HEADER OXIDOREDUCTASE 25-APR-22 7XMD TITLE CRYO-EM STRUCTURE OF CYTOCHROME BO3 FROM ESCHERICHIA COLI, THE TITLE 2 STRUCTURE COMPLEXED WITH AN ALLOSTERIC INHIBITOR N4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B562-O COMPLEX SUBUNIT I,CYTOCHROME O UBIQUINOL COMPND 5 OXIDASE SUBUNIT 1,CYTOCHROME O SUBUNIT 1,OXIDASE BO(3) SUBUNIT 1, COMPND 6 UBIQUINOL OXIDASE CHAIN A,UBIQUINOL OXIDASE POLYPEPTIDE I,UBIQUINOL COMPND 7 OXIDASE SUBUNIT 1; COMPND 8 EC: 7.1.1.3; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UBIQUINOL OXIDASE SUBUNIT 2; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 3; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: CYTOCHROME O UBIQUINOL OXIDASE SUBUNIT 3,CYTOCHROME O COMPND 18 SUBUNIT 3,OXIDASE BO(3) SUBUNIT 3,UBIQUINOL OXIDASE CHAIN C,UBIQUINOL COMPND 19 OXIDASE POLYPEPTIDE III,UBIQUINOL OXIDASE SUBUNIT 3; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 4; COMPND 23 CHAIN: D; COMPND 24 SYNONYM: CYTOCHROME O UBIQUINOL OXIDASE SUBUNIT 4,CYTOCHROME O COMPND 25 SUBUNIT 4,OXIDASE BO(3) SUBUNIT 4,UBIQUINOL OXIDASE CHAIN D,UBIQUINOL COMPND 26 OXIDASE POLYPEPTIDE IV,UBIQUINOL OXIDASE SUBUNIT 4; COMPND 27 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 GENE: CYOA, ACU57_11830, AM464_19145, APX88_10780, AWP93_14560, SOURCE 10 BANRA_03634, BEA19_24285, BJI68_14080, BJJ90_20095, BK383_14750, SOURCE 11 BMC79_002872, BO068_001687, BOB65_000403, BON66_08870, BON73_06180, SOURCE 12 BON74_21890, BON77_14335, BON80_10695, BON86_25900, BON87_05825, SOURCE 13 BON89_00395, BON92_15695, BON93_19065, BON98_18690, BSR05_07160, SOURCE 14 BXT93_14110, BZL69_16590, C2121_000756, C5N07_12950, CA593_00980, SOURCE 15 CDC27_01080, CDL36_18475, CDL37_08970, CQP61_20675, CR539_06390, SOURCE 16 CT143_00345, CXJ73_004380, D0X26_07630, D3822_17775, D3Y67_14555, SOURCE 17 D9E34_22950, D9J03_07430, DAH17_06675, DAH34_12595, DAH36_12985, SOURCE 18 DD762_23785, DKP82_19825, DN627_04300, DNQ45_18500, DNX30_04955, SOURCE 19 DTM16_23740, DTM45_11185, DU321_07410, DXT70_02705, E2119_01520, SOURCE 20 E2122_05970, E2131_02675, E2135_01205, E4K51_12275, E5P26_04320, SOURCE 21 E5P27_05630, E5P28_11110, E5P29_09785, E5P31_06375, E5P32_04100, SOURCE 22 E5P34_04850, E5P35_04720, E5P36_01955, E5P40_03855, E5S36_14935, SOURCE 23 E5S46_14035, E5S51_13330, E5S58_14090, E5S61_17450, EC3234A_4C01010, SOURCE 24 EI021_16450, EIA08_09775, EIZ93_01035, EL79_3413, EL80_3367, SOURCE 25 ELT17_06040, ELT20_08135, ELT41_07160, ELT49_07745, ELT51_19775, SOURCE 26 ELU85_09175, ELV10_08020, ELV16_21785, ELX48_13290, ELX76_14920, SOURCE 27 ELX85_08605, EVY14_00280, EXPECSC038_03272, EYV17_02895, SOURCE 28 EYV18_09930, EYY21_23390, F2N31_13445, F3N40_15010, F9S83_01735, SOURCE 29 F9V24_00335, FA849_16035, FA868_02450, FE587_05330, FEJ01_04230, SOURCE 30 FEL34_02865, FGG80_03370, FGY90_08715, FHD44_10295, FJQ51_12155, SOURCE 31 FQF29_11475, FTV93_12140, FV293_05915, FWK02_10070, G3813_001713, SOURCE 32 G4A38_05615, G5603_08425, GIB53_01940, GKF86_04705, GKF89_04260, SOURCE 33 GLW94_08520, GQM13_16545, GQW68_14795, GQW80_03945, GRW05_22945, SOURCE 34 GRW57_14390, GRW81_04315, GSY44_02240, GTP88_03650, GUB08_11340, SOURCE 35 H0O53_01600, HIN64_001359, HJQ60_002319, HJS37_002124, HJU54_001612, SOURCE 36 HL601_03105, HLZ50_08430, HMJ82_07910, HMU48_15410, HMV41_13070, SOURCE 37 HMV95_11775, HNC36_06575, HNC59_10400, HNC66_06810, HNC99_09295, SOURCE 38 HND12_08495, HVW04_08795, HVX16_19275, HX136_19320, IA00_004007, SOURCE 39 IH772_12955, IT029_003268, J0541_001708, JNP96_06590, SOURCE 40 NCTC10082_01037, NCTC10764_05312, NCTC10974_04302, NCTC11112_03815, SOURCE 41 NCTC12950_04133, NCTC13148_06650, NCTC8008_03342, NCTC8450_01418, SOURCE 42 NCTC8500_04220, NCTC8621_03944, NCTC9037_03917, NCTC9044_03552, SOURCE 43 NCTC9117_04753, PGD_02879, SAMEA3472067_03229, SAMEA3751407_02102, SOURCE 44 WP2S18E08_34950; SOURCE 45 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 46 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 47 MOL_ID: 3; SOURCE 48 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 49 ORGANISM_TAXID: 562; SOURCE 50 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 51 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 52 MOL_ID: 4; SOURCE 53 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 54 ORGANISM_TAXID: 562; SOURCE 55 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 56 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RESPIRATORY ENZYME, MEMBRANE PROTEIN, HEME PROTEIN, ALLOSTERIC KEYWDS 2 INHIBITOR, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR Y.NISHIDA,H.SHIGEMATSU,T.IWAMOTO,S.TAKASHIMA,Y.SHINTANI REVDAT 1 21-DEC-22 7XMD 0 JRNL AUTH Y.NISHIDA,S.YANAGISAWA,R.MORITA,H.SHIGEMATSU, JRNL AUTH 2 K.SHINZAWA-ITOH,H.YUKI,S.OGASAWARA,K.SHIMUTA,T.IWAMOTO, JRNL AUTH 3 C.NAKABAYASHI,W.MATSUMURA,H.KATO,C.GOPALASINGAM,T.NAGAO, JRNL AUTH 4 T.QAQORH,Y.TAKAHASHI,S.YAMAZAKI,K.KAMIYA,R.HARADA,N.MIZUNO, JRNL AUTH 5 H.TAKAHASHI,Y.AKEDA,M.OHNISHI,Y.ISHII,T.KUMASAKA,T.MURATA, JRNL AUTH 6 K.MURAMOTO,T.TOSHA,Y.SHIRO,T.HONMA,Y.SHIGETA,M.KUBO, JRNL AUTH 7 S.TAKASHIMA,Y.SHINTANI JRNL TITL IDENTIFYING ANTIBIOTICS BASED ON STRUCTURAL DIFFERENCES IN JRNL TITL 2 THE CONSERVED ALLOSTERY FROM MITOCHONDRIAL HEME-COPPER JRNL TITL 3 OXIDASES. JRNL REF NAT COMMUN V. 13 7591 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36481732 JRNL DOI 10.1038/S41467-022-34771-Y REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, COOT, PHENIX, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.990 REMARK 3 NUMBER OF PARTICLES : 67692 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7XMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029143. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CYTOCHROME BO3 UBIQUINOL REMARK 245 OXIDASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 13.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7173 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PHE A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 661 REMARK 465 GLY A 662 REMARK 465 ASN A 663 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 LEU B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 5 REMARK 465 TYR B 6 REMARK 465 ASN B 7 REMARK 465 LYS B 8 REMARK 465 SER B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 TRP B 12 REMARK 465 LEU B 13 REMARK 465 SER B 14 REMARK 465 LEU B 15 REMARK 465 PHE B 16 REMARK 465 ALA B 17 REMARK 465 GLY B 18 REMARK 465 THR B 19 REMARK 465 VAL B 20 REMARK 465 LEU B 21 REMARK 465 LEU B 22 REMARK 465 HIS B 284 REMARK 465 GLY B 285 REMARK 465 LYS B 286 REMARK 465 SER B 287 REMARK 465 MET B 288 REMARK 465 ASP B 289 REMARK 465 MET B 290 REMARK 465 THR B 291 REMARK 465 GLN B 292 REMARK 465 PRO B 293 REMARK 465 GLU B 294 REMARK 465 GLY B 295 REMARK 465 GLU B 296 REMARK 465 HIS B 297 REMARK 465 SER B 298 REMARK 465 ALA B 299 REMARK 465 HIS B 300 REMARK 465 GLU B 301 REMARK 465 GLY B 302 REMARK 465 MET B 303 REMARK 465 GLU B 304 REMARK 465 GLY B 305 REMARK 465 MET B 306 REMARK 465 ASP B 307 REMARK 465 MET B 308 REMARK 465 SER B 309 REMARK 465 HIS B 310 REMARK 465 ALA B 311 REMARK 465 GLU B 312 REMARK 465 SER B 313 REMARK 465 ALA B 314 REMARK 465 HIS B 315 REMARK 465 HIS B 316 REMARK 465 HIS B 317 REMARK 465 HIS B 318 REMARK 465 HIS B 319 REMARK 465 HIS B 320 REMARK 465 HIS B 321 REMARK 465 HIS B 322 REMARK 465 HIS B 323 REMARK 465 ARG B 324 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 THR C 3 REMARK 465 ASP C 4 REMARK 465 THR C 5 REMARK 465 LEU C 6 REMARK 465 THR C 7 REMARK 465 HIS C 8 REMARK 465 ALA C 9 REMARK 465 THR C 10 REMARK 465 ALA C 11 REMARK 465 HIS C 12 REMARK 465 ALA C 13 REMARK 465 HIS C 14 REMARK 465 GLU C 15 REMARK 465 HIS C 16 REMARK 465 GLY C 17 REMARK 465 HIS C 18 REMARK 465 HIS C 19 REMARK 465 ASP C 20 REMARK 465 ALA C 21 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 HIS D 3 REMARK 465 SER D 4 REMARK 465 THR D 5 REMARK 465 ASP D 6 REMARK 465 HIS D 7 REMARK 465 SER D 8 REMARK 465 GLY D 9 REMARK 465 ALA D 10 REMARK 465 SER D 11 REMARK 465 HIS D 12 REMARK 465 GLY D 13 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 HIS A 284 CE2 TYR A 288 1.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 6 -133.01 62.63 REMARK 500 ALA A 9 -165.62 56.41 REMARK 500 PHE A 12 -73.56 -87.89 REMARK 500 HIS A 13 26.89 -148.33 REMARK 500 LEU A 49 -5.41 70.53 REMARK 500 VAL A 114 -62.53 -121.00 REMARK 500 ALA A 172 73.62 51.35 REMARK 500 ASP A 522 36.84 -97.40 REMARK 500 ASP A 532 65.37 -159.56 REMARK 500 ASN A 551 -7.13 69.10 REMARK 500 GLU A 572 52.62 -92.87 REMARK 500 ALA A 657 -166.97 -117.04 REMARK 500 ASP B 31 63.86 -158.41 REMARK 500 ARG B 70 -139.81 40.76 REMARK 500 ALA B 71 -27.93 -152.32 REMARK 500 ASN B 81 17.00 49.86 REMARK 500 SER B 83 -62.52 -95.09 REMARK 500 LEU B 120 -11.07 72.66 REMARK 500 MET B 134 -160.75 -123.11 REMARK 500 ILE B 183 130.15 15.01 REMARK 500 GLN B 240 49.49 -81.67 REMARK 500 TYR B 260 75.58 -102.01 REMARK 500 MET C 128 53.87 -91.43 REMARK 500 ALA C 203 34.39 -99.81 REMARK 500 PRO D 43 43.14 -76.61 REMARK 500 ALA D 44 -38.09 -132.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 702 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 NE2 REMARK 620 2 HEM A 702 NA 97.1 REMARK 620 3 HEM A 702 NB 79.2 87.7 REMARK 620 4 HEM A 702 NC 82.1 174.1 86.4 REMARK 620 5 HEM A 702 ND 102.0 94.1 177.7 91.8 REMARK 620 6 HIS A 421 NE2 167.6 91.7 92.5 88.2 86.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 703 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 284 ND1 REMARK 620 2 HIS A 333 NE2 104.4 REMARK 620 3 HIS A 334 NE2 107.7 75.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEO A 701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 419 NE2 REMARK 620 2 HEO A 701 NA 84.7 REMARK 620 3 HEO A 701 NB 93.5 87.5 REMARK 620 4 HEO A 701 NC 100.9 171.7 86.0 REMARK 620 5 HEO A 701 ND 94.5 94.6 171.9 91.2 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33294 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CYTOCHROME BO3 FROM ESCHERICHIA COLI, THE REMARK 900 STRUCTURE COMPLEXED WITH AN ALLOSTERIC INHIBITOR N4 DBREF 7XMD A 1 663 UNP P0ABI8 CYOB_ECOLI 1 663 DBREF1 7XMD B 1 315 UNP A0A024L5V9_ECOLX DBREF2 7XMD B A0A024L5V9 1 315 DBREF 7XMD C 1 204 UNP P0ABJ3 CYOC_ECOLI 1 204 DBREF 7XMD D 1 109 UNP P0ABJ6 CYOD_ECOLI 1 109 SEQADV 7XMD HIS B 316 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 317 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 318 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 319 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 320 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 321 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 322 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD HIS B 323 UNP A0A024L5V EXPRESSION TAG SEQADV 7XMD ARG B 324 UNP A0A024L5V EXPRESSION TAG SEQRES 1 A 663 MET PHE GLY LYS LEU SER LEU ASP ALA VAL PRO PHE HIS SEQRES 2 A 663 GLU PRO ILE VAL MET VAL THR ILE ALA GLY ILE ILE LEU SEQRES 3 A 663 GLY GLY LEU ALA LEU VAL GLY LEU ILE THR TYR PHE GLY SEQRES 4 A 663 LYS TRP THR TYR LEU TRP LYS GLU TRP LEU THR SER VAL SEQRES 5 A 663 ASP HIS LYS ARG LEU GLY ILE MET TYR ILE ILE VAL ALA SEQRES 6 A 663 ILE VAL MET LEU LEU ARG GLY PHE ALA ASP ALA ILE MET SEQRES 7 A 663 MET ARG SER GLN GLN ALA LEU ALA SER ALA GLY GLU ALA SEQRES 8 A 663 GLY PHE LEU PRO PRO HIS HIS TYR ASP GLN ILE PHE THR SEQRES 9 A 663 ALA HIS GLY VAL ILE MET ILE PHE PHE VAL ALA MET PRO SEQRES 10 A 663 PHE VAL ILE GLY LEU MET ASN LEU VAL VAL PRO LEU GLN SEQRES 11 A 663 ILE GLY ALA ARG ASP VAL ALA PHE PRO PHE LEU ASN ASN SEQRES 12 A 663 LEU SER PHE TRP PHE THR VAL VAL GLY VAL ILE LEU VAL SEQRES 13 A 663 ASN VAL SER LEU GLY VAL GLY GLU PHE ALA GLN THR GLY SEQRES 14 A 663 TRP LEU ALA TYR PRO PRO LEU SER GLY ILE GLU TYR SER SEQRES 15 A 663 PRO GLY VAL GLY VAL ASP TYR TRP ILE TRP SER LEU GLN SEQRES 16 A 663 LEU SER GLY ILE GLY THR THR LEU THR GLY ILE ASN PHE SEQRES 17 A 663 PHE VAL THR ILE LEU LYS MET ARG ALA PRO GLY MET THR SEQRES 18 A 663 MET PHE LYS MET PRO VAL PHE THR TRP ALA SER LEU CYS SEQRES 19 A 663 ALA ASN VAL LEU ILE ILE ALA SER PHE PRO ILE LEU THR SEQRES 20 A 663 VAL THR VAL ALA LEU LEU THR LEU ASP ARG TYR LEU GLY SEQRES 21 A 663 THR HIS PHE PHE THR ASN ASP MET GLY GLY ASN MET MET SEQRES 22 A 663 MET TYR ILE ASN LEU ILE TRP ALA TRP GLY HIS PRO GLU SEQRES 23 A 663 VAL TYR ILE LEU ILE LEU PRO VAL PHE GLY VAL PHE SER SEQRES 24 A 663 GLU ILE ALA ALA THR PHE SER ARG LYS ARG LEU PHE GLY SEQRES 25 A 663 TYR THR SER LEU VAL TRP ALA THR VAL CYS ILE THR VAL SEQRES 26 A 663 LEU SER PHE ILE VAL TRP LEU HIS HIS PHE PHE THR MET SEQRES 27 A 663 GLY ALA GLY ALA ASN VAL ASN ALA PHE PHE GLY ILE THR SEQRES 28 A 663 THR MET ILE ILE ALA ILE PRO THR GLY VAL LYS ILE PHE SEQRES 29 A 663 ASN TRP LEU PHE THR MET TYR GLN GLY ARG ILE VAL PHE SEQRES 30 A 663 HIS SER ALA MET LEU TRP THR ILE GLY PHE ILE VAL THR SEQRES 31 A 663 PHE SER VAL GLY GLY MET THR GLY VAL LEU LEU ALA VAL SEQRES 32 A 663 PRO GLY ALA ASP PHE VAL LEU HIS ASN SER LEU PHE LEU SEQRES 33 A 663 ILE ALA HIS PHE HIS ASN VAL ILE ILE GLY GLY VAL VAL SEQRES 34 A 663 PHE GLY CYS PHE ALA GLY MET THR TYR TRP TRP PRO LYS SEQRES 35 A 663 ALA PHE GLY PHE LYS LEU ASN GLU THR TRP GLY LYS ARG SEQRES 36 A 663 ALA PHE TRP PHE TRP ILE ILE GLY PHE PHE VAL ALA PHE SEQRES 37 A 663 MET PRO LEU TYR ALA LEU GLY PHE MET GLY MET THR ARG SEQRES 38 A 663 ARG LEU SER GLN GLN ILE ASP PRO GLN PHE HIS THR MET SEQRES 39 A 663 LEU MET ILE ALA ALA SER GLY ALA VAL LEU ILE ALA LEU SEQRES 40 A 663 GLY ILE LEU CYS LEU VAL ILE GLN MET TYR VAL SER ILE SEQRES 41 A 663 ARG ASP ARG ASP GLN ASN ARG ASP LEU THR GLY ASP PRO SEQRES 42 A 663 TRP GLY GLY ARG THR LEU GLU TRP ALA THR SER SER PRO SEQRES 43 A 663 PRO PRO PHE TYR ASN PHE ALA VAL VAL PRO HIS VAL HIS SEQRES 44 A 663 GLU ARG ASP ALA PHE TRP GLU MET LYS GLU LYS GLY GLU SEQRES 45 A 663 ALA TYR LYS LYS PRO ASP HIS TYR GLU GLU ILE HIS MET SEQRES 46 A 663 PRO LYS ASN SER GLY ALA GLY ILE VAL ILE ALA ALA PHE SEQRES 47 A 663 SER THR ILE PHE GLY PHE ALA MET ILE TRP HIS ILE TRP SEQRES 48 A 663 TRP LEU ALA ILE VAL GLY PHE ALA GLY MET ILE ILE THR SEQRES 49 A 663 TRP ILE VAL LYS SER PHE ASP GLU ASP VAL ASP TYR TYR SEQRES 50 A 663 VAL PRO VAL ALA GLU ILE GLU LYS LEU GLU ASN GLN HIS SEQRES 51 A 663 PHE ASP GLU ILE THR LYS ALA GLY LEU LYS ASN GLY ASN SEQRES 1 B 324 MET ARG LEU ARG LYS TYR ASN LYS SER LEU GLY TRP LEU SEQRES 2 B 324 SER LEU PHE ALA GLY THR VAL LEU LEU SER GLY CYS ASN SEQRES 3 B 324 SER ALA LEU LEU ASP PRO LYS GLY GLN ILE GLY LEU GLU SEQRES 4 B 324 GLN ARG SER LEU ILE LEU THR ALA PHE GLY LEU MET LEU SEQRES 5 B 324 ILE VAL VAL ILE PRO ALA ILE LEU MET ALA VAL GLY PHE SEQRES 6 B 324 ALA TRP LYS TYR ARG ALA SER ASN LYS ASP ALA LYS TYR SEQRES 7 B 324 SER PRO ASN TRP SER HIS SER ASN LYS VAL GLU ALA VAL SEQRES 8 B 324 VAL TRP THR VAL PRO ILE LEU ILE ILE ILE PHE LEU ALA SEQRES 9 B 324 VAL LEU THR TRP LYS THR THR HIS ALA LEU GLU PRO SER SEQRES 10 B 324 LYS PRO LEU ALA HIS ASP GLU LYS PRO ILE THR ILE GLU SEQRES 11 B 324 VAL VAL SER MET ASP TRP LYS TRP PHE PHE ILE TYR PRO SEQRES 12 B 324 GLU GLN GLY ILE ALA THR VAL ASN GLU ILE ALA PHE PRO SEQRES 13 B 324 ALA ASN THR PRO VAL TYR PHE LYS VAL THR SER ASN SER SEQRES 14 B 324 VAL MET ASN SER PHE PHE ILE PRO ARG LEU GLY SER GLN SEQRES 15 B 324 ILE TYR ALA MET ALA GLY MET GLN THR ARG LEU HIS LEU SEQRES 16 B 324 ILE ALA ASN GLU PRO GLY THR TYR ASP GLY ILE SER ALA SEQRES 17 B 324 SER TYR SER GLY PRO GLY PHE SER GLY MET LYS PHE LYS SEQRES 18 B 324 ALA ILE ALA THR PRO ASP ARG ALA ALA PHE ASP GLN TRP SEQRES 19 B 324 VAL ALA LYS ALA LYS GLN SER PRO ASN THR MET SER ASP SEQRES 20 B 324 MET ALA ALA PHE GLU LYS LEU ALA ALA PRO SER GLU TYR SEQRES 21 B 324 ASN GLN VAL GLU TYR PHE SER ASN VAL LYS PRO ASP LEU SEQRES 22 B 324 PHE ALA ASP VAL ILE ASN LYS PHE MET ALA HIS GLY LYS SEQRES 23 B 324 SER MET ASP MET THR GLN PRO GLU GLY GLU HIS SER ALA SEQRES 24 B 324 HIS GLU GLY MET GLU GLY MET ASP MET SER HIS ALA GLU SEQRES 25 B 324 SER ALA HIS HIS HIS HIS HIS HIS HIS HIS HIS ARG SEQRES 1 C 204 MET ALA THR ASP THR LEU THR HIS ALA THR ALA HIS ALA SEQRES 2 C 204 HIS GLU HIS GLY HIS HIS ASP ALA GLY GLY THR LYS ILE SEQRES 3 C 204 PHE GLY PHE TRP ILE TYR LEU MET SER ASP CYS ILE LEU SEQRES 4 C 204 PHE SER ILE LEU PHE ALA THR TYR ALA VAL LEU VAL ASN SEQRES 5 C 204 GLY THR ALA GLY GLY PRO THR GLY LYS ASP ILE PHE GLU SEQRES 6 C 204 LEU PRO PHE VAL LEU VAL GLU THR PHE LEU LEU LEU PHE SEQRES 7 C 204 SER SER ILE THR TYR GLY MET ALA ALA ILE ALA MET TYR SEQRES 8 C 204 LYS ASN ASN LYS SER GLN VAL ILE SER TRP LEU ALA LEU SEQRES 9 C 204 THR TRP LEU PHE GLY ALA GLY PHE ILE GLY MET GLU ILE SEQRES 10 C 204 TYR GLU PHE HIS HIS LEU ILE VAL ASN GLY MET GLY PRO SEQRES 11 C 204 ASP ARG SER GLY PHE LEU SER ALA PHE PHE ALA LEU VAL SEQRES 12 C 204 GLY THR HIS GLY LEU HIS VAL THR SER GLY LEU ILE TRP SEQRES 13 C 204 MET ALA VAL LEU MET VAL GLN ILE ALA ARG ARG GLY LEU SEQRES 14 C 204 THR SER THR ASN ARG THR ARG ILE MET CYS LEU SER LEU SEQRES 15 C 204 PHE TRP HIS PHE LEU ASP VAL VAL TRP ILE CYS VAL PHE SEQRES 16 C 204 THR VAL VAL TYR LEU MET GLY ALA MET SEQRES 1 D 109 MET SER HIS SER THR ASP HIS SER GLY ALA SER HIS GLY SEQRES 2 D 109 SER VAL LYS THR TYR MET THR GLY PHE ILE LEU SER ILE SEQRES 3 D 109 ILE LEU THR VAL ILE PRO PHE TRP MET VAL MET THR GLY SEQRES 4 D 109 ALA ALA SER PRO ALA VAL ILE LEU GLY THR ILE LEU ALA SEQRES 5 D 109 MET ALA VAL VAL GLN VAL LEU VAL HIS LEU VAL CYS PHE SEQRES 6 D 109 LEU HIS MET ASN THR LYS SER ASP GLU GLY TRP ASN MET SEQRES 7 D 109 THR ALA PHE VAL PHE THR VAL LEU ILE ILE ALA ILE LEU SEQRES 8 D 109 VAL VAL GLY SER ILE TRP ILE MET TRP ASN LEU ASN TYR SEQRES 9 D 109 ASN MET MET MET HIS HET HEO A 701 59 HET HEM A 702 43 HET CU A 703 1 HET PEE A 704 51 HET JYR A 705 17 HET UNX B 401 1 HET PEE C 301 51 HETNAM HEO HEME O HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CU COPPER (II) ION HETNAM PEE 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE HETNAM JYR METHYL 3-OXIDANYL-5-[OXIDANYL(OXIDANYLIDENE)-$L^{4}- HETNAM 2 JYR AZANYL]-1-BENZOTHIOPHENE-2-CARBOXYLATE HETNAM UNX UNKNOWN ATOM OR ION HETSYN HEM HEME HETSYN PEE DOPE FORMUL 5 HEO C49 H58 FE N4 O5 2+ FORMUL 6 HEM C34 H32 FE N4 O4 FORMUL 7 CU CU 2+ FORMUL 8 PEE 2(C41 H78 N O8 P) FORMUL 9 JYR C10 H7 N O5 S FORMUL 10 UNX X HELIX 1 AA1 MET A 18 PHE A 38 1 21 HELIX 2 AA2 TRP A 41 GLU A 47 1 7 HELIX 3 AA3 ASP A 53 SER A 87 1 35 HELIX 4 AA4 PRO A 95 VAL A 114 1 20 HELIX 5 AA5 VAL A 114 ILE A 131 1 18 HELIX 6 AA6 PHE A 138 LEU A 160 1 23 HELIX 7 AA7 TYR A 173 GLY A 178 1 6 HELIX 8 AA8 VAL A 185 MET A 215 1 31 HELIX 9 AA9 PRO A 226 LEU A 259 1 34 HELIX 10 AB1 MET A 272 HIS A 284 1 13 HELIX 11 AB2 HIS A 284 SER A 306 1 23 HELIX 12 AB3 GLY A 312 SER A 327 1 16 HELIX 13 AB4 PHE A 328 ILE A 329 5 2 HELIX 14 AB5 VAL A 330 GLY A 339 5 10 HELIX 15 AB6 GLY A 341 ILE A 355 1 15 HELIX 16 AB7 ILE A 355 MET A 370 1 16 HELIX 17 AB8 HIS A 378 VAL A 403 1 26 HELIX 18 AB9 VAL A 403 HIS A 411 1 9 HELIX 19 AC1 SER A 413 GLY A 426 1 14 HELIX 20 AC2 GLY A 427 TRP A 440 1 14 HELIX 21 AC3 TRP A 440 GLY A 445 1 6 HELIX 22 AC4 ASN A 449 GLY A 478 1 30 HELIX 23 AC5 ASP A 488 GLN A 490 5 3 HELIX 24 AC6 PHE A 491 ASP A 522 1 32 HELIX 25 AC7 THR A 538 THR A 543 5 6 HELIX 26 AC8 ASP A 562 GLY A 571 1 10 HELIX 27 AC9 GLY A 590 TRP A 608 1 19 HELIX 28 AD1 ILE A 610 ASP A 631 1 22 HELIX 29 AD2 PRO A 639 LYS A 656 1 18 HELIX 30 AD3 GLY B 34 ARG B 70 1 37 HELIX 31 AD4 SER B 85 LEU B 114 1 30 HELIX 32 AD5 GLY B 212 MET B 218 5 7 HELIX 33 AD6 ASP B 227 GLN B 240 1 14 HELIX 34 AD7 ASP B 247 ALA B 255 1 9 HELIX 35 AD8 ASP B 272 ALA B 283 1 12 HELIX 36 AD9 GLY C 23 VAL C 51 1 29 HELIX 37 AE1 GLU C 65 LYS C 92 1 28 HELIX 38 AE2 ASN C 94 ASN C 126 1 33 HELIX 39 AE3 SER C 133 GLY C 168 1 36 HELIX 40 AE4 THR C 170 VAL C 198 1 29 HELIX 41 AE5 LEU C 200 MET C 204 5 5 HELIX 42 AE6 VAL D 15 GLY D 39 1 25 HELIX 43 AE7 ALA D 44 CYS D 64 1 21 HELIX 44 AE8 LYS D 71 GLY D 75 5 5 HELIX 45 AE9 ASN D 77 MET D 106 1 30 SHEET 1 AA1 2 ILE A 583 PRO A 586 0 SHEET 2 AA1 2 ASP A 635 VAL A 638 -1 O TYR A 636 N MET A 585 SHEET 1 AA2 6 THR B 191 ILE B 196 0 SHEET 2 AA2 6 PRO B 160 SER B 167 -1 N PHE B 163 O LEU B 193 SHEET 3 AA2 6 ILE B 127 SER B 133 1 N ILE B 127 O PRO B 160 SHEET 4 AA2 6 TRP B 138 ILE B 141 -1 O ILE B 141 N GLU B 130 SHEET 5 AA2 6 ALA B 148 VAL B 150 -1 O THR B 149 N PHE B 140 SHEET 6 AA2 6 GLU B 264 PHE B 266 -1 O PHE B 266 N ALA B 148 SHEET 1 AA3 5 GLU B 152 PRO B 156 0 SHEET 2 AA3 5 PHE B 220 THR B 225 1 O ILE B 223 N ILE B 153 SHEET 3 AA3 5 GLY B 201 SER B 207 -1 N GLY B 201 O ALA B 224 SHEET 4 AA3 5 ASN B 172 PHE B 175 -1 N PHE B 175 O ILE B 206 SHEET 5 AA3 5 TYR B 184 ALA B 185 -1 O ALA B 185 N ASN B 172 LINK NE2 HIS A 106 FE HEM A 702 1555 1555 1.99 LINK ND1 HIS A 284 CU CU A 703 1555 1555 2.00 LINK NE2 HIS A 333 CU CU A 703 1555 1555 2.00 LINK NE2 HIS A 334 CU CU A 703 1555 1555 2.00 LINK NE2 HIS A 419 FE HEO A 701 1555 1555 2.05 LINK NE2 HIS A 421 FE HEM A 702 1555 1555 1.97 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000