HEADER IMMUNE SYSTEM 28-JAN-25 9I5N TITLE SINGLE PARTICLE CRYO ELECTRON MICROSCOPY OF A FAB FRAGMENT BOUND TO TITLE 2 RECOMBINANT HUMAN CD40 LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB20 HEAVY CHAIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FAB FRAGMENT HEAVY CHAIN, ONLY THE VARIABLE REGION; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FAB20 LIGHT CHAIN; COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: FAB FRAGMENT LIGHT CHAIN, ONLY THE VARIABLE REGION; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: CD40 LIGAND, SOLUBLE FORM; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: SCD40L; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: ONE SUBUNIT OF EXTRACELLULAR DOMAIN OF TRIMERIC HCD40L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PCDNA3.4; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PCDNA3.4; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: CD40LG, CD40L, TNFSF5, TRAP; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CD40 LIGAND INHIBITOR, CD154 INHIBITOR, AUTOIMMUNITY, FAB FRAGMENT, KEYWDS 2 IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR E.L.KRISTOFFERSEN,T.SCHINKEL,E.S.ANDERSEN REVDAT 1 25-FEB-26 9I5N 0 JRNL AUTH K.PEDERSEN,N.S.LAURSEN,K.GREEN,A.G.HANSEN,Y.PALARASAH, JRNL AUTH 2 A.B.ROVSING,E.L.KRISTOFFERSEN,T.SCHINKEL,E.S.ANDERSEN, JRNL AUTH 3 J.VALERO,L.CIVIT,A.TROLDBORG,S.E.DEGN,S.THIEL JRNL TITL CURBING AUTOIMMUNITY: A FAB FRAGMENT TARGETING CD40-CD40L JRNL TITL 2 HALTS B-CELL ACTIVATION AND DIFFERENTIATION JRNL REF EUR.J.IMMUNOL. 2026 JRNL REFN ISSN 0014-2980 JRNL DOI 10.1002/EJI.70158 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, ISOLDE, REMARK 3 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 311649 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 9I5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292144669. 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 : INCUBATED SAMPLE CONTAINING FAB REMARK 245 FRAGMENT AND RECOMBINANT HUMAN REMARK 245 CD40 LIGAND. 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 : BUFFER: 1X PBS, 1 MM MGCL2; 1:3 REMARK 245 MOLAR RATIO, 2.47 UM RHCD40L AND 7.42 UM FAB20 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5673 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 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 : 2.70 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 : 130000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C 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 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 SER B 19 77.63 -116.79 REMARK 500 SER A 26 31.99 -71.10 REMARK 500 ASP A 31 -62.23 -90.58 REMARK 500 MET A 33 108.58 -163.08 REMARK 500 ASN A 52 0.75 90.35 REMARK 500 SER A 60 23.37 -76.13 REMARK 500 THR C 134 40.41 -85.86 REMARK 500 GLU C 142 98.12 -62.56 REMARK 500 ASN C 150 -161.64 -165.55 REMARK 500 GLU C 202 108.36 -58.31 REMARK 500 LEU C 205 -124.21 -79.93 REMARK 500 PRO C 233 41.21 -75.16 REMARK 500 ASP C 243 81.18 -155.17 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD1 REMARK 620 2 ASP A 31 OD2 63.6 REMARK 620 3 ASP A 92 OD2 96.7 156.3 REMARK 620 4 GLU C 202 OE1 139.8 96.3 107.4 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-52634 RELATED DB: EMDB REMARK 900 SINGLE PARTICLE CRYO ELECTRON MICROSCOPY OF A FAB FRAGMENT BOUND TO REMARK 900 RECOMBINANT HUMAN CD40 LIGAND DBREF 9I5N B 1 118 PDB 9I5N 9I5N 1 118 DBREF 9I5N A 1 107 PDB 9I5N 9I5N 1 107 DBREF 9I5N C 119 261 UNP P29965 CD40L_HUMAN 119 261 SEQRES 1 B 118 GLN VAL GLN LEU LYS GLN SER GLY PRO GLY LEU VAL GLN SEQRES 2 B 118 PRO SER GLN SER LEU SER ILE THR CYS THR VAL SER GLY SEQRES 3 B 118 PHE SER LEU THR GLY TYR GLY VAL HIS TRP VAL ARG GLN SEQRES 4 B 118 SER PRO GLY LYS GLY LEU GLU TRP LEU GLY MET ILE TRP SEQRES 5 B 118 SER GLY GLY SER THR ASP TYR ASN ALA ALA PHE ILE SER SEQRES 6 B 118 ARG LEU SER ILE SER LYS ASP SER SER LYS SER GLN VAL SEQRES 7 B 118 PHE PHE LYS MET ASN SER LEU GLN ALA ASN ASP THR ALA SEQRES 8 B 118 ILE TYR TYR CYS ALA ARG SER SER GLY ASN TYR GLY GLU SEQRES 9 B 118 ASP ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR SEQRES 10 B 118 VAL SEQRES 1 A 107 GLU THR THR VAL THR GLN SER PRO ALA SER LEU SER MET SEQRES 2 A 107 ALA ILE GLY GLU LYS VAL THR ILE ARG CYS ILE THR SER SEQRES 3 A 107 THR ASP ILE ASP ASP ASP MET ASN TRP TYR GLN GLN LYS SEQRES 4 A 107 PRO GLY GLU PRO PRO GLU LEU LEU ILE SER GLU ASP ASN SEQRES 5 A 107 THR LEU ARG PRO GLY VAL PRO SER ARG PHE SER SER SER SEQRES 6 A 107 GLY TYR GLY THR ASP PHE VAL PHE ALA ILE GLU ASN MET SEQRES 7 A 107 LEU PRO GLU ASP VAL ALA ASP TYR PHE CYS LEU GLN SER SEQRES 8 A 107 ASP ASN LEU PRO PHE THR PHE GLY SER GLY THR LYS LEU SEQRES 9 A 107 GLU ILE LYS SEQRES 1 C 143 ASN PRO GLN ILE ALA ALA HIS VAL ILE SER GLU ALA SER SEQRES 2 C 143 SER LYS THR THR SER VAL LEU GLN TRP ALA GLU LYS GLY SEQRES 3 C 143 TYR TYR THR MET SER ASN ASN LEU VAL THR LEU GLU ASN SEQRES 4 C 143 GLY LYS GLN LEU THR VAL LYS ARG GLN GLY LEU TYR TYR SEQRES 5 C 143 ILE TYR ALA GLN VAL THR PHE CYS SER ASN ARG GLU ALA SEQRES 6 C 143 SER SER GLN ALA PRO PHE ILE ALA SER LEU CYS LEU LYS SEQRES 7 C 143 SER PRO GLY ARG PHE GLU ARG ILE LEU LEU ARG ALA ALA SEQRES 8 C 143 ASN THR HIS SER SER ALA LYS PRO CYS GLY GLN GLN SER SEQRES 9 C 143 ILE HIS LEU GLY GLY VAL PHE GLU LEU GLN PRO GLY ALA SEQRES 10 C 143 SER VAL PHE VAL ASN VAL THR ASP PRO SER GLN VAL SER SEQRES 11 C 143 HIS GLY THR GLY PHE THR SER PHE GLY LEU LEU LYS LEU HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *13(H2 O) HELIX 1 AA1 ASN B 60 ILE B 64 5 5 HELIX 2 AA2 GLN B 86 THR B 90 5 5 HELIX 3 AA3 LEU A 79 VAL A 83 5 5 SHEET 1 AA1 4 GLN B 6 SER B 7 0 SHEET 2 AA1 4 SER B 19 THR B 23 -1 O THR B 21 N SER B 7 SHEET 3 AA1 4 GLN B 77 LYS B 81 -1 O VAL B 78 N CYS B 22 SHEET 4 AA1 4 SER B 68 ASP B 72 -1 N SER B 68 O LYS B 81 SHEET 1 AA2 4 GLY B 44 TRP B 47 0 SHEET 2 AA2 4 VAL B 34 SER B 40 -1 N SER B 40 O GLY B 44 SHEET 3 AA2 4 ALA B 91 SER B 98 -1 O TYR B 94 N VAL B 37 SHEET 4 AA2 4 MET B 107 TRP B 110 -1 O TYR B 109 N ARG B 97 SHEET 1 AA3 4 GLY B 44 TRP B 47 0 SHEET 2 AA3 4 VAL B 34 SER B 40 -1 N SER B 40 O GLY B 44 SHEET 3 AA3 4 ALA B 91 SER B 98 -1 O TYR B 94 N VAL B 37 SHEET 4 AA3 4 THR B 114 VAL B 116 -1 O THR B 114 N TYR B 93 SHEET 1 AA4 4 VAL A 4 SER A 7 0 SHEET 2 AA4 4 VAL A 19 THR A 25 -1 O ARG A 22 N SER A 7 SHEET 3 AA4 4 ASP A 70 ILE A 75 -1 O PHE A 73 N ILE A 21 SHEET 4 AA4 4 PHE A 62 GLY A 66 -1 N SER A 63 O ALA A 74 SHEET 1 AA5 5 SER A 10 MET A 13 0 SHEET 2 AA5 5 THR A 102 ILE A 106 1 O GLU A 105 N LEU A 11 SHEET 3 AA5 5 ASP A 85 LEU A 89 -1 N TYR A 86 O THR A 102 SHEET 4 AA5 5 ASN A 34 GLN A 38 -1 N TYR A 36 O PHE A 87 SHEET 5 AA5 5 GLU A 45 ILE A 48 -1 O GLU A 45 N GLN A 37 SHEET 1 AA6 3 TRP C 140 ALA C 141 0 SHEET 2 AA6 3 ALA C 123 SER C 128 -1 N ILE C 127 O ALA C 141 SHEET 3 AA6 3 THR C 147 MET C 148 -1 O THR C 147 N HIS C 125 SHEET 1 AA7 5 TRP C 140 ALA C 141 0 SHEET 2 AA7 5 ALA C 123 SER C 128 -1 N ILE C 127 O ALA C 141 SHEET 3 AA7 5 SER C 255 LYS C 260 -1 O LEU C 258 N ALA C 124 SHEET 4 AA7 5 GLY C 167 SER C 179 -1 N GLN C 174 O SER C 255 SHEET 5 AA7 5 GLY C 219 LEU C 231 -1 O LEU C 225 N ALA C 173 SHEET 1 AA8 5 VAL C 153 GLU C 156 0 SHEET 2 AA8 5 GLN C 160 VAL C 163 -1 O THR C 162 N THR C 154 SHEET 3 AA8 5 SER C 236 VAL C 241 -1 O VAL C 237 N LEU C 161 SHEET 4 AA8 5 PHE C 189 LYS C 196 -1 N LYS C 196 O SER C 236 SHEET 5 AA8 5 ARG C 207 ASN C 210 -1 O ALA C 208 N ALA C 191 SSBOND 1 CYS B 22 CYS B 95 1555 1555 2.01 SSBOND 2 CYS A 23 CYS A 88 1555 1555 2.04 SSBOND 3 CYS C 178 CYS C 218 1555 1555 2.03 LINK OD1 ASP A 31 MG MG A 201 1555 1555 2.03 LINK OD2 ASP A 31 MG MG A 201 1555 1555 2.02 LINK OD2 ASP A 92 MG MG A 201 1555 1555 1.87 LINK MG MG A 201 OE1 GLU C 202 1555 1555 1.87 CISPEP 1 SER A 7 PRO A 8 0 -2.59 CISPEP 2 LEU A 94 PRO A 95 0 1.27 CISPEP 3 LYS C 216 PRO C 217 0 -9.71 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 323 1433 CONECT 1433 323 CONECT 2094 3076 CONECT 2206 5560 CONECT 2207 5560 CONECT 3076 2094 CONECT 3135 5560 CONECT 4323 4930 CONECT 4679 5560 CONECT 4930 4323 CONECT 5560 2206 2207 3135 4679 MASTER 148 0 1 3 34 0 0 6 2833 3 11 30 END