4 RELION 2.0

166793 particles, 62.3% in total, were used for final 3D reconstruction

emd_3951.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 230 230 230 0 0 0 230 230 230 243.79999 243.79999 243.79999 90.0 90.0 90.0 X Y Z -0.020596072 0.080156974 0.0008213509 0.0040123253 1.06 1.06 1.06 0.0156 AUTHOR ::::EMDATABANK.org::::EMD-3951:::: Cryo-EM images of Reaction centre-light harvesting complex 1 (RC-LH1) from Blc. viridis were processed using RELION 2.0. The 3D cryo-EM map was produced after Post-processing to 2.87 Angstrom. BACKBONE TRACE REAL emd_3951_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 230 230 230 0 0 0 230 230 230 243.79999 243.79999 243.79999 90.0 90.0 90.0 X Y Z -0.018971715 0.077884465 0.00068648835 0.0039250073 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-3951:::: First half of map from last round of calculation Refine3D in RELION. emd_3951_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 230 230 230 0 0 0 230 230 230 243.79999 243.79999 243.79999 90.0 90.0 90.0 X Y Z -0.019273961 0.075988844 0.0006863464 0.003878339 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-3951:::: Second half of map from last round of calculation Refine3D in RELION.