HEADER IMMUNE SYSTEM 26-AUG-23 8W5D TITLE CRYO-EM STRUCTURE OF QB-AB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF AB1; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MINOR CAPSID PROTEIN A1; COMPND 7 CHAIN: c, C; COMPND 8 SYNONYM: QB COAT PROTEIN; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF AB1; COMPND 12 CHAIN: L; 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: ESCHERICHIA PHAGE QBETA; SOURCE 8 ORGANISM_TAXID: 2789016; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS QB, CRYO-EM, ANTIBODY, 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 8W5D 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. 4.30 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 63988 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 8W5D 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_1300040588. 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-AB1 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) : 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) : 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: H, c, C, L 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 H 1 REMARK 465 HIS H 2 REMARK 465 SER H 3 REMARK 465 GLN H 4 REMARK 465 VAL H 5 REMARK 465 GLN H 6 REMARK 465 TRP H 116 REMARK 465 GLY H 117 REMARK 465 GLN H 118 REMARK 465 GLY H 119 REMARK 465 THR H 120 REMARK 465 THR H 121 REMARK 465 LEU H 122 REMARK 465 SER c 56 REMARK 465 ARG c 57 REMARK 465 ASN c 58 REMARK 465 ARG c 59 REMARK 465 SER C 56 REMARK 465 ARG C 57 REMARK 465 ASN C 58 REMARK 465 ARG C 59 REMARK 465 VAL L 1 REMARK 465 THR L 8 REMARK 465 GLN L 9 REMARK 465 SER L 10 REMARK 465 PRO L 11 REMARK 465 ALA L 12 REMARK 465 SER L 13 REMARK 465 LEU L 14 REMARK 465 ALA L 15 REMARK 465 GLU L 86 REMARK 465 GLU L 87 REMARK 465 ASP L 88 REMARK 465 ASP L 89 REMARK 465 THR L 90 REMARK 465 ALA L 91 REMARK 465 MET L 92 REMARK 465 TYR L 93 REMARK 465 PHE L 94 REMARK 465 THR L 109 REMARK 465 LYS L 110 REMARK 465 LEU L 111 REMARK 465 GLU L 112 REMARK 465 ILE L 113 REMARK 465 LYS L 114 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 CG2 VAL L 6 O THR L 23 1.88 REMARK 500 CG2 VAL L 6 CA ILE L 24 2.13 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 LEU H 48 CA - CB - CG ANGL. DEV. = 16.1 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 PHE H 30 -179.86 -69.02 REMARK 500 GLU H 49 -155.88 -137.39 REMARK 500 TRP H 50 160.78 -49.17 REMARK 500 ARG H 69 -159.85 -136.87 REMARK 500 LEU H 70 65.45 61.87 REMARK 500 ASN H 76 14.01 -141.07 REMARK 500 ASP H 92 57.93 -97.69 REMARK 500 GLN H 103 49.17 -92.00 REMARK 500 ASN H 104 49.98 -144.86 REMARK 500 PHE H 113 70.35 57.78 REMARK 500 LYS c 13 -20.73 68.15 REMARK 500 ASP c 14 153.45 179.17 REMARK 500 ASN c 61 -167.13 -161.50 REMARK 500 ALA c 88 51.14 -142.14 REMARK 500 ASN C 10 65.25 60.04 REMARK 500 LYS C 13 -20.77 68.11 REMARK 500 ASP C 14 153.51 179.21 REMARK 500 ASN C 61 -167.17 -161.49 REMARK 500 ALA C 88 51.14 -142.10 REMARK 500 LEU L 18 -8.71 71.88 REMARK 500 GLU L 30 70.52 47.36 REMARK 500 ASP L 33 -165.86 -127.13 REMARK 500 TYR L 35 -6.15 68.40 REMARK 500 ILE L 37 -48.43 -130.76 REMARK 500 ALA L 58 -11.14 70.33 REMARK 500 SER L 59 24.07 -150.21 REMARK 500 GLN L 61 72.05 56.83 REMARK 500 GLU L 100 -81.50 -83.08 REMARK 500 PHE L 105 -175.96 -171.91 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 ASP c 14 GLY c 15 149.24 REMARK 500 ASP C 14 GLY C 15 149.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37286 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF QB-AB1 DBREF 8W5D H 1 122 PDB 8W5D 8W5D 1 122 DBREF 8W5D c 1 131 UNP Q8LTE1 A1_BPQBE 2 132 DBREF 8W5D C 1 131 UNP Q8LTE1 A1_BPQBE 2 132 DBREF 8W5D L 1 114 PDB 8W5D 8W5D 1 114 SEQRES 1 H 122 VAL HIS SER GLN VAL GLN LEU LYS GLN SER GLY PRO GLY SEQRES 2 H 122 LEU VAL GLN PRO SER GLN SER LEU SER ILE THR CYS THR SEQRES 3 H 122 VAL SER GLY PHE SER LEU THR SER TYR GLY VAL HIS TRP SEQRES 4 H 122 VAL ARG GLN SER PRO GLY LYS GLY LEU GLU TRP LEU GLY SEQRES 5 H 122 VAL ILE TRP SER GLY GLY ASN THR ASP TYR ASP ALA ALA SEQRES 6 H 122 PHE ILE SER ARG LEU SER ILE ARG LYS ASP ASN SER LYS SEQRES 7 H 122 ASN GLN VAL PHE PHE LYS MET ASN SER LEU GLN ALA ASP SEQRES 8 H 122 ASP THR ALA ILE TYR TYR CYS ALA ARG GLU SER GLN ASN SEQRES 9 H 122 TYR TYR GLY ASN THR TRP ASN TYR PHE ASP TYR TRP GLY SEQRES 10 H 122 GLN GLY THR THR LEU SEQRES 1 c 131 ALA LYS LEU GLU THR VAL THR LEU GLY ASN ILE GLY LYS SEQRES 2 c 131 ASP GLY LYS GLN THR LEU VAL LEU ASN PRO ARG GLY VAL SEQRES 3 c 131 ASN PRO THR ASN GLY VAL ALA SER LEU SER GLN ALA GLY SEQRES 4 c 131 ALA VAL PRO ALA LEU GLU LYS ARG VAL THR VAL SER VAL SEQRES 5 c 131 SER GLN PRO SER ARG ASN ARG LYS ASN TYR LYS VAL GLN SEQRES 6 c 131 VAL LYS ILE GLN ASN PRO THR ALA CYS THR ALA ASN GLY SEQRES 7 c 131 SER CYS ASP PRO SER VAL THR ARG GLN ALA TYR ALA ASP SEQRES 8 c 131 VAL THR PHE SER PHE THR GLN TYR SER THR ASP GLU GLU SEQRES 9 c 131 ARG ALA PHE VAL ARG THR GLU LEU ALA ALA LEU LEU ALA SEQRES 10 c 131 SER PRO LEU LEU ILE ASP ALA ILE ASP GLN LEU ASN PRO SEQRES 11 c 131 ALA SEQRES 1 C 131 ALA LYS LEU GLU THR VAL THR LEU GLY ASN ILE GLY LYS SEQRES 2 C 131 ASP GLY LYS GLN THR LEU VAL LEU ASN PRO ARG GLY VAL SEQRES 3 C 131 ASN PRO THR ASN GLY VAL ALA SER LEU SER GLN ALA GLY SEQRES 4 C 131 ALA VAL PRO ALA LEU GLU LYS ARG VAL THR VAL SER VAL SEQRES 5 C 131 SER GLN PRO SER ARG ASN ARG LYS ASN TYR LYS VAL GLN SEQRES 6 C 131 VAL LYS ILE GLN ASN PRO THR ALA CYS THR ALA ASN GLY SEQRES 7 C 131 SER CYS ASP PRO SER VAL THR ARG GLN ALA TYR ALA ASP SEQRES 8 C 131 VAL THR PHE SER PHE THR GLN TYR SER THR ASP GLU GLU SEQRES 9 C 131 ARG ALA PHE VAL ARG THR GLU LEU ALA ALA LEU LEU ALA SEQRES 10 C 131 SER PRO LEU LEU ILE ASP ALA ILE ASP GLN LEU ASN PRO SEQRES 11 C 131 ALA SEQRES 1 L 114 VAL HIS SER ASP ILE VAL LEU THR GLN SER PRO ALA SER SEQRES 2 L 114 LEU ALA VAL SER LEU GLY GLN ARG ALA THR ILE SER CYS SEQRES 3 L 114 ARG ALA SER GLU SER VAL ASP ASN TYR GLY ILE SER PHE SEQRES 4 L 114 MET ASN TRP PHE GLN GLN LYS PRO GLY GLN PRO PRO LYS SEQRES 5 L 114 LEU LEU ILE TYR ALA ALA SER ASN GLN GLY SER GLY VAL SEQRES 6 L 114 PRO ALA ARG PHE SER GLY SER GLY SER GLY THR ASP PHE SEQRES 7 L 114 SER LEU ASN ILE HIS PRO VAL GLU GLU ASP ASP THR ALA SEQRES 8 L 114 MET TYR PHE CYS GLN GLN SER LYS GLU VAL PRO TYR THR SEQRES 9 L 114 PHE GLY GLY GLY THR LYS LEU GLU ILE LYS HELIX 1 AA1 SER H 31 THR H 33 5 3 HELIX 2 AA2 THR c 101 LEU c 116 1 16 HELIX 3 AA3 SER c 118 GLN c 127 1 10 HELIX 4 AA4 THR C 101 LEU C 116 1 16 HELIX 5 AA5 SER C 118 GLN C 127 1 10 SHEET 1 AA1 2 LEU H 21 ILE H 23 0 SHEET 2 AA1 2 PHE H 83 MET H 85 -1 O PHE H 83 N ILE H 23 SHEET 1 AA2 3 ILE H 54 TRP H 55 0 SHEET 2 AA2 3 TYR H 35 GLN H 42 -1 N VAL H 37 O ILE H 54 SHEET 3 AA2 3 ILE H 95 SER H 102 -1 O TYR H 97 N VAL H 40 SHEET 1 AA3 2 ASN H 104 TYR H 106 0 SHEET 2 AA3 2 VAL C 6 LEU C 8 -1 O THR C 7 N TYR H 105 SHEET 1 AA410 ASN c 22 VAL c 26 0 SHEET 2 AA410 ALA c 33 SER c 36 -1 O SER c 36 N ASN c 22 SHEET 3 AA410 ARG c 47 VAL c 50 -1 O VAL c 50 N ALA c 33 SHEET 4 AA410 VAL c 64 GLN c 69 -1 O GLN c 69 N ARG c 47 SHEET 5 AA410 ALA c 90 PHE c 94 -1 O VAL c 92 N VAL c 66 SHEET 6 AA410 ALA C 90 PHE C 94 -1 O THR C 93 N ASP c 91 SHEET 7 AA410 VAL C 64 GLN C 69 -1 N VAL C 66 O VAL C 92 SHEET 8 AA410 ARG C 47 VAL C 50 -1 N ARG C 47 O GLN C 69 SHEET 9 AA410 ALA C 33 SER C 36 -1 N ALA C 33 O VAL C 50 SHEET 10 AA410 ASN C 22 VAL C 26 -1 N ASN C 22 O SER C 36 SHEET 1 AA5 2 THR c 72 CYS c 74 0 SHEET 2 AA5 2 SER c 83 ARG c 86 -1 N SER c 83 O CYS c 74 SHEET 1 AA6 2 THR C 72 CYS C 74 0 SHEET 2 AA6 2 SER C 83 ARG C 86 -1 N SER C 83 O CYS C 74 SHEET 1 AA7 2 ASP L 4 ILE L 5 0 SHEET 2 AA7 2 SER L 25 CYS L 26 -1 O SER L 25 N ILE L 5 SHEET 1 AA8 4 LYS L 52 LEU L 53 0 SHEET 2 AA8 4 ASN L 41 GLN L 44 -1 N GLN L 44 O LYS L 52 SHEET 3 AA8 4 GLN L 96 GLN L 97 -1 O GLN L 97 N ASN L 41 SHEET 4 AA8 4 PHE L 105 GLY L 106 -1 O GLY L 106 N GLN L 96 SHEET 1 AA9 2 GLY L 71 SER L 72 0 SHEET 2 AA9 2 SER L 79 LEU L 80 -1 O SER L 79 N SER L 72 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