HEADER PROTEIN TRANSPORT 19-NOV-24 9KNX TITLE CRYO-EM STRUCTURE OF HUMAN MITOCHONDRIAL PYRUVATE CARRIER IN THE TITLE 2 OCCLUDED CONFORMATION AT PH 6.8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL PYRUVATE CARRIER 2; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: BRAIN PROTEIN 44; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MITOCHONDRIAL PYRUVATE CARRIER 1; COMPND 8 CHAIN: A; COMPND 9 SYNONYM: BRAIN PROTEIN 44-LIKE PROTEIN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MPC SPECIFIC NANOBODY 1; COMPND 13 CHAIN: C; COMPND 14 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: MPC2, BRP44; 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: MPC1, BRP44L, CGI-129, HSPC040, PNAS-115; 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_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MITOCHONDRIAL PYRUVATE CARRIER, MPC, PYRUVATE TRANSPORT, PROTEIN KEYWDS 2 TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR J.H.SHI,J.M.LIANG,D.MA REVDAT 1 12-MAR-25 9KNX 0 JRNL AUTH J.H.SHI,J.M.LIANG,D.MA JRNL TITL A MEMBRANE TRANSPORTER COMPLEX WITH SUBSTRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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) : 3.720 REMARK 3 NUMBER OF PARTICLES : 312660 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 9KNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053868. 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 : A MEMBRANE TRANSPORTER COMPLEX 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 : 6.80 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1200.00 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C 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 B 1 REMARK 465 GLY B 128 REMARK 465 SER B 129 REMARK 465 ASP B 130 REMARK 465 TYR B 131 REMARK 465 LYS B 132 REMARK 465 ASP B 133 REMARK 465 HIS B 134 REMARK 465 ASP B 135 REMARK 465 GLY B 136 REMARK 465 ASP B 137 REMARK 465 TYR B 138 REMARK 465 LYS B 139 REMARK 465 ASP B 140 REMARK 465 HIS B 141 REMARK 465 ASP B 142 REMARK 465 ILE B 143 REMARK 465 ASP B 144 REMARK 465 TYR B 145 REMARK 465 LYS B 146 REMARK 465 ASP B 147 REMARK 465 ASP B 148 REMARK 465 ASP B 149 REMARK 465 ASP B 150 REMARK 465 LYS B 151 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 5 REMARK 465 VAL A 6 REMARK 465 ARG A 7 REMARK 465 LYS A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ASP A 11 REMARK 465 TYR A 12 REMARK 465 VAL A 13 REMARK 465 ARG A 14 REMARK 465 SER A 15 REMARK 465 LYS A 16 REMARK 465 ASP A 17 REMARK 465 PHE A 18 REMARK 465 ARG A 19 REMARK 465 ASP A 20 REMARK 465 GLY A 110 REMARK 465 SER A 111 REMARK 465 TYR A 112 REMARK 465 PRO A 113 REMARK 465 TYR A 114 REMARK 465 ASP A 115 REMARK 465 VAL A 116 REMARK 465 PRO A 117 REMARK 465 ASP A 118 REMARK 465 TYR A 119 REMARK 465 ALA A 120 REMARK 465 SER C 115 REMARK 465 LEU C 116 REMARK 465 GLU C 117 REMARK 465 HIS C 118 REMARK 465 HIS C 119 REMARK 465 HIS C 120 REMARK 465 HIS C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 GLY C 125 REMARK 465 GLY C 126 REMARK 465 SER C 127 REMARK 465 GLY C 128 REMARK 465 GLU C 129 REMARK 465 GLN C 130 REMARK 465 LYS C 131 REMARK 465 LEU C 132 REMARK 465 ILE C 133 REMARK 465 SER C 134 REMARK 465 GLU C 135 REMARK 465 GLU C 136 REMARK 465 ASP C 137 REMARK 465 LEU C 138 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 LYS B 27 0.78 -68.96 REMARK 500 LEU A 22 53.75 36.97 REMARK 500 SER C 56 42.31 37.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CDL B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62465 RELATED DB: EMDB REMARK 900 A MEMBRANE TRANSPORTER COMPLEX TREATED WITH SUBSTRATE,PH 6.8 DBREF 9KNX B 1 127 UNP O95563 MPC2_HUMAN 1 127 DBREF 9KNX A 1 109 UNP Q9Y5U8 MPC1_HUMAN 1 109 DBREF 9KNX C 1 138 PDB 9KNX 9KNX 1 138 SEQADV 9KNX GLY B 128 UNP O95563 EXPRESSION TAG SEQADV 9KNX SER B 129 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 130 UNP O95563 EXPRESSION TAG SEQADV 9KNX TYR B 131 UNP O95563 EXPRESSION TAG SEQADV 9KNX LYS B 132 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 133 UNP O95563 EXPRESSION TAG SEQADV 9KNX HIS B 134 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 135 UNP O95563 EXPRESSION TAG SEQADV 9KNX GLY B 136 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 137 UNP O95563 EXPRESSION TAG SEQADV 9KNX TYR B 138 UNP O95563 EXPRESSION TAG SEQADV 9KNX LYS B 139 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 140 UNP O95563 EXPRESSION TAG SEQADV 9KNX HIS B 141 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 142 UNP O95563 EXPRESSION TAG SEQADV 9KNX ILE B 143 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 144 UNP O95563 EXPRESSION TAG SEQADV 9KNX TYR B 145 UNP O95563 EXPRESSION TAG SEQADV 9KNX LYS B 146 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 147 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 148 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 149 UNP O95563 EXPRESSION TAG SEQADV 9KNX ASP B 150 UNP O95563 EXPRESSION TAG SEQADV 9KNX LYS B 151 UNP O95563 EXPRESSION TAG SEQADV 9KNX GLY A 110 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX SER A 111 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX TYR A 112 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX PRO A 113 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX TYR A 114 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX ASP A 115 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX VAL A 116 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX PRO A 117 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX ASP A 118 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX TYR A 119 UNP Q9Y5U8 EXPRESSION TAG SEQADV 9KNX ALA A 120 UNP Q9Y5U8 EXPRESSION TAG SEQRES 1 B 151 MET SER ALA ALA GLY ALA ARG GLY LEU ARG ALA THR TYR SEQRES 2 B 151 HIS ARG LEU LEU ASP LYS VAL GLU LEU MET LEU PRO GLU SEQRES 3 B 151 LYS LEU ARG PRO LEU TYR ASN HIS PRO ALA GLY PRO ARG SEQRES 4 B 151 THR VAL PHE PHE TRP ALA PRO ILE MET LYS TRP GLY LEU SEQRES 5 B 151 VAL CYS ALA GLY LEU ALA ASP MET ALA ARG PRO ALA GLU SEQRES 6 B 151 LYS LEU SER THR ALA GLN SER ALA VAL LEU MET ALA THR SEQRES 7 B 151 GLY PHE ILE TRP SER ARG TYR SER LEU VAL ILE ILE PRO SEQRES 8 B 151 LYS ASN TRP SER LEU PHE ALA VAL ASN PHE PHE VAL GLY SEQRES 9 B 151 ALA ALA GLY ALA SER GLN LEU PHE ARG ILE TRP ARG TYR SEQRES 10 B 151 ASN GLN GLU LEU LYS ALA LYS ALA HIS LYS GLY SER ASP SEQRES 11 B 151 TYR LYS ASP HIS ASP GLY ASP TYR LYS ASP HIS ASP ILE SEQRES 12 B 151 ASP TYR LYS ASP ASP ASP ASP LYS SEQRES 1 A 120 MET ALA GLY ALA LEU VAL ARG LYS ALA ALA ASP TYR VAL SEQRES 2 A 120 ARG SER LYS ASP PHE ARG ASP TYR LEU MET SER THR HIS SEQRES 3 A 120 PHE TRP GLY PRO VAL ALA ASN TRP GLY LEU PRO ILE ALA SEQRES 4 A 120 ALA ILE ASN ASP MET LYS LYS SER PRO GLU ILE ILE SER SEQRES 5 A 120 GLY ARG MET THR PHE ALA LEU CYS CYS TYR SER LEU THR SEQRES 6 A 120 PHE MET ARG PHE ALA TYR LYS VAL GLN PRO ARG ASN TRP SEQRES 7 A 120 LEU LEU PHE ALA CYS HIS ALA THR ASN GLU VAL ALA GLN SEQRES 8 A 120 LEU ILE GLN GLY GLY ARG LEU ILE LYS HIS GLU MET THR SEQRES 9 A 120 LYS THR ALA SER ALA GLY SER TYR PRO TYR ASP VAL PRO SEQRES 10 A 120 ASP TYR ALA SEQRES 1 C 138 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 138 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 138 PHE PRO VAL THR GLU ARG VAL MET TYR TRP TYR ARG GLN SEQRES 4 C 138 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ALA ILE ASP SEQRES 5 C 138 SER GLN GLY SER SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 138 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 C 138 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 C 138 ALA VAL TYR TYR CYS LYS VAL GLU VAL GLY TRP GLY TYR SEQRES 9 C 138 LYS GLY GLN GLY THR GLN VAL THR VAL SER SER LEU GLU SEQRES 10 C 138 HIS HIS HIS HIS HIS HIS HIS GLY GLY SER GLY GLU GLN SEQRES 11 C 138 LYS LEU ILE SER GLU GLU ASP LEU HET CDL B 201 89 HETNAM CDL CARDIOLIPIN HETSYN CDL DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3- HETSYN 2 CDL PHOSPHO)-1',3'-SN-GLYCEROL FORMUL 4 CDL C81 H156 O17 P2 2- HELIX 1 AA1 SER B 2 LEU B 24 1 23 HELIX 2 AA2 PRO B 25 LYS B 27 5 3 HELIX 3 AA3 LEU B 28 ASN B 33 1 6 HELIX 4 AA4 THR B 40 MET B 60 1 21 HELIX 5 AA5 SER B 68 LEU B 87 1 20 HELIX 6 AA6 ASN B 93 LYS B 127 1 35 HELIX 7 AA7 MET A 23 TRP A 34 1 12 HELIX 8 AA8 TRP A 34 MET A 44 1 11 HELIX 9 AA9 SER A 52 VAL A 73 1 22 HELIX 10 AB1 ASN A 77 SER A 108 1 32 HELIX 11 AB2 ASP C 62 LYS C 65 5 4 HELIX 12 AB3 ASN C 74 LYS C 76 5 3 HELIX 13 AB4 LYS C 87 THR C 91 5 5 SHEET 1 AA1 4 GLN C 3 SER C 7 0 SHEET 2 AA1 4 LEU C 18 SER C 25 -1 O ALA C 23 N VAL C 5 SHEET 3 AA1 4 THR C 78 MET C 83 -1 O LEU C 81 N LEU C 20 SHEET 4 AA1 4 PHE C 68 ASP C 73 -1 N THR C 69 O GLN C 82 SHEET 1 AA2 6 GLY C 10 GLN C 13 0 SHEET 2 AA2 6 THR C 109 SER C 114 1 O SER C 114 N VAL C 12 SHEET 3 AA2 6 ALA C 92 VAL C 98 -1 N TYR C 94 O THR C 109 SHEET 4 AA2 6 MET C 34 GLN C 39 -1 N TYR C 37 O TYR C 95 SHEET 5 AA2 6 GLU C 46 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AA2 6 THR C 58 TYR C 60 -1 O TYR C 59 N ALA C 50 SHEET 1 AA3 4 GLY C 10 GLN C 13 0 SHEET 2 AA3 4 THR C 109 SER C 114 1 O SER C 114 N VAL C 12 SHEET 3 AA3 4 ALA C 92 VAL C 98 -1 N TYR C 94 O THR C 109 SHEET 4 AA3 4 TYR C 104 LYS C 105 -1 O TYR C 104 N VAL C 98 SSBOND 1 CYS C 22 CYS C 96 1555 1555 2.02 CISPEP 1 ILE B 90 PRO B 91 0 -11.87 CISPEP 2 GLN A 74 PRO A 75 0 1.63 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