HEADER IMMUNE SYSTEM 27-AUG-23 8W5V TITLE CRYO-EM STRUCTURE OF QBN10K-AB40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF AB40; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF AB40; 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 REVDAT 1 26-FEB-25 8W5V 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. 3.40 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 802733 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 8W5V 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_1300040618. 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 QBN10K-AB40 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) : 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) : 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: 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 LYS L 111 REMARK 465 LEU L 112 REMARK 465 GLU L 113 REMARK 465 ILE L 114 REMARK 465 LYS L 115 REMARK 465 VAL H 1 REMARK 465 HIS H 2 REMARK 465 SER H 3 REMARK 465 GLU H 4 REMARK 465 THR H 118 REMARK 465 VAL H 119 REMARK 465 SER H 120 REMARK 465 SER H 121 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 O LEU c 8 OG1 THR c 18 2.16 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 ALA L 60 -5.18 68.82 REMARK 500 SER L 86 156.13 64.74 REMARK 500 ASP L 91 30.47 -140.06 REMARK 500 ALA L 93 175.45 77.44 REMARK 500 ARG L 102 -96.01 57.13 REMARK 500 SER H 17 -150.03 53.72 REMARK 500 SER H 43 -136.40 54.73 REMARK 500 SER H 47 159.89 69.19 REMARK 500 ILE H 51 -59.32 -121.95 REMARK 500 LYS H 66 24.79 47.45 REMARK 500 ALA C 40 -5.59 67.45 REMARK 500 ALA c 40 -5.12 67.85 REMARK 500 TYR c 99 31.12 -93.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37305 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF QBN10K-AB40 DBREF 8W5V L 1 115 PDB 8W5V 8W5V 1 115 DBREF 8W5V H 1 121 PDB 8W5V 8W5V 1 121 DBREF 8W5V C 0 132 UNP Q8LTE1 A1_BPQBE 1 133 DBREF 8W5V c 0 132 UNP Q8LTE1 A1_BPQBE 1 133 SEQADV 8W5V LYS C 10 UNP Q8LTE1 ASN 11 CONFLICT SEQADV 8W5V LYS c 10 UNP Q8LTE1 ASN 11 CONFLICT SEQRES 1 L 115 VAL HIS SER ASP ILE VAL MET SER GLN SER PRO SER SER SEQRES 2 L 115 LEU ALA VAL SER ILE GLY GLU LYS VAL THR LEU THR CYS SEQRES 3 L 115 LYS SER SER GLN SER LEU LEU PHE SER SER ASN GLN LYS SEQRES 4 L 115 ASN TYR LEU ALA TRP TYR GLN GLN ASN PRO GLY GLN SER SEQRES 5 L 115 PRO LYS LEU LEU ILE TYR TRP ALA SER THR ARG GLU SER SEQRES 6 L 115 GLY VAL PRO ASP ARG PHE THR GLY SER GLY SER GLY THR SEQRES 7 L 115 ASP PHE THR LEU THR ILE SER SER VAL LYS ALA GLU ASP SEQRES 8 L 115 LEU ALA ILE TYR TYR CYS GLN GLN TYR PHE ARG TYR PRO SEQRES 9 L 115 ALA PHE GLY GLY GLY THR LYS LEU GLU ILE LYS SEQRES 1 H 121 VAL HIS SER GLU VAL GLN LEU GLN GLN SER GLY PRO GLU SEQRES 2 H 121 LEU VAL LYS SER GLY THR SER VAL LYS LEU SER CYS LYS SEQRES 3 H 121 ALA SER GLY TYR SER PHE THR ASP HIS SER LEU HIS TRP SEQRES 4 H 121 VAL LYS GLN SER HIS GLY GLU SER LEU GLU TRP ILE GLY SEQRES 5 H 121 TYR PHE SER PRO ASN ASN GLY GLY THR ILE TYR ASN GLN SEQRES 6 H 121 LYS PHE MET GLY LYS ALA THR LEU THR VAL ASP ARG SER SEQRES 7 H 121 SER SER THR ALA TYR MET ASP LEU HIS ASN LEU THR SER SEQRES 8 H 121 ALA ASP SER ALA VAL TYR PHE CYS SER THR GLY TRP ASP SEQRES 9 H 121 TYR GLY PRO PHE ASP SER TRP GLY GLN GLY THR THR LEU SEQRES 10 H 121 THR VAL SER SER SEQRES 1 C 133 MET ALA LYS LEU GLU THR VAL THR LEU GLY LYS 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 LYS 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 LEU c 116 1 16 HELIX 4 AA4 SER c 118 GLN c 127 1 10 SHEET 1 AA1 3 THR L 23 LYS L 27 0 SHEET 2 AA1 3 ASP L 79 ILE L 84 -1 O LEU L 82 N LEU L 24 SHEET 3 AA1 3 PHE L 71 SER L 74 -1 N THR L 72 O THR L 83 SHEET 1 AA2 4 THR L 62 ARG L 63 0 SHEET 2 AA2 4 LYS L 54 TYR L 58 -1 N TYR L 58 O THR L 62 SHEET 3 AA2 4 LEU L 42 GLN L 47 -1 N GLN L 46 O LYS L 54 SHEET 4 AA2 4 ILE L 94 GLN L 99 -1 O TYR L 96 N TYR L 45 SHEET 1 AA3 4 GLN H 6 GLN H 9 0 SHEET 2 AA3 4 VAL H 21 SER H 28 -1 O LYS H 26 N GLN H 8 SHEET 3 AA3 4 THR H 81 LEU H 86 -1 O ALA H 82 N CYS H 25 SHEET 4 AA3 4 THR H 72 ASP H 76 -1 N ASP H 76 O THR H 81 SHEET 1 AA4 5 ILE H 62 TYR H 63 0 SHEET 2 AA4 5 GLY H 52 PHE H 54 -1 N TYR H 53 O ILE H 62 SHEET 3 AA4 5 SER H 36 HIS H 38 -1 N LEU H 37 O PHE H 54 SHEET 4 AA4 5 SER H 100 GLY H 102 -1 O GLY H 102 N SER H 36 SHEET 5 AA4 5 PHE H 108 TRP H 111 -1 O ASP H 109 N THR H 101 SHEET 1 AA512 VAL C 6 ILE C 11 0 SHEET 2 AA512 GLN C 17 VAL C 26 -1 O LEU C 19 N LEU C 8 SHEET 3 AA512 ALA C 33 SER C 36 -1 O SER C 36 N ASN C 22 SHEET 4 AA512 ARG C 47 VAL C 52 -1 O VAL C 50 N ALA C 33 SHEET 5 AA512 VAL C 64 CYS C 74 -1 O GLN C 65 N SER C 51 SHEET 6 AA512 SER C 83 PHE C 94 -1 O PHE C 94 N VAL C 64 SHEET 7 AA512 SER c 83 PHE c 94 -1 O ASP c 91 N THR C 93 SHEET 8 AA512 VAL c 64 CYS c 74 -1 N VAL c 66 O VAL c 92 SHEET 9 AA512 ARG c 47 VAL c 52 -1 N SER c 51 O GLN c 65 SHEET 10 AA512 VAL c 32 SER c 36 -1 N ALA c 33 O VAL c 50 SHEET 11 AA512 GLN c 17 ASN c 27 -1 N ASN c 22 O SER c 36 SHEET 12 AA512 VAL c 6 ILE c 11 -1 N VAL c 6 O LEU c 21 SSBOND 1 CYS H 25 CYS H 99 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