HEADER PROTEIN BINDING 03-JUN-24 9FKQ TITLE CRYO-EM STRUCTURE OF MBP HOMO-DIMER ASSEMBLED BY HOMO DI-GLUEBODY - TITLE 2 MBP LOCAL REFINEMENT 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 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 GLUEBODY, NANOBODY, CRYO-EM SPA, SMALL PROTEIN, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR G.YI,M.YE,D.MAMALIS,L.CARRIQUE,M.FAIRHEAD,H.LI,K.DUERR,P.ZHANG, AUTHOR 2 D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT REVDAT 2 24-DEC-25 9FKQ 1 JRNL REVDAT 1 18-JUN-25 9FKQ 0 JRNL AUTH G.YI,D.MAMALIS,M.YE,L.CARRIQUE,M.FAIRHEAD,H.LI,K.L.DUERR, JRNL AUTH 2 P.ZHANG,D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT JRNL TITL COVALENTLY CONSTRAINED 'DI-GEMBODIES' ENABLE PARALLEL JRNL TITL 2 STRUCTURE SOLUTIONS BY CRYO-EM. JRNL REF NAT.CHEM.BIOL. 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40817135 JRNL DOI 10.1038/S41589-025-01972-7 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, UCSF CHIMERAX, REMARK 3 PHENIX, CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5M13 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) : 2.450 REMARK 3 NUMBER OF PARTICLES : 197442 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 9FKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292139122. 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 : MBP HOMO-DIMER ASSEMBLED BY REMARK 245 HOMO DI-GLUEBODY GBMBP - MBP REMARK 245 LOCAL REFINEMENT 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 : 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) : 2600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 0 REMARK 465 LYS A 1 REMARK 465 ILE A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 367 REMARK 465 SER A 368 REMARK 465 GLY A 369 REMARK 465 GLY A 370 REMARK 465 SER A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 SER A 378 REMARK 465 SER A 379 REMARK 465 GLY A 380 REMARK 465 VAL A 381 REMARK 465 ASP A 382 REMARK 465 LEU A 383 REMARK 465 GLY A 384 REMARK 465 THR A 385 REMARK 465 GLU A 386 REMARK 465 ASN A 387 REMARK 465 LEU A 388 REMARK 465 TYR A 389 REMARK 465 PHE A 390 REMARK 465 GLN A 391 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 O GLU A 28 H GLY A 32 1.59 REMARK 500 OE1 GLN A 72 OH TYR A 99 1.99 REMARK 500 OE2 GLU A 214 ND2 ASN A 218 2.07 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 LYS A 256 77.91 -112.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50525 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MBP HOMO-DIMER ASSEMBLED BY HOMO DI-GLUEBODY - REMARK 900 MBP LOCAL REFINEMENT DBREF 9FKQ A 1 366 UNP P0AEX9 MALE_ECOLI 27 392 SEQADV 9FKQ MET A 0 UNP P0AEX9 INITIATING METHIONINE SEQADV 9FKQ ASN A 367 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ SER A 368 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLY A 369 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLY A 370 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ SER A 371 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 372 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 373 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 374 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 375 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 376 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ HIS A 377 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ SER A 378 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ SER A 379 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLY A 380 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ VAL A 381 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ ASP A 382 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ LEU A 383 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLY A 384 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ THR A 385 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLU A 386 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ ASN A 387 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ LEU A 388 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ TYR A 389 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ PHE A 390 UNP P0AEX9 EXPRESSION TAG SEQADV 9FKQ GLN A 391 UNP P0AEX9 EXPRESSION TAG SEQRES 1 A 392 MET LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN SEQRES 2 A 392 GLY ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS SEQRES 3 A 392 LYS PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU SEQRES 4 A 392 HIS PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA SEQRES 5 A 392 ALA THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS SEQRES 6 A 392 ASP ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA SEQRES 7 A 392 GLU ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR SEQRES 8 A 392 PRO PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU SEQRES 9 A 392 ILE ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE SEQRES 10 A 392 TYR ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP SEQRES 11 A 392 GLU GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS SEQRES 12 A 392 GLY LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR SEQRES 13 A 392 PHE THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA SEQRES 14 A 392 PHE LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL SEQRES 15 A 392 GLY VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE SEQRES 16 A 392 LEU VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP SEQRES 17 A 392 THR ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY SEQRES 18 A 392 GLU THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER SEQRES 19 A 392 ASN ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL SEQRES 20 A 392 LEU PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL SEQRES 21 A 392 GLY VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN SEQRES 22 A 392 LYS GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU SEQRES 23 A 392 THR ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO SEQRES 24 A 392 LEU GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU SEQRES 25 A 392 ALA LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA SEQRES 26 A 392 GLN LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER SEQRES 27 A 392 ALA PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA SEQRES 28 A 392 ALA SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP SEQRES 29 A 392 ALA GLN THR ASN SER GLY GLY SER HIS HIS HIS HIS HIS SEQRES 30 A 392 HIS SER SER GLY VAL ASP LEU GLY THR GLU ASN LEU TYR SEQRES 31 A 392 PHE GLN HELIX 1 AA1 GLY A 16 GLY A 32 1 17 HELIX 2 AA2 LYS A 42 ALA A 52 1 11 HELIX 3 AA3 HIS A 64 SER A 73 1 10 HELIX 4 AA4 ASP A 82 ASP A 87 1 6 HELIX 5 AA5 TYR A 90 VAL A 97 1 8 HELIX 6 AA6 GLU A 130 LYS A 142 1 13 HELIX 7 AA7 GLU A 153 ALA A 162 1 10 HELIX 8 AA8 ASN A 185 ASN A 201 1 17 HELIX 9 AA9 ASP A 209 LYS A 219 1 11 HELIX 10 AB1 GLY A 228 TRP A 230 5 3 HELIX 11 AB2 ALA A 231 LYS A 239 1 9 HELIX 12 AB3 ASN A 272 TYR A 283 1 12 HELIX 13 AB4 THR A 286 LYS A 297 1 12 HELIX 14 AB5 LEU A 304 ALA A 312 1 9 HELIX 15 AB6 ASP A 314 GLY A 327 1 14 HELIX 16 AB7 GLN A 335 SER A 352 1 18 HELIX 17 AB8 THR A 356 THR A 366 1 11 SHEET 1 AA1 6 VAL A 35 GLU A 38 0 SHEET 2 AA1 6 LEU A 7 TRP A 10 1 N ILE A 9 O THR A 36 SHEET 3 AA1 6 ILE A 59 ALA A 63 1 O ILE A 59 N TRP A 10 SHEET 4 AA1 6 PHE A 258 ILE A 266 -1 O SER A 263 N TRP A 62 SHEET 5 AA1 6 ALA A 105 GLU A 111 -1 N TYR A 106 O ALA A 264 SHEET 6 AA1 6 ALA A 301 VAL A 302 -1 O ALA A 301 N VAL A 110 SHEET 1 AA2 5 VAL A 35 GLU A 38 0 SHEET 2 AA2 5 LEU A 7 TRP A 10 1 N ILE A 9 O THR A 36 SHEET 3 AA2 5 ILE A 59 ALA A 63 1 O ILE A 59 N TRP A 10 SHEET 4 AA2 5 PHE A 258 ILE A 266 -1 O SER A 263 N TRP A 62 SHEET 5 AA2 5 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259 SHEET 1 AA3 2 ARG A 98 TYR A 99 0 SHEET 2 AA3 2 LYS A 102 LEU A 103 -1 O LYS A 102 N TYR A 99 SHEET 1 AA4 4 SER A 145 LEU A 147 0 SHEET 2 AA4 4 THR A 222 ASN A 227 1 O ALA A 223 N SER A 145 SHEET 3 AA4 4 SER A 114 ASN A 118 -1 N ASN A 118 O ALA A 223 SHEET 4 AA4 4 TYR A 242 THR A 245 -1 O GLY A 243 N TYR A 117 SHEET 1 AA5 2 LYS A 170 GLU A 172 0 SHEET 2 AA5 2 LYS A 175 ASP A 177 -1 O LYS A 175 N GLU A 172 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 TER 5603 THR A 366 MASTER 171 0 0 17 19 0 0 6 2807 1 0 31 END