HEADER IMMUNE SYSTEM 26-AUG-23 8W5F TITLE CRYO-EM STRUCTURE OF QB-AB6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF AB6; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF AB6; 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 8W5F 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. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 241562 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 8W5F 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_1300040591. 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-AB6 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 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: 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 16 REMARK 465 HIS L 17 REMARK 465 SER L 18 REMARK 465 ASP L 19 REMARK 465 GLU L 123 REMARK 465 ILE L 124 REMARK 465 LYS L 125 REMARK 465 VAL H 17 REMARK 465 HIS H 18 REMARK 465 SER H 19 REMARK 465 GLN H 20 REMARK 465 SER H 141 REMARK 465 SER H 142 REMARK 465 MET c 0 REMARK 465 TYR c 132 REMARK 465 MET C 0 REMARK 465 TYR C 132 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 PRO L 26 130.81 -37.40 REMARK 500 LEU L 29 -6.61 66.21 REMARK 500 SER L 30 -92.77 44.39 REMARK 500 VAL L 31 124.39 45.41 REMARK 500 ALA L 69 -49.08 160.01 REMARK 500 ALA L 73 -71.28 -80.65 REMARK 500 ASP L 74 -59.29 -125.56 REMARK 500 GLN L 97 166.83 62.56 REMARK 500 GLU L 99 -30.33 162.10 REMARK 500 SER L 103 69.67 61.31 REMARK 500 PHE L 116 174.74 65.22 REMARK 500 PRO H 26 -146.07 -3.31 REMARK 500 LYS H 32 145.96 95.69 REMARK 500 TYR H 46 28.70 -141.29 REMARK 500 THR H 47 70.46 57.80 REMARK 500 THR H 49 48.83 -81.60 REMARK 500 TRP H 66 73.57 59.33 REMARK 500 ASN H 74 -8.71 75.04 REMARK 500 GLN H 101 -60.16 -92.80 REMARK 500 GLU H 108 57.75 -92.96 REMARK 500 LYS c 13 -66.83 75.91 REMARK 500 ARG c 59 154.65 62.77 REMARK 500 PRO c 130 -173.91 -69.31 REMARK 500 GLU C 4 -169.37 -126.58 REMARK 500 LYS C 13 -13.30 63.22 REMARK 500 ASP C 14 160.83 177.47 REMARK 500 ASN C 61 146.57 -170.83 REMARK 500 ALA C 90 115.11 -163.66 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 L 25 PRO L 26 -137.47 REMARK 500 ILE c 11 GLY c 12 -138.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37290 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF QB-AB6 DBREF 8W5F L 16 125 PDB 8W5F 8W5F 16 125 DBREF 8W5F H 17 142 PDB 8W5F 8W5F 17 142 DBREF 8W5F c 0 132 UNP Q8LTE1 A1_BPQBE 1 133 DBREF 8W5F 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 VAL SER VAL GLY GLU THR VAL THR LEU THR CYS SEQRES 3 L 110 ARG ALA SER GLU ASN ILE TYR SER ASN LEU ALA TRP TYR SEQRES 4 L 110 HIS GLN LYS GLN GLY ILE SER PRO GLN LEU LEU VAL TYR SEQRES 5 L 110 ALA ALA ALA LYS LEU ALA ASP GLY VAL PRO SER ARG PHE SEQRES 6 L 110 SER GLY SER GLY SER GLY THR GLN TYR SER PHE LYS ILE SEQRES 7 L 110 ASN SER LEU GLN SER GLU ASP PHE GLY SER TYR TYR CYS SEQRES 8 L 110 GLN HIS PHE TRP GLY 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 GLN VAL GLN LEU GLN GLN PRO GLY THR GLU SEQRES 2 H 126 LEU VAL LYS PRO GLY ALA SER VAL LYS LEU SER CYS LYS SEQRES 3 H 126 ALA SER GLY TYR THR PHE THR SER TYR SER VAL HIS TRP SEQRES 4 H 126 VAL LYS GLN ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY SEQRES 5 H 126 SER ILE ASN PRO ASN ASN ASP VAL ALA TYR PHE ASN GLU SEQRES 6 H 126 LYS PHE LYS THR LYS ALA THR LEU THR VAL ASP ARG SER SEQRES 7 H 126 SER SER THR ALA TYR MET GLN LEU SER SER LEU THR PHE SEQRES 8 H 126 GLU ASP SER ALA VAL TYR TYR CYS ALA ARG GLY GLY ILE SEQRES 9 H 126 HIS TYR THR TYR ASP GLY TYR TYR PHE ASP 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 GLN c 127 1 10 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 23 GLN L 24 0 SHEET 2 AA1 4 VAL L 37 ARG L 42 -1 O ARG L 42 N THR L 23 SHEET 3 AA1 4 GLN L 88 ILE L 93 -1 O PHE L 91 N LEU L 39 SHEET 4 AA1 4 PHE L 80 GLY L 84 -1 N SER L 83 O SER L 90 SHEET 1 AA2 2 LEU L 51 ALA L 52 0 SHEET 2 AA2 2 GLN L 107 HIS L 108 -1 O GLN L 107 N ALA L 52 SHEET 1 AA3 4 GLN H 22 GLN H 24 0 SHEET 2 AA3 4 LEU H 39 SER H 44 -1 O LYS H 42 N GLN H 24 SHEET 3 AA3 4 THR H 97 MET H 100 -1 O ALA H 98 N CYS H 41 SHEET 4 AA3 4 LEU H 89 ASP H 92 -1 N THR H 90 O TYR H 99 SHEET 1 AA4 2 GLU H 29 LEU H 30 0 SHEET 2 AA4 2 LEU H 138 THR H 139 1 O THR H 139 N GLU H 29 SHEET 1 AA5 4 ALA H 77 PHE H 79 0 SHEET 2 AA5 4 GLY H 68 ILE H 70 -1 N SER H 69 O TYR H 78 SHEET 3 AA5 4 VAL H 53 GLN H 58 -1 N TRP H 55 O GLY H 68 SHEET 4 AA5 4 VAL H 112 ARG H 117 -1 O ALA H 116 N HIS H 54 SHEET 1 AA612 VAL c 6 ILE c 11 0 SHEET 2 AA612 GLN c 17 PRO c 23 -1 O LEU c 21 N VAL c 6 SHEET 3 AA612 LEU c 35 SER c 36 -1 O SER c 36 N ASN c 22 SHEET 4 AA612 ARG c 47 VAL c 52 -1 O VAL c 48 N LEU c 35 SHEET 5 AA612 VAL c 64 CYS c 74 -1 O GLN c 65 N SER c 51 SHEET 6 AA612 SER c 83 PHE c 94 -1 O PHE c 94 N VAL c 64 SHEET 7 AA612 SER C 83 THR C 97 -1 O ASP C 91 N THR c 93 SHEET 8 AA612 ASN C 61 CYS C 74 -1 N THR C 72 O ARG C 86 SHEET 9 AA612 ARG C 47 VAL C 52 -1 N THR C 49 O LYS C 67 SHEET 10 AA612 ALA C 33 GLN C 37 -1 N ALA C 33 O VAL C 50 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 L 41 CYS L 106 1555 1555 2.03 SSBOND 2 CYS H 41 CYS H 115 1555 1555 2.03 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