HEADER IMMUNE SYSTEM 06-MAR-26 11OR TITLE OMI32 FAB IN COMPLEX WITH LC-KAPPA VHH COMPND MOL_ID: 1; COMPND 2 MOLECULE: OMI32 HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: OMI32 LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LC-KAPPA VHH; COMPND 11 CHAIN: K; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; 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: LAMA GLAMA; SOURCE 13 ORGANISM_TAXID: 9844; SOURCE 14 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS ANTIBODY, FAB, EVOLVED, BROADLY NEUTRALIZING, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR G.KANG,A.M.PHILLIPS,C.CATALANO,G.SCAPIN REVDAT 1 08-APR-26 11OR 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 : 71518 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 11OR 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_1000305789. 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 FAB IN COMPLEX WITH LC REMARK 245 -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) : 5054.00 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: H, L, K 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 GLY H 136 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 H 1 CG CD OE1 OE2 REMARK 470 LYS H 43 CG CD CE NZ REMARK 470 LYS H 132 CG CD CE NZ REMARK 470 LYS H 217 CG CD CE NZ REMARK 470 GLU K 1 CG CD OE1 OE2 REMARK 470 GLN K 3 CG CD OE1 NE2 REMARK 470 GLN K 13 CG CD OE1 NE2 REMARK 470 GLN K 113 CG CD OE1 NE2 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 OE1 GLN K 39 O LYS K 43 2.05 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 SER H 116 57.20 -91.41 REMARK 500 PHE L 33 57.91 -97.74 REMARK 500 VAL K 48 -56.01 -122.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75892 RELATED DB: EMDB REMARK 900 OMI32 FAB IN COMPLEX WITH LC-KAPPA VHH DBREF 11OR H 1 217 PDB 11OR 11OR 1 217 DBREF 11OR L 4 214 PDB 11OR 11OR 4 214 DBREF 11OR K 1 120 PDB 11OR 11OR 1 120 SEQRES 1 H 217 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 217 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 217 PHE THR PHE SER ASN TYR GLY MET HIS TRP VAL ARG GLN SEQRES 4 H 217 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL TYR TRP SEQRES 5 H 217 TYR ASP GLY GLY ASN LYS PHE TYR ALA ASP SER VAL LYS SEQRES 6 H 217 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 217 LEU TYR LEU GLN MET ASN SER LEU ARG VAL GLU ASP THR SEQRES 8 H 217 ALA VAL TYR TYR CYS ALA ARG ASP THR ALA PRO PRO ASP SEQRES 9 H 217 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SEQRES 10 H 217 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SEQRES 11 H 217 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS SEQRES 12 H 217 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 217 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 217 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 217 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN SEQRES 16 H 217 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR SEQRES 17 H 217 LYS VAL ASP LYS ARG VAL GLU PRO LYS SEQRES 1 L 211 MET THR GLN SER PRO GLY THR LEU SER LEU SER PRO GLY SEQRES 2 L 211 GLU ARG ALA THR LEU SER CYS ARG ALA SER GLN SER ILE SEQRES 3 L 211 SER SER SER PHE LEU ALA TRP TYR GLN GLN LYS PRO GLY SEQRES 4 L 211 GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SER ARG SEQRES 5 L 211 ALA THR GLY ILE PRO ASP ARG PHE SER GLY SER GLY SER SEQRES 6 L 211 GLY THR ASP PHE THR LEU THR ILE SER ARG LEU GLU PRO SEQRES 7 L 211 GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR GLY THR SEQRES 8 L 211 SER PRO ARG LEU THR PHE GLY GLY GLY THR LYS VAL ASP SEQRES 9 L 211 ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE PHE SEQRES 10 L 211 PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SER SEQRES 11 L 211 VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA SEQRES 12 L 211 LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER GLY SEQRES 13 L 211 ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS ASP SEQRES 14 L 211 SER THR TYR SER LEU SER SER THR LEU THR LEU SER LYS SEQRES 15 L 211 ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU VAL SEQRES 16 L 211 THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER PHE SEQRES 17 L 211 ASN ARG GLY 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 HELIX 1 AA1 ARG H 87 THR H 91 5 5 HELIX 2 AA2 SER H 159 ALA H 161 5 3 HELIX 3 AA3 SER H 189 GLN H 195 1 7 HELIX 4 AA4 LYS H 204 ASN H 207 5 4 HELIX 5 AA5 GLU L 80 PHE L 84 5 5 HELIX 6 AA6 SER L 123 SER L 129 1 7 HELIX 7 AA7 LYS L 185 LYS L 190 1 6 HELIX 8 AA8 LYS K 87 THR K 91 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 THR H 78 MET H 83 -1 O LEU H 79 N CYS H 22 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA2 6 VAL H 11 VAL H 12 0 SHEET 2 AA2 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA2 6 ALA H 92 ARG H 98 -1 N ALA H 92 O VAL H 112 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 TYR H 51 -1 O ALA H 49 N TRP H 36 SHEET 6 AA2 6 LYS H 58 TYR H 60 -1 O PHE H 59 N VAL H 50 SHEET 1 AA3 4 SER H 123 LEU H 127 0 SHEET 2 AA3 4 THR H 138 TYR H 148 -1 O LYS H 146 N SER H 123 SHEET 3 AA3 4 TYR H 179 PRO H 188 -1 O VAL H 187 N ALA H 139 SHEET 4 AA3 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 AA4 4 SER H 123 LEU H 127 0 SHEET 2 AA4 4 THR H 138 TYR H 148 -1 O LYS H 146 N SER H 123 SHEET 3 AA4 4 TYR H 179 PRO H 188 -1 O VAL H 187 N ALA H 139 SHEET 4 AA4 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 AA5 3 THR H 154 TRP H 157 0 SHEET 2 AA5 3 TYR H 197 HIS H 203 -1 O ASN H 200 N SER H 156 SHEET 3 AA5 3 THR H 208 VAL H 214 -1 O VAL H 210 N VAL H 201 SHEET 1 AA6 4 THR L 5 SER L 7 0 SHEET 2 AA6 4 ALA L 19 ARG L 24 -1 O SER L 22 N SER L 7 SHEET 3 AA6 4 ASP L 71 ILE L 76 -1 O LEU L 74 N LEU L 21 SHEET 4 AA6 4 SER L 66 SER L 68 -1 N SER L 66 O THR L 73 SHEET 1 AA7 6 THR L 10 SER L 12 0 SHEET 2 AA7 6 THR L 104 ASP L 107 1 O ASP L 107 N LEU L 11 SHEET 3 AA7 6 VAL L 86 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AA7 6 ALA L 35 GLN L 39 -1 N GLN L 39 O VAL L 86 SHEET 5 AA7 6 ARG L 46 TYR L 50 -1 O LEU L 48 N TRP L 36 SHEET 6 AA7 6 SER L 54 ARG L 55 -1 O SER L 54 N TYR L 50 SHEET 1 AA8 4 THR L 10 SER L 12 0 SHEET 2 AA8 4 THR L 104 ASP L 107 1 O ASP L 107 N LEU L 11 SHEET 3 AA8 4 VAL L 86 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AA8 4 THR L 99 PHE L 100 -1 O THR L 99 N GLN L 91 SHEET 1 AA9 4 SER L 116 PHE L 120 0 SHEET 2 AA9 4 THR L 131 PHE L 141 -1 O ASN L 139 N SER L 116 SHEET 3 AA9 4 TYR L 175 SER L 184 -1 O LEU L 177 N LEU L 138 SHEET 4 AA9 4 SER L 161 VAL L 165 -1 N GLN L 162 O THR L 180 SHEET 1 AB1 3 ALA L 146 VAL L 152 0 SHEET 2 AB1 3 VAL L 193 HIS L 200 -1 O GLU L 197 N GLN L 149 SHEET 3 AB1 3 VAL L 207 ASN L 212 -1 O PHE L 211 N TYR L 194 SHEET 1 AB2 4 GLN K 3 SER K 7 0 SHEET 2 AB2 4 SER K 17 SER K 25 -1 O ALA K 23 N GLN K 5 SHEET 3 AB2 4 THR K 78 ASN K 84 -1 O MET K 83 N LEU K 18 SHEET 4 AB2 4 PHE K 68 VAL K 70 -1 N THR K 69 O GLN K 82 SHEET 1 AB3 4 ARG K 45 ALA K 51 0 SHEET 2 AB3 4 ALA K 33 GLN K 39 -1 N MET K 34 O ALA K 51 SHEET 3 AB3 4 ALA K 92 ASP K 99 -1 O TYR K 95 N PHE K 37 SHEET 4 AB3 4 THR K 115 VAL K 117 -1 O VAL K 117 N ALA K 92 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS H 143 CYS H 199 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 89 1555 1555 2.03 SSBOND 4 CYS L 136 CYS L 196 1555 1555 2.03 SSBOND 5 CYS K 22 CYS K 96 1555 1555 2.03 CISPEP 1 ALA H 101 PRO H 102 0 -3.43 CISPEP 2 PHE H 149 PRO H 150 0 -5.12 CISPEP 3 GLU H 151 PRO H 152 0 -3.53 CISPEP 4 SER L 7 PRO L 8 0 -4.04 CISPEP 5 TYR L 142 PRO L 143 0 1.07 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 153 750 CONECT 750 153 CONECT 1050 1464 CONECT 1464 1050 CONECT 1746 2255 CONECT 2255 1746 CONECT 2602 3081 CONECT 3081 2602 CONECT 3362 3947 CONECT 3947 3362 MASTER 153 0 0 8 50 0 0 6 4125 3 10 44 END