HEADER RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA 21-MAR-25 9U5R TITLE HRV14 3C IN COMPLEX WITH SINGLE CHAIN ANTIBODY YDF AND CLOVERLEAFRNA- TITLE 2 CONFORMATION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE 3C; COMPND 3 CHAIN: O; COMPND 4 SYNONYM: PICORNAIN 3C,P3C; COMPND 5 EC: 3.4.22.28; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: YDF HEAVY CHAIN; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: YDF LIGHT CHAIN; COMPND 13 CHAIN: Q; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: RNA (83-MER); COMPND 17 CHAIN: R; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHINOVIRUS B14; SOURCE 3 ORGANISM_TAXID: 12131; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: RHINOVIRUS B14; SOURCE 19 ORGANISM_TAXID: 12131 KEYWDS CLOVERLEAFRNA, 3C, COMPLEX, RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA, KEYWDS 2 RNA BINDING PROTEIN-IMMUNE SYSTEM-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR B.YANG,Q.WANG,S.W.SUN,X.ZHANG REVDAT 1 25-MAR-26 9U5R 0 JRNL AUTH B.YANG,Q.WANG,S.W.SUN,X.ZHANG JRNL TITL HRV14 3C IN COMPLEX WITH SINGLE CHAIN ANTIBODY YDF AND JRNL TITL 2 CLOVERLEAFRNA,CONFORMATION 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC 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 : FLEXIBLE FIT 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) : 3.590 REMARK 3 NUMBER OF PARTICLES : 198810 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 9U5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 25-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057689. 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 : DIMER3C-YDF-RNA-C2 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 : 8.00 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 : DIRECT ELECTRON DE-16 (4K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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 : 2.70 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: O, P, Q, R 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 G R 17 REMARK 465 U R 18 REMARK 465 A R 19 REMARK 465 U R 20 REMARK 465 C R 21 REMARK 465 C R 22 REMARK 465 C R 23 REMARK 465 A R 24 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 G R 16 OP2 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 ASP O 32 -110.43 53.63 REMARK 500 GLN O 42 71.88 48.91 REMARK 500 LEU O 94 52.19 -93.08 REMARK 500 ASN O 106 -132.22 57.49 REMARK 500 VAL P 50 -62.39 -120.21 REMARK 500 ALA P 94 -168.69 -167.12 REMARK 500 ASP P 116 -50.71 -122.59 REMARK 500 GLN Q 49 -110.08 55.54 REMARK 500 ALA Q 83 -166.11 -163.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63881 RELATED DB: EMDB REMARK 900 HRV14 3C IN COMPLEX WITH SINGLE CHAIN ANTIBODY YDF AND REMARK 900 CLOVERLEAFRNA-CONFORMATION 2 DBREF 9U5R O 2 181 UNP P03303 POLG_HRV14 1539 1718 DBREF 9U5R P 3 129 PDB 9U5R 9U5R 3 129 DBREF 9U5R Q 1 107 PDB 9U5R 9U5R 1 107 DBREF 9U5R R 1 83 PDB 9U5R 9U5R 1 83 SEQRES 1 O 180 PRO ASN THR GLU PHE ALA LEU SER LEU LEU ARG LYS ASN SEQRES 2 O 180 ILE MET THR ILE THR THR SER LYS GLY GLU PHE THR GLY SEQRES 3 O 180 LEU GLY ILE HIS ASP ARG VAL CYS VAL ILE PRO THR HIS SEQRES 4 O 180 ALA GLN PRO GLY ASP ASP VAL LEU VAL ASN GLY GLN LYS SEQRES 5 O 180 ILE ARG VAL LYS ASP LYS TYR LYS LEU VAL ASP PRO GLU SEQRES 6 O 180 ASN ILE ASN LEU GLU LEU THR VAL LEU THR LEU ASP ARG SEQRES 7 O 180 ASN GLU LYS PHE ARG ASP ILE ARG GLY PHE ILE SER GLU SEQRES 8 O 180 ASP LEU GLU GLY VAL ASP ALA THR LEU VAL VAL HIS SER SEQRES 9 O 180 ASN ASN PHE THR ASN THR ILE LEU GLU VAL GLY PRO VAL SEQRES 10 O 180 THR MET ALA GLY LEU ILE ASN LEU SER SER THR PRO THR SEQRES 11 O 180 ASN ARG MET ILE ARG TYR ASP TYR ALA THR LYS THR GLY SEQRES 12 O 180 GLN CYS GLY GLY VAL LEU CYS ALA THR GLY LYS ILE PHE SEQRES 13 O 180 GLY ILE HIS VAL GLY GLY ASN GLY ARG GLN GLY PHE SER SEQRES 14 O 180 ALA GLN LEU LYS LYS GLN TYR PHE VAL GLU LYS SEQRES 1 P 127 GLN VAL GLN LEU LEU GLN SER GLY GLY GLY VAL VAL GLN SEQRES 2 P 127 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 P 127 PHE THR PHE SER SER TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 P 127 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL ILE SER SEQRES 5 P 127 TYR ASP GLY SER ASN LYS TYR TYR ALA ASP SER VAL LYS SEQRES 6 P 127 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 P 127 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 P 127 ALA VAL TYR TYR CYS ALA ARG VAL GLY LYS GLY GLY TYR SEQRES 9 P 127 ASP PHE TRP SER GLY SER GLY TYR MET ASP VAL TRP GLY SEQRES 10 P 127 LYS GLY THR THR VAL THR VAL SER SER GLY SEQRES 1 Q 107 SER TYR VAL LEU THR GLN PRO PRO SER VAL SER VAL SER SEQRES 2 Q 107 PRO GLY GLN THR ALA SER ILE THR CYS SER GLY ASP LYS SEQRES 3 Q 107 LEU GLY ASP LYS TYR ALA CYS TRP TYR GLN GLN LYS PRO SEQRES 4 Q 107 GLY GLN SER PRO VAL LEU VAL ILE TYR GLN ASP SER LYS SEQRES 5 Q 107 ARG PRO SER GLY ILE PRO GLU ARG PHE SER GLY SER ASN SEQRES 6 Q 107 SER GLY ASN THR ALA THR LEU THR ILE SER GLY THR GLN SEQRES 7 Q 107 ALA MET ASP GLU ALA ASP TYR TYR CYS GLN ALA TRP ASP SEQRES 8 Q 107 SER SER THR VAL VAL PHE GLY GLY GLY THR LYS LEU THR SEQRES 9 Q 107 VAL LEU GLY SEQRES 1 R 83 G G G A A A C A G C G G A SEQRES 2 R 83 U G G G U A U C C C A C C SEQRES 3 R 83 A U U C G A C C C A U U G SEQRES 4 R 83 G G U G U A G U A C U C U SEQRES 5 R 83 G G U A C U A U G U A C C SEQRES 6 R 83 U U U G U A C G C C U G U SEQRES 7 R 83 U U C C C HELIX 1 AA1 ASN O 3 ASN O 14 1 12 HELIX 2 AA2 PRO O 38 GLN O 42 5 5 HELIX 3 AA3 ILE O 86 ILE O 90 5 5 HELIX 4 AA4 ARG P 89 THR P 93 5 5 HELIX 5 AA5 LYS Q 26 LYS Q 30 5 5 HELIX 6 AA6 GLN Q 78 GLU Q 82 5 5 SHEET 1 AA1 7 ILE O 15 THR O 20 0 SHEET 2 AA1 7 GLY O 23 HIS O 31 -1 O GLY O 27 N MET O 16 SHEET 3 AA1 7 VAL O 34 ILE O 37 -1 O VAL O 34 N ILE O 30 SHEET 4 AA1 7 ILE O 68 LEU O 77 -1 O THR O 73 N ILE O 37 SHEET 5 AA1 7 GLN O 52 ASP O 64 -1 N ASP O 64 O ILE O 68 SHEET 6 AA1 7 ASP O 46 VAL O 49 -1 N VAL O 47 O ILE O 54 SHEET 7 AA1 7 ILE O 15 THR O 20 -1 N THR O 19 O LEU O 48 SHEET 1 AA2 8 THR O 119 MET O 120 0 SHEET 2 AA2 8 MET O 134 ASP O 138 -1 O ARG O 136 N THR O 119 SHEET 3 AA2 8 GLN O 167 GLN O 172 -1 O GLY O 168 N TYR O 137 SHEET 4 AA2 8 LYS O 155 GLY O 163 -1 N GLY O 162 O PHE O 169 SHEET 5 AA2 8 VAL O 149 ALA O 152 -1 N LEU O 150 O GLY O 158 SHEET 6 AA2 8 THR O 100 SER O 105 -1 N THR O 100 O CYS O 151 SHEET 7 AA2 8 PHE O 108 LEU O 113 -1 O THR O 111 N VAL O 103 SHEET 8 AA2 8 GLY P 105 ASP P 107 -1 O TYR P 106 N ILE O 112 SHEET 1 AA3 2 LEU O 123 LEU O 126 0 SHEET 2 AA3 2 THR O 129 ASN O 132 -1 O THR O 129 N LEU O 126 SHEET 1 AA4 4 GLN P 5 GLY P 10 0 SHEET 2 AA4 4 LEU P 20 SER P 27 -1 O SER P 27 N GLN P 5 SHEET 3 AA4 4 THR P 80 MET P 85 -1 O MET P 85 N LEU P 20 SHEET 4 AA4 4 PHE P 70 ASP P 75 -1 N SER P 73 O TYR P 82 SHEET 1 AA5 6 GLY P 12 VAL P 14 0 SHEET 2 AA5 6 THR P 122 VAL P 126 1 O THR P 125 N VAL P 14 SHEET 3 AA5 6 ALA P 94 ALA P 99 -1 N ALA P 94 O VAL P 124 SHEET 4 AA5 6 MET P 36 GLN P 41 -1 N VAL P 39 O TYR P 97 SHEET 5 AA5 6 LEU P 47 ILE P 53 -1 O GLU P 48 N ARG P 40 SHEET 6 AA5 6 LYS P 60 TYR P 62 -1 O TYR P 61 N VAL P 52 SHEET 1 AA6 4 LEU Q 4 THR Q 5 0 SHEET 2 AA6 4 ALA Q 18 GLY Q 24 -1 O SER Q 23 N THR Q 5 SHEET 3 AA6 4 THR Q 69 ILE Q 74 -1 O LEU Q 72 N ILE Q 20 SHEET 4 AA6 4 PHE Q 61 SER Q 66 -1 N SER Q 62 O THR Q 73 SHEET 1 AA7 5 SER Q 9 SER Q 11 0 SHEET 2 AA7 5 THR Q 101 THR Q 104 1 O LYS Q 102 N VAL Q 10 SHEET 3 AA7 5 ASP Q 84 ASP Q 91 -1 N TYR Q 85 O THR Q 101 SHEET 4 AA7 5 TYR Q 31 GLN Q 37 -1 N GLN Q 37 O ASP Q 84 SHEET 5 AA7 5 VAL Q 44 ILE Q 47 -1 O VAL Q 44 N GLN Q 36 SHEET 1 AA8 4 SER Q 9 SER Q 11 0 SHEET 2 AA8 4 THR Q 101 THR Q 104 1 O LYS Q 102 N VAL Q 10 SHEET 3 AA8 4 ASP Q 84 ASP Q 91 -1 N TYR Q 85 O THR Q 101 SHEET 4 AA8 4 THR Q 94 PHE Q 97 -1 O VAL Q 96 N ALA Q 89 SSBOND 1 CYS P 24 CYS P 98 1555 1555 2.99 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 CONECT 1550 2139 CONECT 2139 1550 MASTER 150 0 0 6 40 0 0 6 4743 4 2 40 END