HEADER OXIDOREDUCTASE 05-SEP-22 8GS8 TITLE CRYO-EM STRUCTURE OF THE HUMAN RESPIRATORY COMPLEX II COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: FLAVOPROTEIN SUBUNIT OF COMPLEX II,FP; COMPND 6 EC: 1.3.5.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, COMPND 10 MITOCHONDRIAL; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, COMPND 15 MITOCHONDRIAL; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: INTEGRAL MEMBRANE PROTEIN CII-3,QPS-1,QPS1,SUCCINATE COMPND 18 DEHYDROGENASE COMPLEX SUBUNIT C,SUCCINATE-UBIQUINONE OXIDOREDUCTASE COMPND 19 CYTOCHROME B LARGE SUBUNIT,CYBL; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL COMPND 23 SUBUNIT, MITOCHONDRIAL; COMPND 24 CHAIN: D; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SDHA, SDH2, SDHF; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: SDHB; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: SDHC, CYB560, SDH3; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 GENE: SDHD; SOURCE 27 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SUCCINATE DEHYDROGENASE, ELECTRON TRANSPORT CHAIN, HUMAN KEYWDS 2 MITOCHONDRIA, OXIDOREDUCTASE, OXIDATIVE PHOSPHORYLATION EXPDTA ELECTRON MICROSCOPY AUTHOR Z.DU,X.ZHOU,Y.LAI,J.XU,Y.ZHANG,S.ZHOU,F.LIU,Y.GAO,H.GONG,Z.RAO REVDAT 1 10-MAY-23 8GS8 0 JRNL AUTH Z.DU,X.ZHOU,Y.LAI,J.XU,Y.ZHANG,S.ZHOU,Z.FENG,L.YU,Y.TANG, JRNL AUTH 2 W.WANG,L.YU,C.TIAN,T.RAN,H.CHEN,L.W.GUDDAT,F.LIU,Y.GAO, JRNL AUTH 3 Z.RAO,H.GONG JRNL TITL STRUCTURE OF THE HUMAN RESPIRATORY COMPLEX II. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 13120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37098072 JRNL DOI 10.1073/PNAS.2216713120 REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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 : NULL 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) : 2.860 REMARK 3 NUMBER OF PARTICLES : 114967 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 8GS8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032005. 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 : THE HUMAN MITOCHONDRIAL COMPLEX REMARK 245 II, COMPOSED OF SDHA, SDHB, REMARK 245 SDHC AND SDHD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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) : 300 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 SER A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 ARG A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 SER A 12 REMARK 465 ALA A 13 REMARK 465 ARG A 14 REMARK 465 ARG A 15 REMARK 465 LEU A 16 REMARK 465 ALA A 17 REMARK 465 LEU A 18 REMARK 465 ALA A 19 REMARK 465 LYS A 20 REMARK 465 ALA A 21 REMARK 465 TRP A 22 REMARK 465 PRO A 23 REMARK 465 THR A 24 REMARK 465 VAL A 25 REMARK 465 LEU A 26 REMARK 465 GLN A 27 REMARK 465 THR A 28 REMARK 465 GLY A 29 REMARK 465 THR A 30 REMARK 465 ARG A 31 REMARK 465 GLY A 32 REMARK 465 PHE A 33 REMARK 465 HIS A 34 REMARK 465 PHE A 35 REMARK 465 THR A 36 REMARK 465 VAL A 37 REMARK 465 ASP A 38 REMARK 465 GLY A 39 REMARK 465 ASN A 40 REMARK 465 LYS A 41 REMARK 465 ARG A 42 REMARK 465 ALA A 43 REMARK 465 SER A 44 REMARK 465 ALA A 45 REMARK 465 LYS A 46 REMARK 465 VAL A 47 REMARK 465 SER A 48 REMARK 465 ASP A 49 REMARK 465 SER A 50 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 VAL B 4 REMARK 465 VAL B 5 REMARK 465 ALA B 6 REMARK 465 LEU B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 ARG B 10 REMARK 465 ARG B 11 REMARK 465 ARG B 12 REMARK 465 LEU B 13 REMARK 465 PRO B 14 REMARK 465 ALA B 15 REMARK 465 THR B 16 REMARK 465 THR B 17 REMARK 465 LEU B 18 REMARK 465 GLY B 19 REMARK 465 GLY B 20 REMARK 465 ALA B 21 REMARK 465 CYS B 22 REMARK 465 LEU B 23 REMARK 465 GLN B 24 REMARK 465 ALA B 25 REMARK 465 SER B 26 REMARK 465 ARG B 27 REMARK 465 GLY B 28 REMARK 465 ALA B 29 REMARK 465 GLN B 30 REMARK 465 THR B 31 REMARK 465 ALA B 32 REMARK 465 ALA B 33 REMARK 465 ALA B 34 REMARK 465 LYS B 274 REMARK 465 GLU B 275 REMARK 465 LYS B 276 REMARK 465 LYS B 277 REMARK 465 ALA B 278 REMARK 465 SER B 279 REMARK 465 VAL B 280 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ALA C 3 REMARK 465 LEU C 4 REMARK 465 LEU C 5 REMARK 465 LEU C 6 REMARK 465 ARG C 7 REMARK 465 HIS C 8 REMARK 465 VAL C 9 REMARK 465 GLY C 10 REMARK 465 ARG C 11 REMARK 465 HIS C 12 REMARK 465 CYS C 13 REMARK 465 LEU C 14 REMARK 465 ARG C 15 REMARK 465 ALA C 16 REMARK 465 HIS C 17 REMARK 465 PHE C 18 REMARK 465 SER C 19 REMARK 465 PRO C 20 REMARK 465 GLN C 21 REMARK 465 LEU C 22 REMARK 465 CYS C 23 REMARK 465 ILE C 24 REMARK 465 ARG C 25 REMARK 465 ASN C 26 REMARK 465 ALA C 27 REMARK 465 VAL C 28 REMARK 465 PRO C 29 REMARK 465 LEU C 30 REMARK 465 GLY C 31 REMARK 465 THR C 32 REMARK 465 THR C 33 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 VAL D 3 REMARK 465 LEU D 4 REMARK 465 TRP D 5 REMARK 465 ARG D 6 REMARK 465 LEU D 7 REMARK 465 SER D 8 REMARK 465 ALA D 9 REMARK 465 VAL D 10 REMARK 465 CYS D 11 REMARK 465 GLY D 12 REMARK 465 ALA D 13 REMARK 465 LEU D 14 REMARK 465 GLY D 15 REMARK 465 GLY D 16 REMARK 465 ARG D 17 REMARK 465 ALA D 18 REMARK 465 LEU D 19 REMARK 465 LEU D 20 REMARK 465 LEU D 21 REMARK 465 ARG D 22 REMARK 465 THR D 23 REMARK 465 PRO D 24 REMARK 465 VAL D 25 REMARK 465 VAL D 26 REMARK 465 ARG D 27 REMARK 465 PRO D 28 REMARK 465 ALA D 29 REMARK 465 HIS D 30 REMARK 465 ILE D 31 REMARK 465 SER D 32 REMARK 465 ALA D 33 REMARK 465 PHE D 34 REMARK 465 LEU D 35 REMARK 465 GLN D 36 REMARK 465 ASP D 37 REMARK 465 ARG D 38 REMARK 465 PRO D 39 REMARK 465 ILE D 40 REMARK 465 PRO D 41 REMARK 465 GLU D 42 REMARK 465 TRP D 43 REMARK 465 CYS D 44 REMARK 465 GLY D 45 REMARK 465 VAL D 46 REMARK 465 GLN D 47 REMARK 465 HIS D 48 REMARK 465 ILE D 49 REMARK 465 HIS D 50 REMARK 465 LEU D 51 REMARK 465 SER D 52 REMARK 465 PRO D 53 REMARK 465 SER D 54 REMARK 465 HIS D 55 REMARK 465 HIS D 56 REMARK 465 SER D 57 REMARK 465 GLY D 58 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 99 C8M FAD A 701 1.70 REMARK 500 O GLN A 104 O4 FAD A 701 2.17 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 52 -135.17 68.68 REMARK 500 HIS A 99 -8.52 -59.31 REMARK 500 ALA A 103 53.44 -153.24 REMARK 500 ALA A 110 44.74 -76.91 REMARK 500 ASN A 113 -63.97 -90.22 REMARK 500 ASP A 131 31.94 72.61 REMARK 500 ARG A 171 -162.06 -129.66 REMARK 500 ALA A 193 53.52 35.43 REMARK 500 THR A 308 108.09 46.98 REMARK 500 LYS A 335 -127.56 44.25 REMARK 500 CYS A 357 32.10 -95.54 REMARK 500 ASP A 362 30.03 -141.78 REMARK 500 LEU A 380 59.13 -118.47 REMARK 500 PHE A 390 -72.71 -114.70 REMARK 500 LYS A 397 -65.57 -121.24 REMARK 500 ALA A 454 -0.27 69.08 REMARK 500 ALA A 502 76.81 -101.46 REMARK 500 HIS A 548 38.35 -98.17 REMARK 500 TRP A 558 48.12 35.83 REMARK 500 LYS A 598 36.93 -91.96 REMARK 500 ALA B 36 72.30 52.32 REMARK 500 VAL B 83 -70.82 -120.65 REMARK 500 SER B 85 35.50 -84.40 REMARK 500 SER B 92 -49.64 -154.36 REMARK 500 GLU B 95 -0.20 -141.12 REMARK 500 CYS B 101 43.72 -91.06 REMARK 500 LYS B 137 112.12 -166.20 REMARK 500 ASP B 138 -51.56 68.71 REMARK 500 LEU B 139 -2.67 -145.72 REMARK 500 GLU B 154 70.05 58.53 REMARK 500 ALA B 190 -1.62 63.71 REMARK 500 ASN B 202 52.14 -118.25 REMARK 500 GLN B 235 48.22 -92.32 REMARK 500 PRO B 237 5.29 -68.28 REMARK 500 PHE B 238 -36.78 -130.15 REMARK 500 TYR B 241 45.61 -94.34 REMARK 500 HIS C 55 -73.71 -129.71 REMARK 500 LEU C 91 -60.43 -101.04 REMARK 500 LEU C 92 127.50 -37.80 REMARK 500 LYS D 60 58.77 -99.66 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 FES B 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 93 SG REMARK 620 2 FES B 301 S1 104.0 REMARK 620 3 FES B 301 S2 97.1 91.0 REMARK 620 4 CYS B 98 SG 101.5 143.7 110.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 101 SG REMARK 620 2 FES B 301 S1 115.8 REMARK 620 3 FES B 301 S2 117.8 91.1 REMARK 620 4 CYS B 113 SG 99.8 125.3 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 302 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 186 SG REMARK 620 2 SF4 B 302 S1 133.4 REMARK 620 3 SF4 B 302 S2 117.8 103.1 REMARK 620 4 SF4 B 302 S4 108.1 90.6 92.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 302 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 189 SG REMARK 620 2 SF4 B 302 S1 124.7 REMARK 620 3 SF4 B 302 S2 128.1 102.8 REMARK 620 4 SF4 B 302 S3 108.1 89.2 90.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 302 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 192 SG REMARK 620 2 SF4 B 302 S2 110.1 REMARK 620 3 SF4 B 302 S3 126.5 91.1 REMARK 620 4 SF4 B 302 S4 124.3 93.1 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B 303 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 196 SG REMARK 620 2 F3S B 303 S1 103.5 REMARK 620 3 F3S B 303 S3 98.3 104.3 REMARK 620 4 F3S B 303 S4 132.5 110.8 103.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B 303 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 243 SG REMARK 620 2 F3S B 303 S1 124.3 REMARK 620 3 F3S B 303 S2 94.6 113.9 REMARK 620 4 F3S B 303 S3 114.7 104.4 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S B 303 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 249 SG REMARK 620 2 F3S B 303 S2 113.9 REMARK 620 3 F3S B 303 S3 129.0 102.4 REMARK 620 4 F3S B 303 S4 101.5 104.0 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 302 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 253 SG REMARK 620 2 SF4 B 302 S1 116.7 REMARK 620 3 SF4 B 302 S3 116.2 88.5 REMARK 620 4 SF4 B 302 S4 133.1 90.5 101.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM D 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 127 NE2 REMARK 620 2 HEM D 201 NA 89.9 REMARK 620 3 HEM D 201 NB 98.2 88.1 REMARK 620 4 HEM D 201 NC 95.3 174.6 89.7 REMARK 620 5 HEM D 201 ND 86.4 90.9 175.3 90.9 REMARK 620 6 HIS D 102 NE2 169.7 80.7 85.9 94.2 89.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34225 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE HUMAN RESPIRATORY COMPLEX II DBREF 8GS8 A 1 664 UNP P31040 SDHA_HUMAN 1 664 DBREF 8GS8 B 1 280 UNP P21912 SDHB_HUMAN 1 280 DBREF 8GS8 C 1 169 UNP Q99643 C560_HUMAN 1 169 DBREF 8GS8 D 1 159 UNP O14521 DHSD_HUMAN 1 159 SEQRES 1 A 664 MET SER GLY VAL ARG GLY LEU SER ARG LEU LEU SER ALA SEQRES 2 A 664 ARG ARG LEU ALA LEU ALA LYS ALA TRP PRO THR VAL LEU SEQRES 3 A 664 GLN THR GLY THR ARG GLY PHE HIS PHE THR VAL ASP GLY SEQRES 4 A 664 ASN LYS ARG ALA SER ALA LYS VAL SER ASP SER ILE SER SEQRES 5 A 664 ALA GLN TYR PRO VAL VAL ASP HIS GLU PHE ASP ALA VAL SEQRES 6 A 664 VAL VAL GLY ALA GLY GLY ALA GLY LEU ARG ALA ALA PHE SEQRES 7 A 664 GLY LEU SER GLU ALA GLY PHE ASN THR ALA CYS VAL THR SEQRES 8 A 664 LYS LEU PHE PRO THR ARG SER HIS THR VAL ALA ALA GLN SEQRES 9 A 664 GLY GLY ILE ASN ALA ALA LEU GLY ASN MET GLU GLU ASP SEQRES 10 A 664 ASN TRP ARG TRP HIS PHE TYR ASP THR VAL LYS GLY SER SEQRES 11 A 664 ASP TRP LEU GLY ASP GLN ASP ALA ILE HIS TYR MET THR SEQRES 12 A 664 GLU GLN ALA PRO ALA ALA VAL VAL GLU LEU GLU ASN TYR SEQRES 13 A 664 GLY MET PRO PHE SER ARG THR GLU ASP GLY LYS ILE TYR SEQRES 14 A 664 GLN ARG ALA PHE GLY GLY GLN SER LEU LYS PHE GLY LYS SEQRES 15 A 664 GLY GLY GLN ALA HIS ARG CYS CYS CYS VAL ALA ASP ARG SEQRES 16 A 664 THR GLY HIS SER LEU LEU HIS THR LEU TYR GLY ARG SER SEQRES 17 A 664 LEU ARG TYR ASP THR SER TYR PHE VAL GLU TYR PHE ALA SEQRES 18 A 664 LEU ASP LEU LEU MET GLU ASN GLY GLU CYS ARG GLY VAL SEQRES 19 A 664 ILE ALA LEU CYS ILE GLU ASP GLY SER ILE HIS ARG ILE SEQRES 20 A 664 ARG ALA LYS ASN THR VAL VAL ALA THR GLY GLY TYR GLY SEQRES 21 A 664 ARG THR TYR PHE SER CYS THR SER ALA HIS THR SER THR SEQRES 22 A 664 GLY ASP GLY THR ALA MET ILE THR ARG ALA GLY LEU PRO SEQRES 23 A 664 CYS GLN ASP LEU GLU PHE VAL GLN PHE HIS PRO THR GLY SEQRES 24 A 664 ILE TYR GLY ALA GLY CYS LEU ILE THR GLU GLY CYS ARG SEQRES 25 A 664 GLY GLU GLY GLY ILE LEU ILE ASN SER GLN GLY GLU ARG SEQRES 26 A 664 PHE MET GLU ARG TYR ALA PRO VAL ALA LYS ASP LEU ALA SEQRES 27 A 664 SER ARG ASP VAL VAL SER ARG SER MET THR LEU GLU ILE SEQRES 28 A 664 ARG GLU GLY ARG GLY CYS GLY PRO GLU LYS ASP HIS VAL SEQRES 29 A 664 TYR LEU GLN LEU HIS HIS LEU PRO PRO GLU GLN LEU ALA SEQRES 30 A 664 THR ARG LEU PRO GLY ILE SER GLU THR ALA MET ILE PHE SEQRES 31 A 664 ALA GLY VAL ASP VAL THR LYS GLU PRO ILE PRO VAL LEU SEQRES 32 A 664 PRO THR VAL HIS TYR ASN MET GLY GLY ILE PRO THR ASN SEQRES 33 A 664 TYR LYS GLY GLN VAL LEU ARG HIS VAL ASN GLY GLN ASP SEQRES 34 A 664 GLN ILE VAL PRO GLY LEU TYR ALA CYS GLY GLU ALA ALA SEQRES 35 A 664 CYS ALA SER VAL HIS GLY ALA ASN ARG LEU GLY ALA ASN SEQRES 36 A 664 SER LEU LEU ASP LEU VAL VAL PHE GLY ARG ALA CYS ALA SEQRES 37 A 664 LEU SER ILE GLU GLU SER CYS ARG PRO GLY ASP LYS VAL SEQRES 38 A 664 PRO PRO ILE LYS PRO ASN ALA GLY GLU GLU SER VAL MET SEQRES 39 A 664 ASN LEU ASP LYS LEU ARG PHE ALA ASP GLY SER ILE ARG SEQRES 40 A 664 THR SER GLU LEU ARG LEU SER MET GLN LYS SER MET GLN SEQRES 41 A 664 ASN HIS ALA ALA VAL PHE ARG VAL GLY SER VAL LEU GLN SEQRES 42 A 664 GLU GLY CYS GLY LYS ILE SER LYS LEU TYR GLY ASP LEU SEQRES 43 A 664 LYS HIS LEU LYS THR PHE ASP ARG GLY MET VAL TRP ASN SEQRES 44 A 664 THR ASP LEU VAL GLU THR LEU GLU LEU GLN ASN LEU MET SEQRES 45 A 664 LEU CYS ALA LEU GLN THR ILE TYR GLY ALA GLU ALA ARG SEQRES 46 A 664 LYS GLU SER ARG GLY ALA HIS ALA ARG GLU ASP TYR LYS SEQRES 47 A 664 VAL ARG ILE ASP GLU TYR ASP TYR SER LYS PRO ILE GLN SEQRES 48 A 664 GLY GLN GLN LYS LYS PRO PHE GLU GLU HIS TRP ARG LYS SEQRES 49 A 664 HIS THR LEU SER TYR VAL ASP VAL GLY THR GLY LYS VAL SEQRES 50 A 664 THR LEU GLU TYR ARG PRO VAL ILE ASP LYS THR LEU ASN SEQRES 51 A 664 GLU ALA ASP CYS ALA THR VAL PRO PRO ALA ILE ARG SER SEQRES 52 A 664 TYR SEQRES 1 B 280 MET ALA ALA VAL VAL ALA LEU SER LEU ARG ARG ARG LEU SEQRES 2 B 280 PRO ALA THR THR LEU GLY GLY ALA CYS LEU GLN ALA SER SEQRES 3 B 280 ARG GLY ALA GLN THR ALA ALA ALA THR ALA PRO ARG ILE SEQRES 4 B 280 LYS LYS PHE ALA ILE TYR ARG TRP ASP PRO ASP LYS ALA SEQRES 5 B 280 GLY ASP LYS PRO HIS MET GLN THR TYR GLU VAL ASP LEU SEQRES 6 B 280 ASN LYS CYS GLY PRO MET VAL LEU ASP ALA LEU ILE LYS SEQRES 7 B 280 ILE LYS ASN GLU VAL ASP SER THR LEU THR PHE ARG ARG SEQRES 8 B 280 SER CYS ARG GLU GLY ILE CYS GLY SER CYS ALA MET ASN SEQRES 9 B 280 ILE ASN GLY GLY ASN THR LEU ALA CYS THR ARG ARG ILE SEQRES 10 B 280 ASP THR ASN LEU ASN LYS VAL SER LYS ILE TYR PRO LEU SEQRES 11 B 280 PRO HIS MET TYR VAL ILE LYS ASP LEU VAL PRO ASP LEU SEQRES 12 B 280 SER ASN PHE TYR ALA GLN TYR LYS SER ILE GLU PRO TYR SEQRES 13 B 280 LEU LYS LYS LYS ASP GLU SER GLN GLU GLY LYS GLN GLN SEQRES 14 B 280 TYR LEU GLN SER ILE GLU GLU ARG GLU LYS LEU ASP GLY SEQRES 15 B 280 LEU TYR GLU CYS ILE LEU CYS ALA CYS CYS SER THR SER SEQRES 16 B 280 CYS PRO SER TYR TRP TRP ASN GLY ASP LYS TYR LEU GLY SEQRES 17 B 280 PRO ALA VAL LEU MET GLN ALA TYR ARG TRP MET ILE ASP SEQRES 18 B 280 SER ARG ASP ASP PHE THR GLU GLU ARG LEU ALA LYS LEU SEQRES 19 B 280 GLN ASP PRO PHE SER LEU TYR ARG CYS HIS THR ILE MET SEQRES 20 B 280 ASN CYS THR ARG THR CYS PRO LYS GLY LEU ASN PRO GLY SEQRES 21 B 280 LYS ALA ILE ALA GLU ILE LYS LYS MET MET ALA THR TYR SEQRES 22 B 280 LYS GLU LYS LYS ALA SER VAL SEQRES 1 C 169 MET ALA ALA LEU LEU LEU ARG HIS VAL GLY ARG HIS CYS SEQRES 2 C 169 LEU ARG ALA HIS PHE SER PRO GLN LEU CYS ILE ARG ASN SEQRES 3 C 169 ALA VAL PRO LEU GLY THR THR ALA LYS GLU GLU MET GLU SEQRES 4 C 169 ARG PHE TRP ASN LYS ASN ILE GLY SER ASN ARG PRO LEU SEQRES 5 C 169 SER PRO HIS ILE THR ILE TYR SER TRP SER LEU PRO MET SEQRES 6 C 169 ALA MET SER ILE CYS HIS ARG GLY THR GLY ILE ALA LEU SEQRES 7 C 169 SER ALA GLY VAL SER LEU PHE GLY MET SER ALA LEU LEU SEQRES 8 C 169 LEU PRO GLY ASN PHE GLU SER TYR LEU GLU LEU VAL LYS SEQRES 9 C 169 SER LEU CYS LEU GLY PRO ALA LEU ILE HIS THR ALA LYS SEQRES 10 C 169 PHE ALA LEU VAL PHE PRO LEU MET TYR HIS THR TRP ASN SEQRES 11 C 169 GLY ILE ARG HIS LEU MET TRP ASP LEU GLY LYS GLY LEU SEQRES 12 C 169 LYS ILE PRO GLN LEU TYR GLN SER GLY VAL VAL VAL LEU SEQRES 13 C 169 VAL LEU THR VAL LEU SER SER MET GLY LEU ALA ALA MET SEQRES 1 D 159 MET ALA VAL LEU TRP ARG LEU SER ALA VAL CYS GLY ALA SEQRES 2 D 159 LEU GLY GLY ARG ALA LEU LEU LEU ARG THR PRO VAL VAL SEQRES 3 D 159 ARG PRO ALA HIS ILE SER ALA PHE LEU GLN ASP ARG PRO SEQRES 4 D 159 ILE PRO GLU TRP CYS GLY VAL GLN HIS ILE HIS LEU SER SEQRES 5 D 159 PRO SER HIS HIS SER GLY SER LYS ALA ALA SER LEU HIS SEQRES 6 D 159 TRP THR SER GLU ARG VAL VAL SER VAL LEU LEU LEU GLY SEQRES 7 D 159 LEU LEU PRO ALA ALA TYR LEU ASN PRO CYS SER ALA MET SEQRES 8 D 159 ASP TYR SER LEU ALA ALA ALA LEU THR LEU HIS GLY HIS SEQRES 9 D 159 TRP GLY LEU GLY GLN VAL VAL THR ASP TYR VAL HIS GLY SEQRES 10 D 159 ASP ALA LEU GLN LYS ALA ALA LYS ALA GLY LEU LEU ALA SEQRES 11 D 159 LEU SER ALA LEU THR PHE ALA GLY LEU CYS TYR PHE ASN SEQRES 12 D 159 TYR HIS ASP VAL GLY ILE CYS LYS ALA VAL ALA MET LEU SEQRES 13 D 159 TRP LYS LEU HET FAD A 701 53 HET FES B 301 4 HET SF4 B 302 8 HET F3S B 303 7 HET UQ1 C 201 18 HET HEM D 201 43 HET PEV D 202 49 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM SF4 IRON/SULFUR CLUSTER HETNAM F3S FE3-S4 CLUSTER HETNAM UQ1 UBIQUINONE-1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PEV (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1- HETNAM 2 PEV [(PALMITOYLOXY)METHYL]ETHYL STEARATE HETSYN HEM HEME HETSYN PEV PHOSPHATIDYLETHANOLAMINE; 1-PALMITOYL-2-OLEOYL-SN- HETSYN 2 PEV GLYCERO-3-PHOSPHOETHANOLAMINE FORMUL 5 FAD C27 H33 N9 O15 P2 FORMUL 6 FES FE2 S2 FORMUL 7 SF4 FE4 S4 FORMUL 8 F3S FE3 S4 FORMUL 9 UQ1 C14 H18 O4 FORMUL 10 HEM C34 H32 FE N4 O4 FORMUL 11 PEV C39 H78 N O8 P HELIX 1 AA1 ILE A 51 TYR A 55 5 5 HELIX 2 AA2 GLY A 70 GLY A 84 1 15 HELIX 3 AA3 PHE A 94 ALA A 102 5 9 HELIX 4 AA4 ASN A 118 ASP A 131 1 14 HELIX 5 AA5 ASP A 135 ASN A 155 1 21 HELIX 6 AA6 ARG A 195 LEU A 209 1 15 HELIX 7 AA7 TYR A 259 TYR A 263 5 5 HELIX 8 AA8 GLY A 274 ARG A 282 1 9 HELIX 9 AA9 THR A 308 GLY A 315 1 8 HELIX 10 AB1 PHE A 326 ALA A 331 1 6 HELIX 11 AB2 ASP A 341 ARG A 352 1 12 HELIX 12 AB3 PRO A 372 ARG A 379 1 8 HELIX 13 AB4 LEU A 380 PHE A 390 1 11 HELIX 14 AB5 ALA A 454 CYS A 475 1 22 HELIX 15 AB6 GLY A 489 PHE A 501 1 13 HELIX 16 AB7 THR A 508 ALA A 523 1 16 HELIX 17 AB8 VAL A 528 ASP A 545 1 18 HELIX 18 AB9 ASN A 559 ARG A 585 1 27 HELIX 19 AC1 MET B 71 VAL B 83 1 13 HELIX 20 AC2 LEU B 143 ILE B 153 1 11 HELIX 21 AC3 SER B 173 GLU B 178 1 6 HELIX 22 AC4 LYS B 179 ASP B 181 5 3 HELIX 23 AC5 CYS B 192 SER B 195 5 4 HELIX 24 AC6 CYS B 196 ASN B 202 1 7 HELIX 25 AC7 LEU B 207 ILE B 220 1 14 HELIX 26 AC8 LEU B 231 GLN B 235 5 5 HELIX 27 AC9 MET B 247 CYS B 253 1 7 HELIX 28 AD1 ASN B 258 THR B 272 1 15 HELIX 29 AD2 LYS C 35 SER C 48 1 14 HELIX 30 AD3 SER C 62 LEU C 92 1 31 HELIX 31 AD4 ASN C 95 LEU C 106 1 12 HELIX 32 AD5 GLY C 109 LEU C 139 1 31 HELIX 33 AD6 LYS C 144 ALA C 168 1 25 HELIX 34 AD7 ALA D 62 LEU D 80 1 19 HELIX 35 AD8 LEU D 80 ASN D 86 1 7 HELIX 36 AD9 CYS D 88 VAL D 115 1 28 HELIX 37 AE1 GLY D 117 ASP D 146 1 30 HELIX 38 AE2 VAL D 147 TRP D 157 1 11 SHEET 1 AA1 4 VAL A 57 GLU A 61 0 SHEET 2 AA1 4 ILE A 244 ARG A 248 1 O ARG A 248 N HIS A 60 SHEET 3 AA1 4 GLU A 230 CYS A 238 -1 N ALA A 236 O HIS A 245 SHEET 4 AA1 4 TYR A 219 GLU A 227 -1 N PHE A 220 O LEU A 237 SHEET 1 AA2 5 THR A 87 VAL A 90 0 SHEET 2 AA2 5 ALA A 64 VAL A 67 1 N VAL A 66 O ALA A 88 SHEET 3 AA2 5 ASN A 251 VAL A 254 1 O VAL A 253 N VAL A 67 SHEET 4 AA2 5 ILE A 431 ALA A 437 1 O GLY A 434 N THR A 252 SHEET 5 AA2 5 GLN A 420 LEU A 422 -1 N VAL A 421 O VAL A 432 SHEET 1 AA3 3 ILE A 107 ASN A 108 0 SHEET 2 AA3 3 CYS A 189 CYS A 190 -1 O CYS A 190 N ILE A 107 SHEET 3 AA3 3 GLN A 170 ARG A 171 -1 N ARG A 171 O CYS A 189 SHEET 1 AA4 3 CYS A 287 GLN A 288 0 SHEET 2 AA4 3 LYS A 624 ASP A 631 -1 O SER A 628 N CYS A 287 SHEET 3 AA4 3 LYS A 636 PRO A 643 -1 O GLU A 640 N LEU A 627 SHEET 1 AA5 2 VAL A 293 GLN A 294 0 SHEET 2 AA5 2 TYR A 408 ASN A 409 -1 O TYR A 408 N GLN A 294 SHEET 1 AA6 4 GLY A 299 ILE A 300 0 SHEET 2 AA6 4 ILE A 400 LEU A 403 -1 O LEU A 403 N GLY A 299 SHEET 3 AA6 4 VAL A 364 GLN A 367 -1 N VAL A 364 O VAL A 402 SHEET 4 AA6 4 ILE A 317 ILE A 319 -1 N ILE A 319 O TYR A 365 SHEET 1 AA7 2 ILE A 413 PRO A 414 0 SHEET 2 AA7 2 ALA A 442 CYS A 443 1 O CYS A 443 N ILE A 413 SHEET 1 AA8 2 ILE A 506 ARG A 507 0 SHEET 2 AA8 2 LEU A 549 LYS A 550 1 O LYS A 550 N ILE A 506 SHEET 1 AA9 2 PHE A 526 ARG A 527 0 SHEET 2 AA9 2 ALA A 593 ARG A 594 1 O ALA A 593 N ARG A 527 SHEET 1 AB1 5 HIS B 57 ASP B 64 0 SHEET 2 AB1 5 ILE B 39 ARG B 46 -1 N ILE B 44 O GLN B 59 SHEET 3 AB1 5 VAL B 124 TYR B 128 1 O ILE B 127 N TYR B 45 SHEET 4 AB1 5 ALA B 102 ILE B 105 -1 N ASN B 104 O TYR B 128 SHEET 5 AB1 5 GLY B 108 LEU B 111 -1 O THR B 110 N MET B 103 SHEET 1 AB2 2 VAL B 135 LYS B 137 0 SHEET 2 AB2 2 VAL B 140 PRO B 141 -1 O VAL B 140 N ILE B 136 LINK SG CYS B 93 FE1 FES B 301 1555 1555 2.15 LINK SG CYS B 98 FE1 FES B 301 1555 1555 2.27 LINK SG CYS B 101 FE2 FES B 301 1555 1555 2.12 LINK SG CYS B 113 FE2 FES B 301 1555 1555 2.22 LINK SG CYS B 186 FE3 SF4 B 302 1555 1555 2.18 LINK SG CYS B 189 FE4 SF4 B 302 1555 1555 2.17 LINK SG CYS B 192 FE1 SF4 B 302 1555 1555 2.11 LINK SG CYS B 196 FE3 F3S B 303 1555 1555 2.14 LINK SG CYS B 243 FE1 F3S B 303 1555 1555 2.17 LINK SG CYS B 249 FE4 F3S B 303 1555 1555 2.13 LINK SG CYS B 253 FE2 SF4 B 302 1555 1555 2.20 LINK NE2 HIS C 127 FE HEM D 201 1555 1555 2.22 LINK NE2 HIS D 102 FE HEM D 201 1555 1555 2.22 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