HEADER SUGAR BINDING PROTEIN 14-NOV-24 9KL3 TITLE CRYOEM STRUCTURE OF PLEUROCYBELLA PORRIGENS LECTIN (PPL) IN COMPLEX TITLE 2 WITH GALNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROCYBELLA PORRIGENS; SOURCE 3 ORGANISM_TAXID: 71910; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TREFOIL, LECTIN, SUGAR BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.ISHIMOTO,D.ADACHI,H.KAWABATA,S.Y.PARK,J.R.H.TAME,K.KAMATA REVDAT 3 31-DEC-25 9KL3 1 JRNL REVDAT 2 17-DEC-25 9KL3 1 JRNL REVDAT 1 19-NOV-25 9KL3 0 JRNL AUTH D.ADACHI,N.ISHIMOTO,K.MIZUTANI,K.TAKAHASHI,R.KUBOTA, JRNL AUTH 2 H.KAWABATA,S.Y.PARK,L.VANDEBROEK,A.R.D.VOET,M.YAMADA, JRNL AUTH 3 Y.OZEKI,Y.FUJII,H.FUJITA,J.R.H.TAME,K.KAMATA JRNL TITL CRYSTAL AND CRYO-EM STRUCTURE OF PPL, A NOVEL HEXAMERIC JRNL TITL 2 R-TYPE LECTIN FROM THE POISONOUS MUSHROOM PLEUROCYBELLA JRNL TITL 3 PORRIGENS. JRNL REF GLYCOBIOLOGY V. 36 2025 JRNL REFN ESSN 1460-2423 JRNL PMID 41342409 JRNL DOI 10.1093/GLYCOB/CWAF082 REMARK 2 REMARK 2 RESOLUTION. 3.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, SERIALEM, CRYOSPARC, COOT, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, 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) : 3.240 REMARK 3 NUMBER OF PARTICLES : 74285 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 9KL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300050751. 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 : PLEUROCYBELLA PORRIGENS LECTIN REMARK 245 IN COMPLEX WITH GALNAC 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 : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1542 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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) : 4741.00 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) : 200 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 40 -169.79 -79.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62399 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF PLEUROCYBELLA PORRIGENS LECTIN (PPL) IN COMPLEX REMARK 900 WITH GALNAC DBREF 9KL3 A 1 137 UNP B6ZK51 B6ZK51_9AGAR 1 137 SEQADV 9KL3 GLY A -2 UNP B6ZK51 EXPRESSION TAG SEQADV 9KL3 SER A -1 UNP B6ZK51 EXPRESSION TAG SEQADV 9KL3 HIS A 0 UNP B6ZK51 EXPRESSION TAG SEQRES 1 A 140 GLY SER HIS MET SER ILE PRO ALA GLY THR TYR LEU ILE SEQRES 2 A 140 ARG ASN VAL GLU SER ASN LEU TYR LEU ASP LEU ARG GLY SEQRES 3 A 140 SER ASN PRO ALA PRO GLY THR ASP ALA ILE VAL TRP GLY SEQRES 4 A 140 ARG THR GLY ASN ASN ASN GLN ARG TRP ILE VAL THR THR SEQRES 5 A 140 HIS SER ASP GLY THR ARG THR LEU GLU THR VAL GLY ILE SEQRES 6 A 140 ASN SER SER ALA PHE ILE ALA THR ILE GLN PRO GLY GLY SEQRES 7 A 140 ARG VAL THR GLY HIS PRO ASN ASN GLU THR ARG LEU THR SEQRES 8 A 140 ILE THR ASN VAL ASN PRO GLY GLU TYR SER ILE SER ALA SEQRES 9 A 140 GLY GLY LEU LEU TRP LEU ALA ASN THR PRO VAL GLY GLY SEQRES 10 A 140 THR GLY GLU ALA VAL THR LEU GLN ALA ALA GLY GLY ALA SEQRES 11 A 140 ALA GLN SER LEU TRP VAL PHE GLU ALA VAL HET A2G A 201 15 HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 2 A2G C8 H15 N O6 HELIX 1 AA1 GLY A 23 ASN A 25 5 3 SHEET 1 AA1 6 ARG A 55 THR A 59 0 SHEET 2 AA1 6 TRP A 45 THR A 49 -1 N ILE A 46 O GLU A 58 SHEET 3 AA1 6 GLY A 6 ASN A 12 -1 N GLY A 6 O VAL A 47 SHEET 4 AA1 6 LEU A 17 LEU A 21 -1 O LEU A 17 N ASN A 12 SHEET 5 AA1 6 THR A 30 TRP A 35 -1 O ILE A 33 N ASP A 20 SHEET 6 AA1 6 THR A 78 GLY A 79 -1 O GLY A 79 N THR A 30 SHEET 1 AA2 4 ARG A 55 THR A 59 0 SHEET 2 AA2 4 TRP A 45 THR A 49 -1 N ILE A 46 O GLU A 58 SHEET 3 AA2 4 GLY A 6 ASN A 12 -1 N GLY A 6 O VAL A 47 SHEET 4 AA2 4 TRP A 132 ALA A 136 -1 O GLU A 135 N LEU A 9 SHEET 1 AA3 3 THR A 88 ASN A 91 0 SHEET 2 AA3 3 TYR A 97 ALA A 101 -1 O SER A 100 N THR A 88 SHEET 3 AA3 3 LEU A 104 LEU A 105 -1 O LEU A 104 N ALA A 101 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 TER 1012 VAL A 137 HETATM 1013 O5 A2G A 201 111.167 94.339 114.982 1.00 24.35 O HETATM 1014 C1 A2G A 201 112.248 94.848 114.133 1.00 24.35 C HETATM 1015 O1 A2G A 201 113.104 93.815 113.836 1.00 24.35 O HETATM 1016 C2 A2G A 201 113.041 95.972 114.809 1.00 24.35 C HETATM 1017 N2 A2G A 201 114.231 96.286 113.976 1.00 24.35 N HETATM 1018 C3 A2G A 201 113.505 95.599 116.175 1.00 24.35 C HETATM 1019 O3 A2G A 201 114.053 96.793 116.821 1.00 24.35 O HETATM 1020 C4 A2G A 201 112.422 95.062 117.022 1.00 24.35 C HETATM 1021 O4 A2G A 201 111.507 96.132 117.337 1.00 24.35 O HETATM 1022 C5 A2G A 201 111.648 93.940 116.336 1.00 24.35 C HETATM 1023 C6 A2G A 201 110.475 93.586 117.179 1.00 24.35 C HETATM 1024 O6 A2G A 201 110.356 92.191 117.207 1.00 24.35 O HETATM 1025 C7 A2G A 201 114.222 97.435 113.092 1.00 24.35 C HETATM 1026 O7 A2G A 201 113.264 98.128 113.029 1.00 24.35 O HETATM 1027 C8 A2G A 201 115.448 97.753 112.240 1.00 24.35 C CONECT 1013 1014 1022 CONECT 1014 1013 1015 1016 CONECT 1015 1014 CONECT 1016 1014 1017 1018 CONECT 1017 1016 1025 CONECT 1018 1016 1019 1020 CONECT 1019 1018 CONECT 1020 1018 1021 1022 CONECT 1021 1020 CONECT 1022 1013 1020 1023 CONECT 1023 1022 1024 CONECT 1024 1023 CONECT 1025 1017 1026 1027 CONECT 1026 1025 CONECT 1027 1025 MASTER 129 0 1 1 13 0 0 6 1026 1 15 11 END