HEADER IMMUNE SYSTEM 27-AUG-23 8W5Q TITLE CRYO-EM STRUCTURE OF QB-AB45 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF AB45; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF AB45; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: MINOR CAPSID PROTEIN A1; COMPND 11 CHAIN: C, c; COMPND 12 SYNONYM: QB COAT PROTEIN; COMPND 13 ENGINEERED: YES 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 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE QBETA; SOURCE 13 ORGANISM_TAXID: 2789016; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS QB, ANTIBODY, CRYO-EM, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR K.Y.BAO,R.H.LI,Z.L.HUA,B.D.HOU,P.ZHU REVDAT 1 26-FEB-25 8W5Q 0 JRNL AUTH R.LI,K.BAO,C.LIU,X.MA,Z.HUA,P.ZHU,B.HOU JRNL TITL COMPETITION PROPELS, RATHER THAN LIMITS, THE SUCCESS OF JRNL TITL 2 LOW-AFFINITY B CELLS IN THE GERMINAL CENTER RESPONSE. JRNL REF CELL REP V. 44 15334 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 39955776 JRNL DOI 10.1016/J.CELREP.2025.115334 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 4.100 REMARK 3 NUMBER OF PARTICLES : 530467 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 8W5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040614. 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 : COMPLEX OF QB-AB45 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 : 7.40 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 5000.00 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) : 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, C, 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 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 VAL L 1 REMARK 465 HIS L 2 REMARK 465 SER L 3 REMARK 465 ASP L 4 REMARK 465 ILE L 5 REMARK 465 GLN L 6 REMARK 465 THR L 105 REMARK 465 LYS L 106 REMARK 465 LEU L 107 REMARK 465 GLU L 108 REMARK 465 ILE L 109 REMARK 465 LYS L 110 REMARK 465 VAL H 1 REMARK 465 HIS H 2 REMARK 465 SER H 3 REMARK 465 GLU H 4 REMARK 465 THR H 120 REMARK 465 THR H 121 REMARK 465 LEU H 122 REMARK 465 THR H 123 REMARK 465 VAL H 124 REMARK 465 SER H 125 REMARK 465 SER H 126 REMARK 465 MET C 0 REMARK 465 SER C 56 REMARK 465 ARG C 57 REMARK 465 ASN C 58 REMARK 465 ARG C 59 REMARK 465 LYS C 60 REMARK 465 TYR C 132 REMARK 465 MET c 0 REMARK 465 SER c 56 REMARK 465 ARG c 57 REMARK 465 ASN c 58 REMARK 465 ARG c 59 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 OH TYR L 39 O PHE H 112 2.14 REMARK 500 OG1 THR C 93 OD1 ASP c 91 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO H 17 C - N - CD ANGL. DEV. = -28.2 DEGREES 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 L 10 85.78 -151.17 REMARK 500 SER L 15 -169.49 -129.87 REMARK 500 THR L 21 -54.58 -121.40 REMARK 500 TYR L 33 131.25 95.14 REMARK 500 ALA L 54 -63.62 66.73 REMARK 500 THR L 72 -6.53 72.66 REMARK 500 TRP L 95 -50.51 -124.40 REMARK 500 TRP L 99 161.27 64.90 REMARK 500 PRO H 17 62.86 2.33 REMARK 500 LEU H 21 153.44 67.73 REMARK 500 SER H 33 -100.24 47.92 REMARK 500 ALA H 43 150.34 65.84 REMARK 500 LYS H 46 -95.27 57.56 REMARK 500 THR H 66 17.71 58.40 REMARK 500 PHE H 112 67.87 61.35 REMARK 500 GLU H 114 -12.35 78.05 REMARK 500 TYR H 115 -122.41 24.24 REMARK 500 TRP H 116 140.97 73.14 REMARK 500 ALA C 40 -4.62 67.55 REMARK 500 ASN c 10 50.05 36.03 REMARK 500 ALA c 40 -2.08 66.42 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 LYS H 16 PRO H 17 -147.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37301 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF QB-AB45 DBREF 8W5Q L 1 110 PDB 8W5Q 8W5Q 1 110 DBREF 8W5Q H 1 126 PDB 8W5Q 8W5Q 1 126 DBREF 8W5Q C 0 132 UNP Q8LTE1 A1_BPQBE 1 133 DBREF 8W5Q c 0 132 UNP Q8LTE1 A1_BPQBE 1 133 SEQRES 1 L 110 VAL HIS SER ASP ILE GLN MET THR GLN SER PRO ALA SER SEQRES 2 L 110 LEU SER ALA SER VAL GLY GLU THR VAL THR ILE THR CYS SEQRES 3 L 110 ARG ALA SER GLU ASN ILE TYR ASN TYR LEU ALA TRP TYR SEQRES 4 L 110 GLN ARG LYS GLN GLY LYS SER PRO GLN LEU LEU VAL PHE SEQRES 5 L 110 ASN ALA LYS THR LEU ALA ASP GLY VAL PRO SER ARG PHE SEQRES 6 L 110 SER GLY SER GLY SER GLY THR GLN TYR SER LEU LYS ILE SEQRES 7 L 110 ILE SER LEU GLN PRO GLU ASP PHE GLY THR TYR TYR CYS SEQRES 8 L 110 GLN HIS PHE TRP ARG THR PRO TRP THR PHE GLY GLY GLY SEQRES 9 L 110 THR LYS LEU GLU ILE LYS SEQRES 1 H 126 VAL HIS SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 H 126 LEU VAL LYS PRO GLY GLY SER LEU LYS LEU SER CYS ALA SEQRES 3 H 126 ALA SER GLY PHE THR PHE SER ASP TYR GLY MET TYR TRP SEQRES 4 H 126 VAL ARG GLN ALA PRO GLU LYS GLY LEU GLU TRP VAL ALA SEQRES 5 H 126 TYR ILE GLY SER GLY SER GLY VAL ILE TYR TYR ALA ASP SEQRES 6 H 126 THR VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN GLY SEQRES 7 H 126 LYS ASN THR LEU PHE LEU GLN MET THR SER LEU ARG SER SEQRES 8 H 126 GLU ASP THR ALA ILE TYR TYR CYS ALA ARG LYS ARG GLY SEQRES 9 H 126 TYR GLU TYR ASP GLY GLN TYR PHE PHE GLU TYR TRP GLY SEQRES 10 H 126 GLN GLY THR THR LEU THR VAL SER SER SEQRES 1 C 133 MET ALA LYS LEU GLU THR VAL THR LEU GLY ASN ILE GLY SEQRES 2 C 133 LYS ASP GLY LYS GLN THR LEU VAL LEU ASN PRO ARG GLY SEQRES 3 C 133 VAL ASN PRO THR ASN GLY VAL ALA SER LEU SER GLN ALA SEQRES 4 C 133 GLY ALA VAL PRO ALA LEU GLU LYS ARG VAL THR VAL SER SEQRES 5 C 133 VAL SER GLN PRO SER ARG ASN ARG LYS ASN TYR LYS VAL SEQRES 6 C 133 GLN VAL LYS ILE GLN ASN PRO THR ALA CYS THR ALA ASN SEQRES 7 C 133 GLY SER CYS ASP PRO SER VAL THR ARG GLN ALA TYR ALA SEQRES 8 C 133 ASP VAL THR PHE SER PHE THR GLN TYR SER THR ASP GLU SEQRES 9 C 133 GLU ARG ALA PHE VAL ARG THR GLU LEU ALA ALA LEU LEU SEQRES 10 C 133 ALA SER PRO LEU LEU ILE ASP ALA ILE ASP GLN LEU ASN SEQRES 11 C 133 PRO ALA TYR SEQRES 1 c 133 MET ALA LYS LEU GLU THR VAL THR LEU GLY ASN ILE GLY SEQRES 2 c 133 LYS ASP GLY LYS GLN THR LEU VAL LEU ASN PRO ARG GLY SEQRES 3 c 133 VAL ASN PRO THR ASN GLY VAL ALA SER LEU SER GLN ALA SEQRES 4 c 133 GLY ALA VAL PRO ALA LEU GLU LYS ARG VAL THR VAL SER SEQRES 5 c 133 VAL SER GLN PRO SER ARG ASN ARG LYS ASN TYR LYS VAL SEQRES 6 c 133 GLN VAL LYS ILE GLN ASN PRO THR ALA CYS THR ALA ASN SEQRES 7 c 133 GLY SER CYS ASP PRO SER VAL THR ARG GLN ALA TYR ALA SEQRES 8 c 133 ASP VAL THR PHE SER PHE THR GLN TYR SER THR ASP GLU SEQRES 9 c 133 GLU ARG ALA PHE VAL ARG THR GLU LEU ALA ALA LEU LEU SEQRES 10 c 133 ALA SER PRO LEU LEU ILE ASP ALA ILE ASP GLN LEU ASN SEQRES 11 c 133 PRO ALA TYR HELIX 1 AA1 THR C 101 LEU C 116 1 16 HELIX 2 AA2 SER C 118 LEU C 128 1 11 HELIX 3 AA3 THR c 101 ALA c 117 1 17 HELIX 4 AA4 SER c 118 GLN c 127 1 10 SHEET 1 AA1 4 THR L 56 LEU L 57 0 SHEET 2 AA1 4 GLN L 48 PHE L 52 -1 N PHE L 52 O THR L 56 SHEET 3 AA1 4 LEU L 36 ARG L 41 -1 N TRP L 38 O LEU L 50 SHEET 4 AA1 4 THR L 88 HIS L 93 -1 O THR L 88 N ARG L 41 SHEET 1 AA2 2 SER L 66 SER L 70 0 SHEET 2 AA2 2 GLN L 73 LYS L 77 -1 O SER L 75 N SER L 68 SHEET 1 AA3 2 LEU H 7 VAL H 8 0 SHEET 2 AA3 2 ALA H 27 SER H 28 -1 O SER H 28 N LEU H 7 SHEET 1 AA4 3 LYS H 22 LEU H 23 0 SHEET 2 AA4 3 THR H 81 MET H 86 -1 O LEU H 84 N LEU H 23 SHEET 3 AA4 3 PHE H 71 ASP H 76 -1 N THR H 72 O GLN H 85 SHEET 1 AA5 2 VAL H 40 ARG H 41 0 SHEET 2 AA5 2 TYR H 97 TYR H 98 -1 O TYR H 98 N VAL H 40 SHEET 1 AA612 VAL C 6 THR C 7 0 SHEET 2 AA612 VAL C 20 VAL C 26 -1 O LEU C 21 N VAL C 6 SHEET 3 AA612 ALA C 33 GLN C 37 -1 O SER C 34 N ARG C 24 SHEET 4 AA612 ARG C 47 VAL C 52 -1 O VAL C 50 N ALA C 33 SHEET 5 AA612 LYS C 63 CYS C 74 -1 O GLN C 69 N ARG C 47 SHEET 6 AA612 SER C 83 SER C 95 -1 O ARG C 86 N THR C 72 SHEET 7 AA612 SER c 83 PHE c 94 -1 O THR c 93 N ASP C 91 SHEET 8 AA612 VAL c 64 CYS c 74 -1 N ILE c 68 O ALA c 90 SHEET 9 AA612 ARG c 47 VAL c 52 -1 N ARG c 47 O GLN c 69 SHEET 10 AA612 ALA c 33 SER c 36 -1 N LEU c 35 O VAL c 48 SHEET 11 AA612 LEU c 19 VAL c 26 -1 N ARG c 24 O SER c 34 SHEET 12 AA612 VAL c 6 LEU c 8 -1 N VAL c 6 O LEU c 21 SSBOND 1 CYS H 25 CYS H 99 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