HEADER LYASE 20-MAY-23 8JGA TITLE CRYO-EM STRUCTURE OF MI3 FUSED WITH FKBP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP1A,2-DEHYDRO-3- COMPND 3 DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXOGLUTARATE ALDOLASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PPIASE FKBP1A,12 KDA FK506-BINDING PROTEIN,12 KDA FKBP,FKBP- COMPND 6 12,CALSTABIN-1,FK506-BINDING PROTEIN 1A,FKBP-1A,IMMUNOPHILIN FKBP12, COMPND 7 ROTAMASE; COMPND 8 EC: 5.2.1.8; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, THERMOTOGA MARITIMA (STRAIN ATCC SOURCE 3 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8); SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606, 243274; SOURCE 6 GENE: FKBP1A, FKBP1, FKBP12, TM_0066; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN CAGE SCAFFOLD, LYASE EXPDTA ELECTRON MICROSCOPY AUTHOR H.W.ZHANG,W.KANG,C.XUE REVDAT 1 24-APR-24 8JGA 0 JRNL AUTH W.KANG,X.MA,H.ZHANG,J.MA,C.LIU,J.LI,H.GUO,D.WANG,R.WANG, JRNL AUTH 2 B.LI,C.XUE JRNL TITL DYNAMIC METABOLONS USING STIMULI-RESPONSIVE PROTEIN CAGES. JRNL REF J.AM.CHEM.SOC. V. 146 6686 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 38425051 JRNL DOI 10.1021/JACS.3C12876 REMARK 2 REMARK 2 RESOLUTION. 3.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 33473 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 8JGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 23-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037820. 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 : FKBP-MI3 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 : 7.80 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -131 REMARK 465 GLY A -130 REMARK 465 SER A -129 REMARK 465 SER A -128 REMARK 465 HIS A -127 REMARK 465 HIS A -126 REMARK 465 HIS A -125 REMARK 465 HIS A -124 REMARK 465 HIS A -123 REMARK 465 HIS A -122 REMARK 465 GLY A -121 REMARK 465 GLY A -120 REMARK 465 SER A -119 REMARK 465 GLY A -118 REMARK 465 VAL A -117 REMARK 465 GLN A -116 REMARK 465 VAL A -115 REMARK 465 GLU A -114 REMARK 465 THR A -113 REMARK 465 ILE A -112 REMARK 465 SER A -111 REMARK 465 PRO A -110 REMARK 465 GLY A -109 REMARK 465 ASP A -108 REMARK 465 GLY A -107 REMARK 465 ARG A -106 REMARK 465 THR A -105 REMARK 465 PHE A -104 REMARK 465 PRO A -103 REMARK 465 LYS A -102 REMARK 465 ARG A -101 REMARK 465 GLY A -100 REMARK 465 GLN A -99 REMARK 465 THR A -98 REMARK 465 CYS A -97 REMARK 465 VAL A -96 REMARK 465 VAL A -95 REMARK 465 HIS A -94 REMARK 465 TYR A -93 REMARK 465 THR A -92 REMARK 465 GLY A -91 REMARK 465 MET A -90 REMARK 465 LEU A -89 REMARK 465 GLU A -88 REMARK 465 ASP A -87 REMARK 465 GLY A -86 REMARK 465 LYS A -85 REMARK 465 LYS A -84 REMARK 465 PHE A -83 REMARK 465 ASP A -82 REMARK 465 SER A -81 REMARK 465 SER A -80 REMARK 465 ARG A -79 REMARK 465 ASP A -78 REMARK 465 ARG A -77 REMARK 465 ASN A -76 REMARK 465 LYS A -75 REMARK 465 PRO A -74 REMARK 465 PHE A -73 REMARK 465 LYS A -72 REMARK 465 PHE A -71 REMARK 465 MET A -70 REMARK 465 LEU A -69 REMARK 465 GLY A -68 REMARK 465 LYS A -67 REMARK 465 GLN A -66 REMARK 465 GLU A -65 REMARK 465 VAL A -64 REMARK 465 ILE A -63 REMARK 465 ARG A -62 REMARK 465 GLY A -61 REMARK 465 TRP A -60 REMARK 465 GLU A -59 REMARK 465 GLU A -58 REMARK 465 GLY A -57 REMARK 465 VAL A -56 REMARK 465 ALA A -55 REMARK 465 GLN A -54 REMARK 465 MET A -53 REMARK 465 SER A -52 REMARK 465 VAL A -51 REMARK 465 GLY A -50 REMARK 465 GLN A -49 REMARK 465 ARG A -48 REMARK 465 ALA A -47 REMARK 465 LYS A -46 REMARK 465 LEU A -45 REMARK 465 THR A -44 REMARK 465 ILE A -43 REMARK 465 SER A -42 REMARK 465 PRO A -41 REMARK 465 ASP A -40 REMARK 465 TYR A -39 REMARK 465 ALA A -38 REMARK 465 TYR A -37 REMARK 465 GLY A -36 REMARK 465 ALA A -35 REMARK 465 THR A -34 REMARK 465 GLY A -33 REMARK 465 HIS A -32 REMARK 465 PRO A -31 REMARK 465 GLY A -30 REMARK 465 ILE A -29 REMARK 465 ILE A -28 REMARK 465 PRO A -27 REMARK 465 PRO A -26 REMARK 465 HIS A -25 REMARK 465 ALA A -24 REMARK 465 THR A -23 REMARK 465 LEU A -22 REMARK 465 VAL A -21 REMARK 465 PHE A -20 REMARK 465 ASP A -19 REMARK 465 VAL A -18 REMARK 465 GLU A -17 REMARK 465 LEU A -16 REMARK 465 LEU A -15 REMARK 465 LYS A -14 REMARK 465 LEU A -13 REMARK 465 GLU A -12 REMARK 465 GLY A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 204 REMARK 465 GLU A 205 REMARK 465 GLY A 206 REMARK 465 SER A 207 REMARK 465 GLY A 208 REMARK 465 GLU A 209 REMARK 465 PRO A 210 REMARK 465 GLU A 211 REMARK 465 ALA A 212 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 2 CB CG CD CE NZ REMARK 470 MET A 3 CB CG SD CE 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 ASN A 19 -158.36 -91.76 REMARK 500 SER A 20 154.29 -43.38 REMARK 500 PHE A 43 0.31 -67.54 REMARK 500 LEU A 181 39.14 -158.49 REMARK 500 VAL A 182 -12.93 -164.47 REMARK 500 PRO A 186 -7.43 -56.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36228 RELATED DB: EMDB REMARK 900 MI3 FUSED WITH FKBP DBREF 8JGA A -118 -12 UNP P62942 FKB1A_HUMAN 2 108 DBREF 8JGA A 1 205 UNP Q9WXS1 Q9WXS1_THEMA 1 205 SEQADV 8JGA MET A -131 UNP P62942 INITIATING METHIONINE SEQADV 8JGA GLY A -130 UNP P62942 EXPRESSION TAG SEQADV 8JGA SER A -129 UNP P62942 EXPRESSION TAG SEQADV 8JGA SER A -128 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -127 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -126 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -125 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -124 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -123 UNP P62942 EXPRESSION TAG SEQADV 8JGA HIS A -122 UNP P62942 EXPRESSION TAG SEQADV 8JGA GLY A -121 UNP P62942 EXPRESSION TAG SEQADV 8JGA GLY A -120 UNP P62942 EXPRESSION TAG SEQADV 8JGA SER A -119 UNP P62942 EXPRESSION TAG SEQADV 8JGA GLY A -11 UNP P62942 LINKER SEQADV 8JGA GLY A -10 UNP P62942 LINKER SEQADV 8JGA SER A -9 UNP P62942 LINKER SEQADV 8JGA GLY A -8 UNP P62942 LINKER SEQADV 8JGA GLY A -7 UNP P62942 LINKER SEQADV 8JGA SER A -6 UNP P62942 LINKER SEQADV 8JGA GLY A -5 UNP P62942 LINKER SEQADV 8JGA GLY A -4 UNP P62942 LINKER SEQADV 8JGA SER A -3 UNP P62942 LINKER SEQADV 8JGA GLY A -2 UNP P62942 LINKER SEQADV 8JGA GLY A -1 UNP P62942 LINKER SEQADV 8JGA SER A 0 UNP P62942 LINKER SEQADV 8JGA LYS A 26 UNP Q9WXS1 GLU 26 CONFLICT SEQADV 8JGA LEU A 33 UNP Q9WXS1 GLU 33 CONFLICT SEQADV 8JGA MET A 61 UNP Q9WXS1 LYS 61 CONFLICT SEQADV 8JGA ALA A 76 UNP Q9WXS1 CYS 76 CONFLICT SEQADV 8JGA ALA A 100 UNP Q9WXS1 CYS 100 CONFLICT SEQADV 8JGA VAL A 187 UNP Q9WXS1 ASP 187 CONFLICT SEQADV 8JGA ALA A 190 UNP Q9WXS1 ARG 190 CONFLICT SEQADV 8JGA GLY A 206 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA SER A 207 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA GLY A 208 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA GLU A 209 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA PRO A 210 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA GLU A 211 UNP Q9WXS1 EXPRESSION TAG SEQADV 8JGA ALA A 212 UNP Q9WXS1 EXPRESSION TAG SEQRES 1 A 344 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLY GLY SER SEQRES 2 A 344 GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG SEQRES 3 A 344 THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR SEQRES 4 A 344 THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER SEQRES 5 A 344 ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS SEQRES 6 A 344 GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN SEQRES 7 A 344 MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO SEQRES 8 A 344 ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE SEQRES 9 A 344 PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU SEQRES 10 A 344 LYS LEU GLU GLY GLY SER GLY GLY SER GLY GLY SER GLY SEQRES 11 A 344 GLY SER MET LYS MET GLU GLU LEU PHE LYS LYS HIS LYS SEQRES 12 A 344 ILE VAL ALA VAL LEU ARG ALA ASN SER VAL GLU GLU ALA SEQRES 13 A 344 LYS LYS LYS ALA LEU ALA VAL PHE LEU GLY GLY VAL HIS SEQRES 14 A 344 LEU ILE GLU ILE THR PHE THR VAL PRO ASP ALA ASP THR SEQRES 15 A 344 VAL ILE LYS GLU LEU SER PHE LEU LYS GLU MET GLY ALA SEQRES 16 A 344 ILE ILE GLY ALA GLY THR VAL THR SER VAL GLU GLN ALA SEQRES 17 A 344 ARG LYS ALA VAL GLU SER GLY ALA GLU PHE ILE VAL SER SEQRES 18 A 344 PRO HIS LEU ASP GLU GLU ILE SER GLN PHE ALA LYS GLU SEQRES 19 A 344 LYS GLY VAL PHE TYR MET PRO GLY VAL MET THR PRO THR SEQRES 20 A 344 GLU LEU VAL LYS ALA MET LYS LEU GLY HIS THR ILE LEU SEQRES 21 A 344 LYS LEU PHE PRO GLY GLU VAL VAL GLY PRO GLN PHE VAL SEQRES 22 A 344 LYS ALA MET LYS GLY PRO PHE PRO ASN VAL LYS PHE VAL SEQRES 23 A 344 PRO THR GLY GLY VAL ASN LEU ASP ASN VAL CYS GLU TRP SEQRES 24 A 344 PHE LYS ALA GLY VAL LEU ALA VAL GLY VAL GLY SER ALA SEQRES 25 A 344 LEU VAL LYS GLY THR PRO VAL GLU VAL ALA GLU LYS ALA SEQRES 26 A 344 LYS ALA PHE VAL GLU LYS ILE ARG GLY CYS THR GLU GLY SEQRES 27 A 344 SER GLY GLU PRO GLU ALA HELIX 1 AA1 LYS A 2 LYS A 11 1 10 HELIX 2 AA2 SER A 20 GLY A 35 1 16 HELIX 3 AA3 ASP A 47 SER A 56 1 10 HELIX 4 AA4 SER A 56 GLY A 62 1 7 HELIX 5 AA5 SER A 72 SER A 82 1 11 HELIX 6 AA6 ASP A 93 GLY A 104 1 12 HELIX 7 AA7 THR A 113 GLY A 124 1 12 HELIX 8 AA8 PRO A 132 GLY A 137 1 6 HELIX 9 AA9 GLY A 137 LYS A 145 1 9 HELIX 10 AB1 ASN A 163 LYS A 169 1 7 HELIX 11 AB2 THR A 185 GLY A 202 1 18 SHEET 1 AA1 3 ALA A 14 VAL A 15 0 SHEET 2 AA1 3 LEU A 38 THR A 42 1 O GLU A 40 N ALA A 14 SHEET 3 AA1 3 ILE A 64 GLY A 68 1 O GLY A 66 N ILE A 41 SHEET 1 AA2 2 PHE A 86 VAL A 88 0 SHEET 2 AA2 2 PHE A 106 MET A 108 1 O PHE A 106 N ILE A 87 SHEET 1 AA3 2 ILE A 127 LYS A 129 0 SHEET 2 AA3 2 LYS A 152 VAL A 154 1 O VAL A 154 N LEU A 128 SSBOND 1 CYS A 165 CYS A 203 1555 1555 2.04 CISPEP 1 PHE A 131 PRO A 132 0 -0.89 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