HEADER IMMUNE SYSTEM 06-MAR-26 11OU TITLE OMI32 GERMLINE FAB IN COMPLEX WITH LC-KAPPA VHH COMPND MOL_ID: 1; COMPND 2 MOLECULE: LC-KAPPA VHH; COMPND 3 CHAIN: K; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: OMI32 GERMLINE LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: OMI32 GERMLINE HEAVY CHAIN; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ANTIBODY, FAB, GERMLINE, ANCESTOR, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR G.KANG,A.M.PHILLIPS,C.CATALANO,G.SCAPIN REVDAT 1 08-APR-26 11OU 0 JRNL AUTH C.R.THARP,C.CATALANO,A.KHALIFEH,S.GHAFFARI-KASHANI,R.HUANG, JRNL AUTH 2 G.KANG,G.SCAPIN,A.M.PHILLIPS JRNL TITL BIOPHYSICAL TRADE-OFFS IN ANTIBODY EVOLUTION ARE RESOLVED BY JRNL TITL 2 CONFORMATION-MEDIATED EPISTASIS. JRNL REF BIORXIV 2026 JRNL REFN ISSN 2692-8205 JRNL PMID 41889954 JRNL DOI 10.64898/2026.03.12.711465 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 73477 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 11OU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305792. 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 : OMI32 GERMLINE FAB IN COMPLEX REMARK 245 WITH LC-KAPPA VHH 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 : 7.60 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) : 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 : NULL REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5013.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: K, L, H 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 THR H 134 REMARK 465 SER H 135 REMARK 465 SER H 218 REMARK 465 CYS H 219 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 LYS H 43 CG CD CE NZ REMARK 470 ASN H 57 CG OD1 ND2 REMARK 470 LYS H 132 CG CD CE NZ REMARK 470 LYS H 217 CG CD CE NZ 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 VAL K 48 -60.16 -120.16 REMARK 500 ALA L 52 -1.90 68.21 REMARK 500 SER L 95 150.88 63.46 REMARK 500 ALA H 92 -175.71 -170.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75893 RELATED DB: EMDB REMARK 900 OMI32 GERMLINE FAB IN COMPLEX WITH LC-KAPPA VHH DBREF 11OU K 1 120 PDB 11OU 11OU 1 120 DBREF 11OU L 2 215 PDB 11OU 11OU 2 215 DBREF 11OU H 1 219 PDB 11OU 11OU 1 219 SEQRES 1 K 120 GLU VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 K 120 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 K 120 ARG THR ILE SER ARG TYR ALA MET SER TRP PHE ARG GLN SEQRES 4 K 120 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA THR ALA ARG SEQRES 5 K 120 ARG SER GLY ASP GLY ALA PHE TYR ALA ASP SER VAL GLN SEQRES 6 K 120 GLY ARG PHE THR VAL SER ARG ASP ASP ALA LYS ASN THR SEQRES 7 K 120 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 K 120 ALA VAL TYR TYR CYS ALA ILE ASP SER ASP THR PHE TYR SEQRES 9 K 120 SER GLY SER TYR ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 K 120 THR VAL SER SEQRES 1 L 214 ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SER SEQRES 2 L 214 PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER GLN SEQRES 3 L 214 SER VAL SER SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SEQRES 5 L 214 SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 GLY SER SER PRO ARG LEU THR PHE GLY GLY GLY THR LYS SEQRES 9 L 214 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 214 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 214 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 214 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 214 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 214 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 214 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 214 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 214 SER PHE ASN ARG GLY GLU SEQRES 1 H 219 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 219 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 219 PHE THR PHE SER SER TYR GLY MET HIS TRP VAL ARG GLN SEQRES 4 H 219 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL ILE TRP SEQRES 5 H 219 TYR ASP GLY SER ASN LYS TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 219 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 219 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 219 ALA VAL TYR TYR CYS ALA ARG ASP THR ALA PRO PRO ASP SEQRES 9 H 219 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SEQRES 10 H 219 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SEQRES 11 H 219 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS SEQRES 12 H 219 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 219 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 219 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 219 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN SEQRES 16 H 219 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR SEQRES 17 H 219 LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS HELIX 1 AA1 ASP K 74 LYS K 76 5 3 HELIX 2 AA2 LYS K 87 THR K 91 5 5 HELIX 3 AA3 GLU L 80 PHE L 84 5 5 HELIX 4 AA4 SER L 123 GLY L 130 1 8 HELIX 5 AA5 LYS L 185 HIS L 191 1 7 HELIX 6 AA6 ARG H 87 THR H 91 5 5 HELIX 7 AA7 SER H 159 ALA H 161 5 3 HELIX 8 AA8 SER H 190 GLN H 195 1 6 SHEET 1 AA1 4 GLU K 6 SER K 7 0 SHEET 2 AA1 4 SER K 17 ALA K 23 -1 O SER K 21 N SER K 7 SHEET 3 AA1 4 THR K 78 ASN K 84 -1 O MET K 83 N LEU K 18 SHEET 4 AA1 4 PHE K 68 ARG K 72 -1 N THR K 69 O GLN K 82 SHEET 1 AA2 4 GLU K 46 ALA K 51 0 SHEET 2 AA2 4 MET K 34 GLN K 39 -1 N MET K 34 O ALA K 51 SHEET 3 AA2 4 ALA K 92 ASP K 99 -1 O ALA K 97 N SER K 35 SHEET 4 AA2 4 TYR K 108 TRP K 111 -1 O TYR K 110 N ILE K 98 SHEET 1 AA3 4 GLU K 46 ALA K 51 0 SHEET 2 AA3 4 MET K 34 GLN K 39 -1 N MET K 34 O ALA K 51 SHEET 3 AA3 4 ALA K 92 ASP K 99 -1 O ALA K 97 N SER K 35 SHEET 4 AA3 4 THR K 115 VAL K 117 -1 O THR K 115 N TYR K 94 SHEET 1 AA4 4 LEU L 4 SER L 7 0 SHEET 2 AA4 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 4 ASP L 71 ILE L 76 -1 O PHE L 72 N CYS L 23 SHEET 4 AA4 4 PHE L 63 SER L 68 -1 N SER L 66 O THR L 73 SHEET 1 AA5 6 THR L 10 LEU L 13 0 SHEET 2 AA5 6 THR L 104 ILE L 108 1 O LYS L 105 N LEU L 11 SHEET 3 AA5 6 VAL L 86 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AA5 6 LEU L 34 GLN L 39 -1 N GLN L 39 O VAL L 86 SHEET 5 AA5 6 ARG L 46 TYR L 50 -1 O ARG L 46 N GLN L 38 SHEET 6 AA5 6 SER L 54 ARG L 55 -1 O SER L 54 N TYR L 50 SHEET 1 AA6 4 THR L 10 LEU L 13 0 SHEET 2 AA6 4 THR L 104 ILE L 108 1 O LYS L 105 N LEU L 11 SHEET 3 AA6 4 VAL L 86 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AA6 4 THR L 99 PHE L 100 -1 O THR L 99 N GLN L 91 SHEET 1 AA7 4 SER L 116 PHE L 120 0 SHEET 2 AA7 4 THR L 131 PHE L 141 -1 O LEU L 137 N PHE L 118 SHEET 3 AA7 4 TYR L 175 SER L 184 -1 O LEU L 181 N VAL L 134 SHEET 4 AA7 4 SER L 161 VAL L 165 -1 N GLN L 162 O THR L 180 SHEET 1 AA8 4 ALA L 155 GLN L 157 0 SHEET 2 AA8 4 ALA L 146 VAL L 152 -1 N TRP L 150 O GLN L 157 SHEET 3 AA8 4 VAL L 193 HIS L 200 -1 O GLU L 197 N GLN L 149 SHEET 4 AA8 4 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198 SHEET 1 AA9 4 GLU H 6 SER H 7 0 SHEET 2 AA9 4 LEU H 18 CYS H 22 -1 O SER H 21 N SER H 7 SHEET 3 AA9 4 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA9 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AB1 6 VAL H 11 VAL H 12 0 SHEET 2 AB1 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AB1 6 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 112 SHEET 4 AB1 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AB1 6 LEU H 45 ILE H 51 -1 O VAL H 48 N TRP H 36 SHEET 6 AB1 6 LYS H 58 TYR H 60 -1 O TYR H 59 N VAL H 50 SHEET 1 AB2 4 SER H 123 LEU H 127 0 SHEET 2 AB2 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AB2 4 TYR H 179 PRO H 188 -1 O VAL H 185 N LEU H 141 SHEET 4 AB2 4 HIS H 167 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 AB3 4 SER H 123 LEU H 127 0 SHEET 2 AB3 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AB3 4 TYR H 179 PRO H 188 -1 O VAL H 185 N LEU H 141 SHEET 4 AB3 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 AB4 3 THR H 154 TRP H 157 0 SHEET 2 AB4 3 ILE H 198 HIS H 203 -1 O ASN H 202 N THR H 154 SHEET 3 AB4 3 THR H 208 LYS H 213 -1 O VAL H 210 N VAL H 201 SSBOND 1 CYS K 22 CYS K 96 1555 1555 2.03 SSBOND 2 CYS L 23 CYS L 89 1555 1555 2.03 SSBOND 3 CYS L 136 CYS L 196 1555 1555 2.03 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 5 CYS H 143 CYS H 199 1555 1555 2.03 CISPEP 1 SER L 7 PRO L 8 0 -2.90 CISPEP 2 TYR L 142 PRO L 143 0 1.36 CISPEP 3 ALA H 101 PRO H 102 0 -5.93 CISPEP 4 PHE H 149 PRO H 150 0 -3.21 CISPEP 5 GLU H 151 PRO H 152 0 -0.04 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 153 738 CONECT 738 153 CONECT 1080 1589 CONECT 1589 1080 CONECT 1936 2415 CONECT 2415 1936 CONECT 2718 3307 CONECT 3307 2718 CONECT 3611 4025 CONECT 4025 3611 MASTER 141 0 0 8 55 0 0 6 4163 3 10 44 END