HEADER IMMUNE SYSTEM 15-APR-26 12QJ TITLE PNEUMOCOCCAL CHOLINE BINDING CBPE SURFACE PROTEIN BOUNDS TO 5992-2 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHOLINE BINDING PROTEIN E CBPE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.96; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5992-2 FAB HEAVY CHAIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5992-2 FAB LIGHT CHAIN; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: LYTB_3, SAMEA104154639_00853; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS PNEUMOCOCCAL CHOLINE BINDING, CRYOEM, HUMAN MONOCLONAL ANTIBODY, KEYWDS 2 IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR A.MCCORMICK,B.GHAZI ESFAHANI,J.VIDAL,F.E.LEE,M.TOMPKINS,K.MCCAFFREY, AUTHOR 2 J.MOUSA REVDAT 1 03-JUN-26 12QJ 0 JRNL AUTH A.MCCORMICK,B.GHAZI ESFAHANI,J.VIDA,F.E.LEE,M.TOMPKINS, JRNL AUTH 2 K.MCCAFFREY,J.MOUSA JRNL TITL BROADLY REACTIVE HUMAN MONOCLONAL ANTIBODY TARGETING JRNL TITL 2 CONSERVED PNEUMOCOCCAL CHOLINE BINDING DOMAIN INCREASES JRNL TITL 3 PROTECTION AGAINST LETHAL PNEUMOCOCCAL INFECTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.35 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) : 3.350 REMARK 3 NUMBER OF PARTICLES : 59000 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 12QJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000306145. 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 : PNEUMOCOCCAL CHOLINE BINDING REMARK 245 CBPE SURFACE PROTEIN BOUNDS TO REMARK 245 5992-2 FAB 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 : 6.80 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 : DIRECT ELECTRON APOLLO (4K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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) : 6000.00 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) : 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 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ASP A 31 152.79 69.32 REMARK 500 SER A 42 -162.60 -78.47 REMARK 500 LEU A 60 -149.42 -144.69 REMARK 500 THR A 61 -20.34 83.38 REMARK 500 TRP A 121 -71.85 -57.53 REMARK 500 ASP A 122 61.94 -104.30 REMARK 500 GLN A 147 -106.03 48.65 REMARK 500 ALA A 150 15.24 -144.13 REMARK 500 ASN A 166 48.18 -84.69 REMARK 500 ASP A 201 28.76 -143.93 REMARK 500 PHE A 224 -168.29 -72.28 REMARK 500 ASN A 225 -159.44 -113.01 REMARK 500 HIS A 226 109.36 -43.36 REMARK 500 HIS A 227 -123.08 31.99 REMARK 500 LYS A 232 55.85 -98.98 REMARK 500 SER A 251 -165.30 -162.54 REMARK 500 ASN A 258 -3.53 68.16 REMARK 500 VAL A 260 102.12 41.09 REMARK 500 LYS A 281 46.35 -86.52 REMARK 500 GLN A 292 48.28 -83.98 REMARK 500 TYR A 302 -168.38 -126.32 REMARK 500 PRO A 304 -178.98 -69.30 REMARK 500 GLN A 347 0.88 -68.66 REMARK 500 ILE A 350 101.04 19.42 REMARK 500 LEU A 351 -169.57 -112.29 REMARK 500 ASN A 360 52.16 39.87 REMARK 500 ASP A 368 -140.38 54.33 REMARK 500 ASN A 375 -114.31 59.96 REMARK 500 ALA A 380 -97.74 62.13 REMARK 500 GLN A 391 138.40 -171.35 REMARK 500 ARG B 10 -158.64 -149.27 REMARK 500 LEU B 11 11.94 86.14 REMARK 500 LYS B 13 -166.88 -79.93 REMARK 500 SER B 15 69.81 -105.60 REMARK 500 THR B 17 -63.54 -95.67 REMARK 500 LEU B 18 73.65 48.28 REMARK 500 PRO B 42 42.06 -84.05 REMARK 500 THR B 87 -168.72 -78.09 REMARK 500 ALA B 89 -100.55 32.72 REMARK 500 ALA B 101 97.73 -167.30 REMARK 500 PRO B 102 108.28 -52.08 REMARK 500 PRO B 104 66.39 13.90 REMARK 500 TYR B 109 75.97 46.40 REMARK 500 SER C 2 31.28 -88.85 REMARK 500 ALA C 31 21.66 -140.11 REMARK 500 ARG C 56 69.62 -159.25 REMARK 500 SER C 65 145.57 109.43 REMARK 500 ALA C 86 -176.82 69.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 103 PRO B 104 -138.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-76684 RELATED DB: EMDB REMARK 900 PNEUMOCOCCAL CHOLINE BINDING CBPE SURFACE PROTEIN BOUNDS TO 5992-2 REMARK 900 FAB DBREF1 12QJ A 1 394 UNP A0A0T8F9T1_STREE DBREF2 12QJ A A0A0T8F9T1 28 421 DBREF 12QJ B 1 125 PDB 12QJ 12QJ 1 125 DBREF 12QJ C 1 111 PDB 12QJ 12QJ 1 111 SEQRES 1 A 394 SER SER GLY ASN LYS ILE HIS PHE ILE ASN VAL GLN GLU SEQRES 2 A 394 GLY GLY SER ASP ALA ILE ILE LEU GLU SER ASN GLY HIS SEQRES 3 A 394 PHE ALA MET VAL ASP THR GLY GLU ASP TYR ASP PHE PRO SEQRES 4 A 394 ASP GLY SER ASP SER ARG TYR PRO TRP ARG GLU GLY ILE SEQRES 5 A 394 GLU THR SER TYR LYS HIS VAL LEU THR ASP ARG VAL PHE SEQRES 6 A 394 ARG ARG LEU LYS GLU LEU GLY VAL GLN LYS LEU ASP PHE SEQRES 7 A 394 ILE LEU VAL THR HIS THR HIS SER ASP HIS ILE GLY ASN SEQRES 8 A 394 VAL ASP GLU LEU LEU SER THR TYR PRO VAL ASP ARG VAL SEQRES 9 A 394 TYR LEU LYS LYS TYR SER ASP ASN ARG ILE THR ASN SER SEQRES 10 A 394 GLU ARG LEU TRP ASP ASN LEU TYR GLY TYR ASP LYS VAL SEQRES 11 A 394 LEU GLN THR ALA SER GLU LYS GLY VAL SER VAL ILE GLN SEQRES 12 A 394 ASN ILE THR GLN GLY ASP ALA HIS PHE GLN PHE GLY ASP SEQRES 13 A 394 MET ASP ILE GLN LEU TYR ASN TYR GLU ASN GLU THR ASP SEQRES 14 A 394 SER SER GLY GLU LEU LYS LYS ILE TRP ASP ASP ASN SER SEQRES 15 A 394 ASN SER LEU ILE SER VAL VAL LYS VAL ASN GLY LYS LYS SEQRES 16 A 394 ILE TYR LEU GLY GLY ASP LEU ASP ASN VAL HIS GLY ALA SEQRES 17 A 394 GLU ASP LYS TYR GLY PRO LEU ILE GLY LYS VAL ASP LEU SEQRES 18 A 394 MET LYS PHE ASN HIS HIS HIS ASP THR ASN LYS SER ASN SEQRES 19 A 394 THR LYS ASP PHE ILE LYS ASN LEU SER PRO SER LEU ILE SEQRES 20 A 394 VAL GLN THR SER ASP SER LEU PRO TRP LYS ASN GLY VAL SEQRES 21 A 394 ASP SER GLU TYR VAL ASN TRP LEU LYS GLU ARG GLY ILE SEQRES 22 A 394 GLU ARG ILE ASN ALA ALA SER LYS ASP TYR ASP ALA THR SEQRES 23 A 394 VAL PHE ASP ILE ARG GLN ASP GLY LEU VAL ASN ILE SER SEQRES 24 A 394 THR SER TYR LYS PRO ILE PRO SER PHE GLN ALA GLY TRP SEQRES 25 A 394 HIS LYS SER SER TYR GLY ASN TRP TRP TYR GLN ALA PRO SEQRES 26 A 394 ASP SER THR GLY GLU TYR ALA VAL GLY TRP ASN GLU ILE SEQRES 27 A 394 LYS GLY GLU TRP TYR TYR PHE ASN GLN THR GLY ILE LEU SEQRES 28 A 394 LEU GLN ASN GLN TRP LYS LYS TRP ASN ASN ARG TRP PHE SEQRES 29 A 394 TYR LEU THR ASP SER GLY VAL ALA ALA LYS ASN TRP LYS SEQRES 30 A 394 LYS ILE ALA GLY ILE TRP TYR TYR PHE ASN LYS GLU ASN SEQRES 31 A 394 GLN MET GLU ILE SEQRES 1 B 125 GLN VAL GLN LEU GLN GLU SER GLY PRO ARG LEU VAL LYS SEQRES 2 B 125 VAL SER GLU THR LEU SER LEU THR CYS SER LEU SER GLY SEQRES 3 B 125 HIS SER ILE SER SER GLY HIS HIS TRP ALA TRP ILE ARG SEQRES 4 B 125 GLN SER PRO GLY ARG GLY LEU GLU TRP ILE ALA THR VAL SEQRES 5 B 125 ASP HIS ASN GLY ARG THR TYR TYR ASN PRO SER LEU ARG SEQRES 6 B 125 GLY ARG VAL ILE LEU SER LYS ASP THR THR LYS ASN SER SEQRES 7 B 125 PHE SER VAL GLN LEU THR SER VAL THR ALA ALA ASP THR SEQRES 8 B 125 ALA VAL TYR TYR CYS ALA ARG ARG GLU ALA PRO SER PRO SEQRES 9 B 125 GLY THR GLY TRP TYR PRO PRO PHE GLY GLN TRP GLY GLN SEQRES 10 B 125 GLY ALA LEU VAL THR VAL SER THR SEQRES 1 C 111 GLN SER VAL LEU THR GLN PRO PRO SER LEU SER GLY ALA SEQRES 2 C 111 PRO GLY GLN THR VAL THR ILE SER CYS THR GLY SER SER SEQRES 3 C 111 SER ASN ILE GLY ALA GLY TYR ASP VAL HIS TRP TYR ARG SEQRES 4 C 111 GLN LEU PRO GLY THR ALA PRO THR LEU LEU ILE SER VAL SEQRES 5 C 111 PHE ASP ASN ARG PRO LEU GLY VAL PRO GLY ARG ILE SER SEQRES 6 C 111 GLY SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR SEQRES 7 C 111 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS GLN SEQRES 8 C 111 SER HIS ASP ASN MET LEU SER GLY SER VAL PHE GLY GLY SEQRES 9 C 111 GLY THR LYS LEU THR VAL LEU HELIX 1 AA1 THR A 61 LEU A 71 1 11 HELIX 2 AA2 HIS A 85 GLY A 90 1 6 HELIX 3 AA3 ASN A 91 SER A 97 1 7 HELIX 4 AA4 ASP A 122 GLY A 138 1 17 HELIX 5 AA5 GLY A 207 GLY A 217 1 11 HELIX 6 AA6 THR A 235 SER A 243 1 9 HELIX 7 AA7 GLU A 263 GLY A 272 1 10 HELIX 8 AA8 LEU A 366 VAL A 371 1 6 HELIX 9 AA9 PRO B 62 ARG B 65 5 4 SHEET 1 AA1 2 ILE A 19 SER A 23 0 SHEET 2 AA1 2 HIS A 26 VAL A 30 -1 O HIS A 26 N SER A 23 SHEET 1 AA2 3 PHE A 78 ILE A 79 0 SHEET 2 AA2 3 ARG A 103 VAL A 104 1 O ARG A 103 N ILE A 79 SHEET 3 AA2 3 SER A 140 VAL A 141 1 O SER A 140 N VAL A 104 SHEET 1 AA3 2 LEU A 246 GLN A 249 0 SHEET 2 AA3 2 GLU A 274 ASN A 277 1 O GLU A 274 N ILE A 247 SHEET 1 AA4 2 TRP A 312 HIS A 313 0 SHEET 2 AA4 2 TRP A 321 TYR A 322 -1 O TRP A 321 N HIS A 313 SHEET 1 AA5 3 TRP A 335 ILE A 338 0 SHEET 2 AA5 3 GLU A 341 ASN A 346 -1 O GLU A 341 N ILE A 338 SHEET 3 AA5 3 GLY A 349 LEU A 351 -1 O GLY A 349 N ASN A 346 SHEET 1 AA6 2 LYS A 357 TRP A 359 0 SHEET 2 AA6 2 ARG A 362 PHE A 364 -1 O ARG A 362 N TRP A 359 SHEET 1 AA7 3 LEU B 4 GLU B 6 0 SHEET 2 AA7 3 CYS B 22 LEU B 24 -1 O SER B 23 N GLN B 5 SHEET 3 AA7 3 SER B 78 PHE B 79 -1 O PHE B 79 N CYS B 22 SHEET 1 AA8 4 THR B 58 TYR B 60 0 SHEET 2 AA8 4 GLU B 47 VAL B 52 -1 N THR B 51 O TYR B 59 SHEET 3 AA8 4 TRP B 35 GLN B 40 -1 N TRP B 35 O VAL B 52 SHEET 4 AA8 4 VAL B 93 ALA B 97 -1 O TYR B 95 N ILE B 38 SHEET 1 AA9 2 VAL C 18 THR C 19 0 SHEET 2 AA9 2 ALA C 76 ILE C 77 -1 O ILE C 77 N VAL C 18 SHEET 1 AB1 4 ILE C 50 VAL C 52 0 SHEET 2 AB1 4 VAL C 35 GLN C 40 -1 N TRP C 37 O ILE C 50 SHEET 3 AB1 4 ASP C 87 ASP C 94 -1 O TYR C 89 N TYR C 38 SHEET 4 AB1 4 GLY C 99 VAL C 101 -1 O GLY C 99 N ASP C 94 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 2 CYS C 22 CYS C 90 1555 1555 2.04 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 3390 3970 CONECT 3970 3390 CONECT 4340 4839 CONECT 4839 4340 MASTER 178 0 0 9 27 0 0 6 4987 3 4 50 END