HEADER SUGAR BINDING PROTEIN 06-NOV-25 9XKO TITLE HIGH-RESOLUTION CRYO-EM STRUCTURE OF MALTOSE BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE/MALTODEXTRIN-BINDING PERIPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMBP,MALTODEXTRIN-BINDING PROTEIN,MALTOSE-BINDING PROTEIN, COMPND 5 MBP; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: A313V SUBSTITUTION REFLECTS THE MBP SEQUENCE ENCODED COMPND 8 IN THE PMAL-C5X EXPRESSION VECTOR BACKBONE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MALE, B4034, JW3994; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL PROTEIN-LIGAND COMPLEX, SUGAR BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.PARK,Y.YOO,H.JEON,K.CHOI,E.KWON,H.LIM,D.Y.KIM,K.T.NO REVDAT 1 29-APR-26 9XKO 0 JRNL AUTH K.PARK,Y.YOO,H.JEON,K.CHOI,H.KIM,E.KWON,H.H.LIM,D.Y.KIM, JRNL AUTH 2 K.T.NO JRNL TITL HIGH-RESOLUTION CRYO-EM STRUCTURES OF SMALL PROTEIN-LIGAND JRNL TITL 2 COMPLEXES NEAR THE THEORETICAL SIZE LIMIT. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41980966 JRNL DOI 10.1038/S41467-026-71934-7 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, PHENIX, COOT, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1FQC 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) : 2.350 REMARK 3 NUMBER OF PARTICLES : 509884 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9XKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1300065585. 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 : HIGH-RESOLUTION CRYO-EM REMARK 245 STRUCTURE OF MALTOSEE BINDING REMARK 245 PROTEIN 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 : 7.50 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) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 6000.00 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, B 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 26 REMARK 465 LYS A 27 REMARK 465 SER A 396 REMARK 465 ASN A 397 REMARK 465 ASN A 398 REMARK 465 ASN A 399 REMARK 465 ASN A 400 REMARK 465 ASN A 401 REMARK 465 ASN A 402 REMARK 465 ASN A 403 REMARK 465 ASN A 404 REMARK 465 ASN A 405 REMARK 465 ASN A 406 REMARK 465 LEU A 407 REMARK 465 GLY A 408 REMARK 465 ILE A 409 REMARK 465 GLU A 410 REMARK 465 GLY A 411 REMARK 465 ARG A 412 REMARK 465 ILE A 413 REMARK 465 SER A 414 REMARK 465 HIS A 415 REMARK 465 MET A 416 REMARK 465 GLU A 417 REMARK 465 ASN A 418 REMARK 465 LEU A 419 REMARK 465 TYR A 420 REMARK 465 PHE A 421 REMARK 465 GLN A 422 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 VAL A 209 O 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 ASP A 81 -168.95 -125.82 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 GLC B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66973 RELATED DB: EMDB REMARK 900 HIGH-RESOLUTION CRYO-EM STRUCTURE OF MALTOSE BINDING PROTEIN DBREF 9XKO A 27 392 UNP P0AEX9 MALE_ECOLI 27 392 SEQADV 9XKO MET A 26 UNP P0AEX9 INITIATING METHIONINE SEQADV 9XKO VAL A 338 UNP P0AEX9 ALA 338 CONFLICT SEQADV 9XKO ASN A 393 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO SER A 394 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO SER A 395 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO SER A 396 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 397 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 398 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 399 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 400 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 401 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 402 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 403 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 404 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 405 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 406 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO LEU A 407 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO GLY A 408 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ILE A 409 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO GLU A 410 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO GLY A 411 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ARG A 412 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ILE A 413 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO SER A 414 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO HIS A 415 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO MET A 416 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO GLU A 417 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO ASN A 418 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO LEU A 419 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO TYR A 420 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO PHE A 421 UNP P0AEX9 EXPRESSION TAG SEQADV 9XKO GLN A 422 UNP P0AEX9 EXPRESSION TAG SEQRES 1 A 397 MET LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN SEQRES 2 A 397 GLY ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS SEQRES 3 A 397 LYS PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU SEQRES 4 A 397 HIS PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA SEQRES 5 A 397 ALA THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS SEQRES 6 A 397 ASP ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA SEQRES 7 A 397 GLU ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR SEQRES 8 A 397 PRO PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU SEQRES 9 A 397 ILE ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE SEQRES 10 A 397 TYR ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP SEQRES 11 A 397 GLU GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS SEQRES 12 A 397 GLY LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR SEQRES 13 A 397 PHE THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA SEQRES 14 A 397 PHE LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL SEQRES 15 A 397 GLY VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE SEQRES 16 A 397 LEU VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP SEQRES 17 A 397 THR ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY SEQRES 18 A 397 GLU THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER SEQRES 19 A 397 ASN ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL SEQRES 20 A 397 LEU PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL SEQRES 21 A 397 GLY VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN SEQRES 22 A 397 LYS GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU SEQRES 23 A 397 THR ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO SEQRES 24 A 397 LEU GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU SEQRES 25 A 397 VAL LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA SEQRES 26 A 397 GLN LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER SEQRES 27 A 397 ALA PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA SEQRES 28 A 397 ALA SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP SEQRES 29 A 397 ALA GLN THR ASN SER SER SER ASN ASN ASN ASN ASN ASN SEQRES 30 A 397 ASN ASN ASN ASN LEU GLY ILE GLU GLY ARG ILE SER HIS SEQRES 31 A 397 MET GLU ASN LEU TYR PHE GLN HET GLC B 1 11 HET GLC B 2 11 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 HOH *207(H2 O) HELIX 1 AA1 GLY A 42 GLY A 58 1 17 HELIX 2 AA2 LYS A 68 ALA A 78 1 11 HELIX 3 AA3 ARG A 92 SER A 99 1 8 HELIX 4 AA4 ASP A 108 ASP A 113 1 6 HELIX 5 AA5 TYR A 116 VAL A 123 1 8 HELIX 6 AA6 THR A 154 GLU A 156 5 3 HELIX 7 AA7 GLU A 157 LYS A 166 1 10 HELIX 8 AA8 ALA A 167 GLY A 169 5 3 HELIX 9 AA9 GLU A 179 ASP A 190 1 12 HELIX 10 AB1 ASN A 211 ASN A 227 1 17 HELIX 11 AB2 ASP A 235 LYS A 245 1 11 HELIX 12 AB3 GLY A 254 TRP A 256 5 3 HELIX 13 AB4 ALA A 257 LYS A 265 1 9 HELIX 14 AB5 ASN A 298 TYR A 309 1 12 HELIX 15 AB6 THR A 312 LYS A 323 1 12 HELIX 16 AB7 LEU A 330 VAL A 338 1 9 HELIX 17 AB8 ASP A 340 GLY A 353 1 14 HELIX 18 AB9 GLN A 361 SER A 378 1 18 HELIX 19 AC1 THR A 382 SER A 395 1 14 SHEET 1 AA1 6 LYS A 60 GLU A 64 0 SHEET 2 AA1 6 LYS A 32 TRP A 36 1 N ILE A 35 O GLU A 64 SHEET 3 AA1 6 ILE A 85 ALA A 89 1 O PHE A 87 N TRP A 36 SHEET 4 AA1 6 PHE A 284 ILE A 292 -1 O SER A 289 N TRP A 88 SHEET 5 AA1 6 TYR A 132 GLU A 137 -1 N TYR A 132 O ALA A 290 SHEET 6 AA1 6 ALA A 327 VAL A 328 -1 O ALA A 327 N VAL A 136 SHEET 1 AA2 5 LYS A 60 GLU A 64 0 SHEET 2 AA2 5 LYS A 32 TRP A 36 1 N ILE A 35 O GLU A 64 SHEET 3 AA2 5 ILE A 85 ALA A 89 1 O PHE A 87 N TRP A 36 SHEET 4 AA2 5 PHE A 284 ILE A 292 -1 O SER A 289 N TRP A 88 SHEET 5 AA2 5 GLU A 354 ILE A 355 1 O GLU A 354 N VAL A 285 SHEET 1 AA3 2 ARG A 124 TYR A 125 0 SHEET 2 AA3 2 LYS A 128 LEU A 129 -1 O LYS A 128 N TYR A 125 SHEET 1 AA4 4 SER A 171 LEU A 173 0 SHEET 2 AA4 4 THR A 248 ASN A 253 1 O ALA A 249 N SER A 171 SHEET 3 AA4 4 SER A 140 ASN A 144 -1 N ASN A 144 O ALA A 249 SHEET 4 AA4 4 TYR A 268 THR A 271 -1 O GLY A 269 N TYR A 143 SHEET 1 AA5 2 LYS A 196 GLU A 198 0 SHEET 2 AA5 2 LYS A 201 ASP A 203 -1 O ASP A 203 N LYS A 196 LINK O4 GLC B 1 C1 GLC B 2 1555 1555 1.44 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 CONECT 2856 2857 2865 CONECT 2857 2856 2858 2862 CONECT 2858 2857 2859 2863 CONECT 2859 2858 2860 2864 CONECT 2860 2859 2861 2865 CONECT 2861 2860 2866 CONECT 2862 2857 CONECT 2863 2858 CONECT 2864 2859 2867 CONECT 2865 2856 2860 CONECT 2866 2861 CONECT 2867 2864 2868 2876 CONECT 2868 2867 2869 2873 CONECT 2869 2868 2870 2874 CONECT 2870 2869 2871 2875 CONECT 2871 2870 2872 2876 CONECT 2872 2871 2877 CONECT 2873 2868 CONECT 2874 2869 CONECT 2875 2870 CONECT 2876 2867 2871 CONECT 2877 2872 MASTER 167 0 2 19 19 0 0 6 3083 1 22 31 END