HEADER IMMUNE SYSTEM 27-AUG-25 9XZX TITLE STAPHYLOCOCCAL ENTEROTOXIN C IN COMPLEX WITH NB C107 AND NB C112 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENTEROTOXIN TYPE C-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SEC2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NB C107; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NB C112; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: ENTC2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 9 ORGANISM_TAXID: 9844; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 14 ORGANISM_TAXID: 9844; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, VHH, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR W.HANG,J.KIM,D.J.TAYLOR,Y.SHI REVDAT 2 03-JUN-26 9XZX 1 JRNL REVDAT 1 06-MAY-26 9XZX 0 JRNL AUTH Y.J.J.KIM,N.R.WALTON,W.HUANG,M.LEE,Y.XIANG,Z.SANG,C.SUSSMAN, JRNL AUTH 2 S.K.L.MOORE,D.J.TAYLOR,K.CHEN,J.L.HOOK,J.K.MCCORMICK,Y.SHI JRNL TITL MULTIVALENT NANOBODIES FOR POTENT AND BROAD NEUTRALIZATION JRNL TITL 2 OF STAPHYLOCOCCUS AUREUS TOXINS. JRNL REF NAT COMMUN V. 17 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42161902 JRNL DOI 10.1038/S41467-026-73120-1 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 189726 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9XZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000299642. 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 : HSA-NB33-NB77-NB125-N42 COMPLEX 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 GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 GLN C 17 REMARK 465 GLN D 17 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 OD2 ASP A 107 NE2 HIS A 146 1.32 REMARK 500 O TYR A 136 HE22 GLN A 181 1.49 REMARK 500 OD1 ASN A 162 H THR A 260 1.54 REMARK 500 HG1 THR A 207 OG1 THR A 259 1.56 REMARK 500 H ASP A 79 O TYR A 85 1.56 REMARK 500 H LYS D 102 OD2 ASP D 105 1.56 REMARK 500 H GLY D 31 O LEU D 101 1.58 REMARK 500 O TYR A 160 H LEU A 258 1.59 REMARK 500 HH12 ARG C 82 OD2 ASP C 105 1.59 REMARK 500 OH TYR A 50 O THR C 116 1.94 REMARK 500 OD2 ASP A 184 OH TYR A 241 1.96 REMARK 500 OG1 THR A 173 OE2 GLU A 182 2.04 REMARK 500 OG SER A 39 OE2 GLU A 206 2.05 REMARK 500 OG1 THR A 207 OG1 THR A 259 2.09 REMARK 500 OG1 THR A 90 O GLY A 137 2.12 REMARK 500 OG1 THR D 108 OE1 GLN D 135 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 TYR A 56 142.74 -171.31 REMARK 500 TRP A 221 148.36 -172.21 REMARK 500 GLN D 117 19.63 59.81 REMARK 500 TRP D 118 -0.68 71.38 REMARK 500 THR D 123 10.85 -140.46 REMARK 500 ARG D 124 -65.82 62.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD2 REMARK 620 2 HIS A 142 ND1 68.9 REMARK 620 3 HIS A 146 ND1 89.4 141.2 REMARK 620 4 HIS A 146 NE2 38.4 95.4 52.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-72377 RELATED DB: EMDB REMARK 900 STAPHYLOCOCCAL ENTEROTOXIN C IN COMPLEX WITH NB C107 AND NB C112 DBREF 9XZX A 28 263 UNP P34071 ENTC2_STAAU 31 266 DBREF 9XZX C 17 132 PDB 9XZX 9XZX 17 132 DBREF 9XZX D 17 140 PDB 9XZX 9XZX 17 140 SEQRES 1 A 236 PRO ASP PRO THR PRO ASP GLU LEU HIS LYS SER SER GLU SEQRES 2 A 236 PHE THR GLY THR MET GLY ASN MET LYS TYR LEU TYR ASP SEQRES 3 A 236 ASP HIS TYR VAL SER ALA THR LYS VAL MET SER VAL ASP SEQRES 4 A 236 LYS PHE LEU ALA HIS ASP LEU ILE TYR ASN ILE SER ASP SEQRES 5 A 236 LYS LYS LEU LYS ASN TYR ASP LYS VAL LYS THR GLU LEU SEQRES 6 A 236 LEU ASN GLU ASP LEU ALA LYS LYS TYR LYS ASP GLU VAL SEQRES 7 A 236 VAL ASP VAL TYR GLY SER ASN TYR TYR VAL ASN CYS TYR SEQRES 8 A 236 PHE SER SER LYS ASP ASN VAL GLY LYS VAL THR GLY GLY SEQRES 9 A 236 LYS THR CYS MET TYR GLY GLY ILE THR LYS HIS GLU GLY SEQRES 10 A 236 ASN HIS PHE ASP ASN GLY ASN LEU GLN ASN VAL LEU ILE SEQRES 11 A 236 ARG VAL TYR GLU ASN LYS ARG ASN THR ILE SER PHE GLU SEQRES 12 A 236 VAL GLN THR ASP LYS LYS SER VAL THR ALA GLN GLU LEU SEQRES 13 A 236 ASP ILE LYS ALA ARG ASN PHE LEU ILE ASN LYS LYS ASN SEQRES 14 A 236 LEU TYR GLU PHE ASN SER SER PRO TYR GLU THR GLY TYR SEQRES 15 A 236 ILE LYS PHE ILE GLU ASN ASN GLY ASN THR PHE TRP TYR SEQRES 16 A 236 ASP MET MET PRO ALA PRO GLY ASP LYS PHE ASP GLN SER SEQRES 17 A 236 LYS TYR LEU MET MET TYR ASN ASP ASN LYS THR VAL ASP SEQRES 18 A 236 SER LYS SER VAL LYS ILE GLU VAL HIS LEU THR THR LYS SEQRES 19 A 236 ASN GLY SEQRES 1 C 116 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA PRO SER GLY SEQRES 3 C 116 SER THR SER GLY ILE TYR ALA SER GLY TRP TYR ARG GLN SEQRES 4 C 116 VAL PRO GLY LYS PRO GLN GLU TRP LEU ALA ASP ILE SER SEQRES 5 C 116 ARG GLY GLY SER THR LYS TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 116 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 C 116 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 116 THR TYR TYR CYS ARG VAL ILE ASP THR LEU GLY ALA GLU SEQRES 9 C 116 TYR ARG GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 D 124 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 124 ALA GLY GLY SER LEU ARG LEU SER CYS THR ALA SER GLU SEQRES 3 D 124 ARG MET TYR GLY ILE GLU MET GLY TRP PHE ARG GLN ALA SEQRES 4 D 124 PRO GLY LYS GLU ARG GLU LEU VAL ALA ALA ILE THR TRP SEQRES 5 D 124 SER GLY VAL VAL SER HIS LEU GLN GLU SER VAL LYS GLY SEQRES 6 D 124 ARG PHE THR ILE SER ARG ASP ASN PRO LYS LYS THR VAL SEQRES 7 D 124 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 D 124 THR TYR TYR CYS ALA GLY HIS ARG LEU GLN TRP ALA SER SEQRES 9 D 124 GLY TYR THR ARG HIS ASP TYR GLY SER TRP GLY GLN GLY SEQRES 10 D 124 THR GLN VAL THR VAL SER SER HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 AA1 MET A 45 LEU A 51 1 7 HELIX 2 AA2 ASN A 94 ASP A 103 1 10 HELIX 3 AA3 PHE A 147 ASN A 151 5 5 HELIX 4 AA4 ALA A 180 ASN A 196 1 17 HELIX 5 AA5 ASP A 233 MET A 239 1 7 HELIX 6 AA6 MET A 240 ASN A 242 5 3 HELIX 7 AA7 ASP C 77 LYS C 80 5 4 HELIX 8 AA8 LYS C 102 THR C 106 5 5 HELIX 9 AA9 GLU D 77 LYS D 80 5 4 HELIX 10 AB1 LYS D 102 THR D 106 5 5 SHEET 1 AA1 3 VAL A 57 VAL A 62 0 SHEET 2 AA1 3 VAL A 106 GLY A 110 -1 O VAL A 106 N VAL A 62 SHEET 3 AA1 3 ILE A 139 LYS A 141 -1 O THR A 140 N ASP A 107 SHEET 1 AA2 5 SER A 64 ASP A 66 0 SHEET 2 AA2 5 ASP A 72 TYR A 75 -1 O ILE A 74 N ASP A 66 SHEET 3 AA2 5 TYR A 85 GLU A 91 -1 O THR A 90 N LEU A 73 SHEET 4 AA2 5 GLY A 131 TYR A 136 1 O GLY A 131 N ASP A 86 SHEET 5 AA2 5 ASN A 112 TYR A 113 -1 N TYR A 113 O CYS A 134 SHEET 1 AA3 5 ARG A 164 THR A 173 0 SHEET 2 AA3 5 GLN A 153 GLU A 161 -1 N ILE A 157 O PHE A 169 SHEET 3 AA3 5 LYS A 253 THR A 259 1 O LEU A 258 N TYR A 160 SHEET 4 AA3 5 THR A 207 ILE A 213 -1 N LYS A 211 O GLU A 255 SHEET 5 AA3 5 THR A 219 ASP A 223 -1 O TYR A 222 N ILE A 210 SHEET 1 AA4 2 SER A 177 THR A 179 0 SHEET 2 AA4 2 THR A 246 ASP A 248 -1 O VAL A 247 N VAL A 178 SHEET 1 AA5 4 GLN C 19 SER C 23 0 SHEET 2 AA5 4 LEU C 34 SER C 41 -1 O ALA C 39 N VAL C 21 SHEET 3 AA5 4 THR C 93 MET C 98 -1 O VAL C 94 N CYS C 38 SHEET 4 AA5 4 PHE C 83 ASP C 88 -1 N ASP C 88 O THR C 93 SHEET 1 AA6 6 LEU C 27 VAL C 28 0 SHEET 2 AA6 6 THR C 126 VAL C 130 1 O THR C 129 N VAL C 28 SHEET 3 AA6 6 ALA C 107 ASP C 115 -1 N TYR C 109 O THR C 126 SHEET 4 AA6 6 ILE C 47 GLN C 55 -1 N GLN C 55 O THR C 108 SHEET 5 AA6 6 GLU C 62 ILE C 67 -1 O GLU C 62 N ARG C 54 SHEET 6 AA6 6 THR C 73 TYR C 75 -1 O LYS C 74 N ASP C 66 SHEET 1 AA7 4 LEU C 27 VAL C 28 0 SHEET 2 AA7 4 THR C 126 VAL C 130 1 O THR C 129 N VAL C 28 SHEET 3 AA7 4 ALA C 107 ASP C 115 -1 N TYR C 109 O THR C 126 SHEET 4 AA7 4 GLU C 120 ARG C 122 -1 O TYR C 121 N VAL C 113 SHEET 1 AA8 4 LEU D 20 SER D 23 0 SHEET 2 AA8 4 LEU D 34 ALA D 40 -1 O THR D 39 N VAL D 21 SHEET 3 AA8 4 THR D 93 MET D 98 -1 O MET D 98 N LEU D 34 SHEET 4 AA8 4 PHE D 83 ASP D 88 -1 N ASP D 88 O THR D 93 SHEET 1 AA9 6 LEU D 27 GLN D 29 0 SHEET 2 AA9 6 THR D 134 SER D 139 1 O THR D 137 N VAL D 28 SHEET 3 AA9 6 ALA D 107 HIS D 114 -1 N ALA D 107 O VAL D 136 SHEET 4 AA9 6 GLU D 48 GLN D 54 -1 N GLN D 54 O THR D 108 SHEET 5 AA9 6 GLU D 61 ILE D 66 -1 O ILE D 66 N MET D 49 SHEET 6 AA9 6 VAL D 72 LEU D 75 -1 O HIS D 74 N ALA D 65 SHEET 1 AB1 4 LEU D 27 GLN D 29 0 SHEET 2 AB1 4 THR D 134 SER D 139 1 O THR D 137 N VAL D 28 SHEET 3 AB1 4 ALA D 107 HIS D 114 -1 N ALA D 107 O VAL D 136 SHEET 4 AB1 4 SER D 129 TRP D 130 -1 O SER D 129 N GLY D 113 SSBOND 1 CYS A 117 CYS A 134 1555 1555 2.03 SSBOND 2 CYS C 38 CYS C 111 1555 1555 2.04 SSBOND 3 CYS D 38 CYS D 111 1555 1555 2.03 LINK OD2 ASP A 107 ZN ZN A 301 1555 1555 2.00 LINK ND1 HIS A 142 ZN ZN A 301 1555 1555 2.02 LINK ND1 HIS A 146 ZN ZN A 301 1555 1555 2.64 LINK NE2 HIS A 146 ZN ZN A 301 1555 1555 2.02 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 1288 7359 CONECT 1439 1685 CONECT 1685 1439 CONECT 1803 7359 CONECT 1856 7359 CONECT 1859 7359 CONECT 4059 5167 CONECT 5167 4059 CONECT 5763 6926 CONECT 6926 5763 CONECT 7359 1288 1803 1856 1859 MASTER 168 0 1 10 43 0 0 6 3734 3 11 38 END