HEADER SUGAR BINDING PROTEIN 13-FEB-26 28QM TITLE MBP BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE-BINDING PERIPLASMIC PROTEIN,PIGG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DARPIN; COMPND 7 CHAIN: B; COMPND 8 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: MALE, JW3994; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MBP, DARPIN, SCAFFOLD, SUGAR BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,M.FAIRHEAD,O.GITTINS,F.VON DELFT, AUTHOR 2 J.ENDICOTT,A.C.W.PIKE,D.B.SAUER,M.MARTIN,L.S.DLAMINI REVDAT 1 25-FEB-26 28QM 0 JRNL AUTH D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,O.GITTINS,M.MARTIN, JRNL AUTH 2 J.ENDICOTT,M.FAIRHEAD,F.VON DELFT,A.C.W.PIKE,D.B.SAUER, JRNL AUTH 3 L.S.DLAMINI JRNL TITL AN ENGINEERED SYMMETRICAL SCAFFOLD SYSTEM ENABLES HIGH JRNL TITL 2 RESOLUTION IMAGING OF SMALL CARGO PROTEINS BY CRYO-ELECTRON JRNL TITL 3 MICROSCOPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 180813 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 28QM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1292153849. 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 BOUND TO DARPIN ON AN AHIR REMARK 245 DODECAMER SCAFFOLD SYSTEM.; REMARK 245 DARPIN; MBP 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 5050.00 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 29 CG CD OE1 OE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 ASN A 101 CG OD1 ND2 REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 GLU A 275 CG CD OE1 OE2 REMARK 470 ARG A 355 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 20 CG CD OE1 OE2 REMARK 470 ASP B 27 CG OD1 OD2 REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 61 CG CD OE1 OE2 REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 GLU B 166 CG CD OE1 OE2 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 ND2 ASN A 350 OE1 GLN A 356 2.19 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 ILE A 109 -58.98 -123.23 REMARK 500 GLU A 173 -158.69 -157.20 REMARK 500 SER A 370 30.26 -96.00 REMARK 500 ALA A 373 32.90 -146.88 REMARK 500 ASN B 107 31.70 -97.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-56750 RELATED DB: EMDB REMARK 900 MBP BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) DBREF1 28QM A 2 368 UNP A0ACD6BAW2_SERSF DBREF2 28QM A A0ACD6BAW2 3 369 DBREF 28QM B 13 171 PDB 28QM 28QM 13 171 SEQADV 28QM ALA A 83 UNP A0ACD6BAW ASP 84 CONFLICT SEQADV 28QM ALA A 84 UNP A0ACD6BAW LYS 85 CONFLICT SEQADV 28QM ALA A 240 UNP A0ACD6BAW LYS 241 CONFLICT SEQADV 28QM ALA A 360 UNP A0ACD6BAW GLU 361 CONFLICT SEQADV 28QM ALA A 363 UNP A0ACD6BAW LYS 364 CONFLICT SEQADV 28QM ALA A 364 UNP A0ACD6BAW ASP 365 CONFLICT SEQADV 28QM GLY A 369 UNP A0ACD6BAW EXPRESSION TAG SEQADV 28QM SER A 370 UNP A0ACD6BAW EXPRESSION TAG SEQADV 28QM HIS A 371 UNP A0ACD6BAW EXPRESSION TAG SEQADV 28QM HIS A 372 UNP A0ACD6BAW EXPRESSION TAG SEQADV 28QM ALA A 373 UNP A0ACD6BAW EXPRESSION TAG SEQADV 28QM HIS A 374 UNP A0ACD6BAW EXPRESSION TAG SEQRES 1 A 373 LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN GLY SEQRES 2 A 373 ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS LYS SEQRES 3 A 373 PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU HIS SEQRES 4 A 373 PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA ALA SEQRES 5 A 373 THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS ASP SEQRES 6 A 373 ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA GLU SEQRES 7 A 373 ILE THR PRO ALA ALA ALA PHE GLN ASP LYS LEU TYR PRO SEQRES 8 A 373 PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU ILE SEQRES 9 A 373 ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE TYR SEQRES 10 A 373 ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP GLU SEQRES 11 A 373 GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS GLY SEQRES 12 A 373 LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR PHE SEQRES 13 A 373 THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA PHE SEQRES 14 A 373 LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL GLY SEQRES 15 A 373 VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE LEU SEQRES 16 A 373 VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP THR SEQRES 17 A 373 ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY GLU SEQRES 18 A 373 THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER ASN SEQRES 19 A 373 ILE ASP THR SER ALA VAL ASN TYR GLY VAL THR VAL LEU SEQRES 20 A 373 PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL GLY SEQRES 21 A 373 VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN LYS SEQRES 22 A 373 GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU THR SEQRES 23 A 373 ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO LEU SEQRES 24 A 373 GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU ALA SEQRES 25 A 373 LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA GLN SEQRES 26 A 373 LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER ALA SEQRES 27 A 373 PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA ALA SEQRES 28 A 373 SER GLY ARG GLN THR VAL ASP ALA ALA LEU ALA ALA ALA SEQRES 29 A 373 GLN THR ASN GLY SER HIS HIS ALA HIS SEQRES 1 B 159 ASP LEU GLY ARG LYS LEU LEU GLU ALA ALA ARG ALA GLY SEQRES 2 B 159 GLN ASP ASP GLU VAL ARG ILE LEU MET ALA ASN GLY ALA SEQRES 3 B 159 ASP VAL ASN ALA ALA ASP ASN THR GLY THR THR PRO LEU SEQRES 4 B 159 HIS LEU ALA ALA TYR SER GLY HIS LEU GLU ILE VAL GLU SEQRES 5 B 159 VAL LEU LEU LYS HIS GLY ALA ASP VAL ASP ALA SER ASP SEQRES 6 B 159 VAL PHE GLY TYR THR PRO LEU HIS LEU ALA ALA TYR TRP SEQRES 7 B 159 GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS ASN GLY SEQRES 8 B 159 ALA ASP VAL ASN ALA MET ASP SER ASP GLY MET THR PRO SEQRES 9 B 159 LEU HIS LEU ALA ALA LYS TRP GLY TYR LEU GLU ILE VAL SEQRES 10 B 159 GLU VAL LEU LEU LYS HIS GLY ALA ASP VAL ASN ALA GLN SEQRES 11 B 159 ASP LYS PHE GLY LYS THR PRO LYS ASP LEU ALA ARG ASP SEQRES 12 B 159 ASN GLY ASN GLN TRP ILE TYR GLU LEU LEU GLU ALA ALA SEQRES 13 B 159 GLY ARG ALA HET EOH B 201 3 HETNAM EOH ETHANOL FORMUL 3 EOH C2 H6 O HELIX 1 AA1 GLY A 17 THR A 32 1 16 HELIX 2 AA2 LYS A 43 ALA A 53 1 11 HELIX 3 AA3 HIS A 65 SER A 74 1 10 HELIX 4 AA4 ALA A 83 ASP A 88 1 6 HELIX 5 AA5 TYR A 91 ASP A 96 1 6 HELIX 6 AA6 THR A 129 GLU A 131 5 3 HELIX 7 AA7 GLU A 132 ALA A 142 1 11 HELIX 8 AA8 GLU A 154 ASP A 165 1 12 HELIX 9 AA9 ASN A 186 ASN A 202 1 17 HELIX 10 AB1 ASP A 210 LYS A 220 1 11 HELIX 11 AB2 GLY A 229 TRP A 231 5 3 HELIX 12 AB3 ALA A 232 ALA A 240 1 9 HELIX 13 AB4 ASN A 273 TYR A 284 1 12 HELIX 14 AB5 THR A 287 LYS A 298 1 12 HELIX 15 AB6 LEU A 305 ALA A 313 1 9 HELIX 16 AB7 ASP A 315 GLY A 328 1 14 HELIX 17 AB8 GLN A 336 GLY A 354 1 19 HELIX 18 AB9 THR A 357 SER A 370 1 14 HELIX 19 AC1 LEU B 14 GLY B 25 1 12 HELIX 20 AC2 GLN B 26 MET B 34 1 9 HELIX 21 AC3 THR B 49 GLY B 58 1 10 HELIX 22 AC4 HIS B 59 HIS B 69 1 11 HELIX 23 AC5 THR B 82 GLY B 91 1 10 HELIX 24 AC6 HIS B 92 ASN B 102 1 11 HELIX 25 AC7 THR B 115 GLY B 124 1 10 HELIX 26 AC8 TYR B 125 HIS B 135 1 11 HELIX 27 AC9 THR B 148 ASN B 156 1 9 HELIX 28 AD1 ASN B 158 LEU B 165 1 8 HELIX 29 AD2 GLU B 166 ARG B 170 5 5 SHEET 1 AA1 6 VAL A 36 GLU A 39 0 SHEET 2 AA1 6 LEU A 8 TRP A 11 1 N ILE A 10 O THR A 37 SHEET 3 AA1 6 ILE A 60 ALA A 64 1 O PHE A 62 N TRP A 11 SHEET 4 AA1 6 PHE A 259 ILE A 267 -1 O SER A 264 N TRP A 63 SHEET 5 AA1 6 ALA A 106 GLU A 112 -1 N GLU A 112 O GLY A 261 SHEET 6 AA1 6 ALA A 302 VAL A 303 -1 O ALA A 302 N VAL A 111 SHEET 1 AA2 5 VAL A 36 GLU A 39 0 SHEET 2 AA2 5 LEU A 8 TRP A 11 1 N ILE A 10 O THR A 37 SHEET 3 AA2 5 ILE A 60 ALA A 64 1 O PHE A 62 N TRP A 11 SHEET 4 AA2 5 PHE A 259 ILE A 267 -1 O SER A 264 N TRP A 63 SHEET 5 AA2 5 GLU A 329 ILE A 330 1 O GLU A 329 N VAL A 260 SHEET 1 AA3 2 ARG A 99 TYR A 100 0 SHEET 2 AA3 2 LYS A 103 LEU A 104 -1 O LYS A 103 N TYR A 100 SHEET 1 AA4 3 MET A 225 ASN A 228 0 SHEET 2 AA4 3 SER A 115 ASN A 119 -1 N ILE A 117 O THR A 226 SHEET 3 AA4 3 TYR A 243 THR A 246 -1 O GLY A 244 N TYR A 118 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 4034 4035 4036 CONECT 4035 4034 CONECT 4036 4034 MASTER 152 0 1 29 16 0 0 6 4031 2 3 42 END