HEADER PROTEIN BINDING/IMMUNE SYSTEM 14-APR-25 9UHQ TITLE LOCAL REFINEMENT OF JN.1 SPIKE IN COMPLEX WITH ANTIBODY BA5-39 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN (RBD); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BA5-39-L; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: BA5-39-H; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 STRAIN: OMICRON/JN.1; SOURCE 7 GENE: S, 2; SOURCE 8 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, COMPLEX, VIRAL PROTEIN, ANTIBODY, PROTEIN BINDING/IMMUNE KEYWDS 2 SYSTEM, PROTEIN BINDING-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.YUE,X.MAO REVDAT 1 22-JUL-26 9UHQ 0 JRNL AUTH C.YUE,X.MAO JRNL TITL LOCAL REFINEMENT OF JN.1 SPIKE IN COMPLEX WITH ANTIBODY JRNL TITL 2 BA5-39 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.62 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) : 4.620 REMARK 3 NUMBER OF PARTICLES : 161866 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9UHQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300058512. 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 : JN.1 SPIKE IN COMPLEX WITH REMARK 245 ANTIBODY BA5-39 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DARK 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: 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 ASP B 70 CB - CG - OD2 ANGL. DEV. = 5.4 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 VAL A 10 -61.87 -97.71 REMARK 500 ASN A 29 63.61 61.78 REMARK 500 TYR A 38 46.80 -82.82 REMARK 500 PRO A 42 7.83 -67.89 REMARK 500 TYR A 92 111.66 -160.93 REMARK 500 ASP A 97 32.85 -97.09 REMARK 500 ASN A 155 19.10 59.00 REMARK 500 CYS A 193 -171.03 -172.31 REMARK 500 ASN B 30 -115.10 59.94 REMARK 500 PHE B 32 72.96 -100.32 REMARK 500 VAL C 48 -63.00 -109.33 REMARK 500 SER C 84 69.06 61.21 REMARK 500 ALA C 91 -171.05 -171.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64172 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF JN.1 SPIKE IN COMPLEX WITH ANTIBODY BA5-39 DBREF 9UHQ A 1 198 UNP P0DTC2 SPIKE_SARS2 332 530 DBREF 9UHQ B 1 107 PDB 9UHQ 9UHQ 1 107 DBREF 9UHQ C 1 119 PDB 9UHQ 9UHQ 1 119 SEQADV 9UHQ VAL A 1 UNP P0DTC2 ILE 332 CONFLICT SEQADV 9UHQ HIS A 8 UNP P0DTC2 GLY 339 VARIANT SEQADV 9UHQ THR A 25 UNP P0DTC2 LYS 356 CONFLICT SEQADV 9UHQ PHE A 40 UNP P0DTC2 SER 371 VARIANT SEQADV 9UHQ PRO A 42 UNP P0DTC2 SER 373 VARIANT SEQADV 9UHQ PHE A 44 UNP P0DTC2 SER 375 VARIANT SEQADV 9UHQ ALA A 45 UNP P0DTC2 THR 376 VARIANT SEQADV 9UHQ LYS A 72 UNP P0DTC2 ARG 403 CONFLICT SEQADV 9UHQ ASN A 74 UNP P0DTC2 ASP 405 VARIANT SEQADV 9UHQ SER A 77 UNP P0DTC2 ARG 408 VARIANT SEQADV 9UHQ ASN A 86 UNP P0DTC2 LYS 417 VARIANT SEQADV 9UHQ LYS A 109 UNP P0DTC2 ASN 440 VARIANT SEQADV 9UHQ HIS A 114 UNP P0DTC2 VAL 445 CONFLICT SEQADV 9UHQ SER A 115 UNP P0DTC2 GLY 446 VARIANT SEQADV 9UHQ ASP A 119 UNP P0DTC2 ASN 450 CONFLICT SEQADV 9UHQ TRP A 121 UNP P0DTC2 LEU 452 CONFLICT SEQADV 9UHQ SER A 124 UNP P0DTC2 LEU 455 CONFLICT SEQADV 9UHQ LYS A 129 UNP P0DTC2 ASN 460 VARIANT SEQADV 9UHQ ASN A 146 UNP P0DTC2 SER 477 VARIANT SEQADV 9UHQ LYS A 147 UNP P0DTC2 THR 478 VARIANT SEQADV 9UHQ LYS A 150 UNP P0DTC2 ASN 481 CONFLICT SEQADV 9UHQ A UNP P0DTC2 VAL 483 DELETION SEQADV 9UHQ LYS A 152 UNP P0DTC2 GLU 484 VARIANT SEQADV 9UHQ PRO A 154 UNP P0DTC2 PHE 486 VARIANT SEQADV 9UHQ ARG A 166 UNP P0DTC2 GLN 498 VARIANT SEQADV 9UHQ TYR A 169 UNP P0DTC2 ASN 501 VARIANT SEQADV 9UHQ HIS A 173 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 198 VAL THR ASN LEU CYS PRO PHE HIS GLU VAL PHE ASN ALA SEQRES 2 A 198 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG THR ARG SEQRES 3 A 198 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 4 A 198 PHE ALA PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER SEQRES 5 A 198 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 6 A 198 ALA ASP SER PHE VAL ILE LYS GLY ASN GLU VAL SER GLN SEQRES 7 A 198 ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN SEQRES 8 A 198 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 9 A 198 TRP ASN SER ASN LYS LEU ASP SER LYS HIS SER GLY ASN SEQRES 10 A 198 TYR ASP TYR TRP TYR ARG SER PHE ARG LYS SER LYS LEU SEQRES 11 A 198 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 12 A 198 ALA GLY ASN LYS PRO CYS LYS GLY LYS GLY PRO ASN CYS SEQRES 13 A 198 TYR PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR SEQRES 14 A 198 GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 198 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 A 198 LYS LYS SER SEQRES 1 B 107 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 107 PHE VAL GLY ASP ARG VAL THR ILE THR CYS GLN ALA SER SEQRES 3 B 107 GLN ASP ILE ASN ASN PHE LEU ASN TRP TYR GLN GLN LYS SEQRES 4 B 107 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 B 107 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 107 GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER LEU SEQRES 7 B 107 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS HIS GLN TYR SEQRES 8 B 107 ASP ASN LEU PRO ARG THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 B 107 GLU ILE LYS SEQRES 1 C 119 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 C 119 PRO GLY GLY SER LEU ARG VAL SER CYS ALA ALA SER GLY SEQRES 3 C 119 LEU THR VAL SER ARG ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 C 119 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER LEU ILE TYR SEQRES 5 C 119 PRO GLY GLY SER SER TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 119 ARG PHE THR VAL SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 C 119 PHE LEU GLN MET ASN SER LEU THR ALA GLU ASP THR ALA SEQRES 8 C 119 VAL TYR TYR CYS ALA ARG ASP ILE VAL GLY GLY ARG ALA SEQRES 9 C 119 GLY MET ASP VAL TRP GLY GLN GLY THR THR VAL ILE VAL SEQRES 10 C 119 SER SER HELIX 1 AA1 PRO A 6 VAL A 10 5 5 HELIX 2 AA2 SER A 18 TRP A 22 5 5 HELIX 3 AA3 ASP A 33 PHE A 40 5 8 HELIX 4 AA4 SER A 52 ASP A 58 5 7 HELIX 5 AA5 GLY A 73 ILE A 79 5 7 HELIX 6 AA6 GLY A 85 ASN A 91 1 7 HELIX 7 AA7 SER A 107 SER A 112 1 6 HELIX 8 AA8 GLY A 170 GLN A 174 5 5 HELIX 9 AA9 PRO A 195 SER A 198 5 4 HELIX 10 AB1 GLN B 79 ILE B 83 5 5 HELIX 11 AB2 THR C 28 ASN C 32 5 5 HELIX 12 AB3 THR C 86 THR C 90 5 5 SHEET 1 AA1 5 ASN A 23 ILE A 27 0 SHEET 2 AA1 5 ASN A 63 ILE A 71 -1 O ALA A 66 N THR A 25 SHEET 3 AA1 5 TYR A 176 GLU A 184 -1 O VAL A 178 N PHE A 69 SHEET 4 AA1 5 GLY A 100 ASN A 106 -1 N ILE A 103 O VAL A 179 SHEET 5 AA1 5 PHE A 44 TYR A 49 -1 N TYR A 49 O GLY A 100 SHEET 1 AA2 2 CYS A 60 PHE A 61 0 SHEET 2 AA2 2 VAL A 192 CYS A 193 -1 O VAL A 192 N PHE A 61 SHEET 1 AA3 2 TRP A 121 ARG A 123 0 SHEET 2 AA3 2 LEU A 160 SER A 162 -1 O GLN A 161 N TYR A 122 SHEET 1 AA4 2 TYR A 142 GLN A 143 0 SHEET 2 AA4 2 CYS A 156 TYR A 157 -1 O TYR A 157 N TYR A 142 SHEET 1 AA5 4 MET B 4 SER B 7 0 SHEET 2 AA5 4 VAL B 19 ALA B 25 -1 O THR B 22 N SER B 7 SHEET 3 AA5 4 ASP B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA5 4 PHE B 62 SER B 67 -1 N SER B 63 O THR B 74 SHEET 1 AA6 6 SER B 10 ALA B 13 0 SHEET 2 AA6 6 THR B 102 ILE B 106 1 O LYS B 103 N LEU B 11 SHEET 3 AA6 6 THR B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA6 6 LEU B 33 GLN B 38 -1 N ASN B 34 O HIS B 89 SHEET 5 AA6 6 LYS B 45 TYR B 49 -1 O LYS B 45 N GLN B 37 SHEET 6 AA6 6 ASN B 53 LEU B 54 -1 O ASN B 53 N TYR B 49 SHEET 1 AA7 4 SER B 10 ALA B 13 0 SHEET 2 AA7 4 THR B 102 ILE B 106 1 O LYS B 103 N LEU B 11 SHEET 3 AA7 4 THR B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA7 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AA8 4 GLN C 3 SER C 7 0 SHEET 2 AA8 4 LEU C 18 SER C 25 -1 O SER C 21 N SER C 7 SHEET 3 AA8 4 THR C 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AA8 4 PHE C 67 ASP C 72 -1 N ASP C 72 O THR C 77 SHEET 1 AA9 6 LEU C 11 ILE C 12 0 SHEET 2 AA9 6 THR C 113 VAL C 117 1 O ILE C 116 N ILE C 12 SHEET 3 AA9 6 ALA C 91 ALA C 96 -1 N ALA C 91 O VAL C 115 SHEET 4 AA9 6 MET C 34 GLN C 39 -1 N VAL C 37 O TYR C 94 SHEET 5 AA9 6 LEU C 45 ILE C 51 -1 O SER C 49 N TRP C 36 SHEET 6 AA9 6 SER C 57 TYR C 59 -1 O TYR C 58 N LEU C 50 SSBOND 1 CYS A 5 CYS A 30 1555 1555 2.04 SSBOND 2 CYS A 48 CYS A 101 1555 1555 2.04 SSBOND 3 CYS A 60 CYS A 193 1555 1555 2.04 SSBOND 4 CYS A 149 CYS A 156 1555 1555 2.04 SSBOND 5 CYS B 23 CYS B 88 1555 1555 2.04 SSBOND 6 CYS C 22 CYS C 95 1555 1555 2.04 CISPEP 1 SER B 7 PRO B 8 0 -5.26 CISPEP 2 LEU B 94 PRO B 95 0 -6.06 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 36 247 CONECT 247 36 CONECT 396 801 CONECT 486 1553 CONECT 801 396 CONECT 1207 1254 CONECT 1254 1207 CONECT 1553 486 CONECT 1759 2266 CONECT 2266 1759 CONECT 2576 3144 CONECT 3144 2576 MASTER 146 0 0 12 35 0 0 6 3312 3 12 35 END