HEADER VIRAL PROTEIN/TRANSFERASE 07-FEB-23 8I9J TITLE THE PKR AND E3L COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN E3; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: P25; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INTERFERON-INDUCED, DOUBLE-STRANDED RNA-ACTIVATED PROTEIN COMPND 8 KINASE; COMPND 9 CHAIN: A; COMPND 10 SYNONYM: EUKARYOTIC TRANSLATION INITIATION FACTOR 2-ALPHA KINASE 2, COMPND 11 EIF-2A PROTEIN KINASE 2,INTERFERON-INDUCIBLE RNA-DEPENDENT PROTEIN COMPND 12 KINASE,P1/EIF-2A PROTEIN KINASE,PROTEIN KINASE RNA-ACTIVATED,PKR, COMPND 13 PROTEIN KINASE R,TYROSINE-PROTEIN KINASE EIF2AK2,P68 KINASE; COMPND 14 EC: 2.7.11.1,2.7.10.2; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: RNA-BINDING PROTEIN E3; COMPND 18 CHAIN: C; COMPND 19 SYNONYM: P25; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS WR; SOURCE 3 ORGANISM_TAXID: 10254; SOURCE 4 STRAIN: WESTERN RESERVE; SOURCE 5 GENE: VACWR059, E3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: EIF2AK2, PKR, PRKR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: VACCINIA VIRUS WR; SOURCE 17 ORGANISM_TAXID: 10254; SOURCE 18 STRAIN: WESTERN RESERVE; SOURCE 19 GENE: VACWR059, E3L; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3L, PKR, VACCINIA VIRUS, VIRAL PROTEIN-TRANSFERASE COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.W.HAN,H.J.KIM REVDAT 1 28-JUN-23 8I9J 0 JRNL AUTH H.J.KIM,C.W.HAN,M.S.JEONG,S.B.JANG JRNL TITL STRUCTURAL STUDY OF NOVEL VACCINIA VIRUS E3L AND JRNL TITL 2 DSRNA-DEPENDENT PROTEIN KINASE COMPLEX. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 665 1 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37146409 JRNL DOI 10.1016/J.BBRC.2023.04.107 REMARK 2 REMARK 2 RESOLUTION. 6.39 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) : 6.390 REMARK 3 NUMBER OF PARTICLES : 307424 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 8I9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035195. 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 : THE PKR AND E3L COMPLEX 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 : 7.10 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 GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 3999.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, 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: 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 C ILE B 28 H GLU B 29 1.33 REMARK 500 O GLU A 67 H ALA A 71 1.58 REMARK 500 OG SER C 134 O ASP C 153 2.07 REMARK 500 NZ LYS A 66 OD1 ASN A 70 2.10 REMARK 500 NE2 GLN A 26 O LEU A 80 2.12 REMARK 500 O GLU A 17 OG1 THR A 21 2.13 REMARK 500 NZ LYS B 24 OG1 THR B 73 2.14 REMARK 500 O ASP A 9 NZ LYS A 69 2.15 REMARK 500 O ARG C 168 N ASN C 172 2.17 REMARK 500 N VAL C 140 O TYR C 149 2.18 REMARK 500 N ALA C 150 O ALA C 162 2.18 REMARK 500 N PHE A 46 O LYS A 65 2.18 REMARK 500 O GLN B 35 NH1 ARG B 38 2.19 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 ASN B 15 -58.59 -123.59 REMARK 500 LEU B 40 -72.43 -67.83 REMARK 500 ASN B 41 -50.27 -139.86 REMARK 500 MET B 42 18.21 -147.53 REMARK 500 ASP B 53 34.60 -89.40 REMARK 500 MET B 59 47.79 -96.95 REMARK 500 ALA A 7 -160.51 -77.23 REMARK 500 PHE A 14 -60.20 -101.06 REMARK 500 ARG A 23 8.02 -69.64 REMARK 500 LYS A 31 64.92 -101.61 REMARK 500 LEU A 35 78.56 -160.30 REMARK 500 THR A 47 65.54 -100.65 REMARK 500 ASP A 53 -61.42 -96.11 REMARK 500 GLU A 59 147.53 -176.44 REMARK 500 LYS A 65 -158.57 -150.52 REMARK 500 LYS A 66 -18.53 -48.34 REMARK 500 ALA A 68 -2.68 -59.69 REMARK 500 LEU A 75 30.23 -86.77 REMARK 500 VAL A 77 -65.12 -91.88 REMARK 500 GLU A 83 -7.78 80.70 REMARK 500 ALA A 86 77.27 -69.25 REMARK 500 PRO A 89 105.90 -59.96 REMARK 500 ASN A 96 51.22 -145.82 REMARK 500 LEU A 101 71.78 55.65 REMARK 500 SER A 102 125.61 -26.07 REMARK 500 TYR A 106 10.80 -143.50 REMARK 500 VAL A 130 -62.37 -95.57 REMARK 500 HIS A 131 -63.00 -96.57 REMARK 500 TYR A 147 73.75 -106.39 REMARK 500 SER A 148 74.75 -103.82 REMARK 500 LEU A 171 38.63 -92.06 REMARK 500 GLU A 174 -32.86 -133.58 REMARK 500 SER C 139 153.47 -49.64 REMARK 500 SER C 145 64.89 60.77 REMARK 500 THR C 147 -156.87 -148.90 REMARK 500 LEU C 182 50.58 -97.23 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 GLN B 35 LEU B 36 -147.00 REMARK 500 MET B 42 GLU B 43 -148.98 REMARK 500 GLU B 46 VAL B 47 -148.60 REMARK 500 ASP B 65 ILE B 66 149.42 REMARK 500 PHE B 71 MET B 72 138.50 REMARK 500 VAL A 28 VAL A 29 -144.62 REMARK 500 PHE A 46 THR A 47 149.88 REMARK 500 THR A 47 PHE A 48 135.18 REMARK 500 GLN A 49 VAL A 50 143.98 REMARK 500 GLU A 59 GLY A 60 128.16 REMARK 500 LYS A 66 GLU A 67 -138.20 REMARK 500 ALA A 76 VAL A 77 -149.08 REMARK 500 SER A 88 PRO A 89 146.37 REMARK 500 THR A 94 THR A 95 -143.09 REMARK 500 THR A 95 ASN A 96 -145.53 REMARK 500 LEU A 101 SER A 102 -134.88 REMARK 500 GLY A 104 ASN A 105 -144.87 REMARK 500 TYR A 106 ILE A 107 -144.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35274 RELATED DB: EMDB REMARK 900 THE PKR AND E3L COMPLEX DBREF 8I9J B 13 74 UNP P21605 E3_VACCW 9 70 DBREF 8I9J A 6 175 UNP P19525 E2AK2_HUMAN 1 170 DBREF 8I9J C 96 183 UNP P21605 E3_VACCW 96 183 SEQADV 8I9J GLY A 1 UNP P19525 EXPRESSION TAG SEQADV 8I9J SER A 2 UNP P19525 EXPRESSION TAG SEQADV 8I9J HIS A 3 UNP P19525 EXPRESSION TAG SEQADV 8I9J MET A 4 UNP P19525 EXPRESSION TAG SEQADV 8I9J GLU A 5 UNP P19525 EXPRESSION TAG SEQADV 8I9J GLY A 176 UNP P19525 EXPRESSION TAG SEQADV 8I9J SER A 177 UNP P19525 EXPRESSION TAG SEQADV 8I9J GLY A 178 UNP P19525 EXPRESSION TAG SEQADV 8I9J CYS A 179 UNP P19525 EXPRESSION TAG SEQRES 1 B 62 ARG SER ASN ALA GLU ILE VAL CYS GLU ALA ILE LYS THR SEQRES 2 B 62 ILE GLY ILE GLU GLY ALA THR ALA ALA GLN LEU THR ARG SEQRES 3 B 62 GLN LEU ASN MET GLU LYS ARG GLU VAL ASN LYS ALA LEU SEQRES 4 B 62 TYR ASP LEU GLN ARG SER ALA MET VAL TYR SER SER ASP SEQRES 5 B 62 ASP ILE PRO PRO ARG TRP PHE MET THR THR SEQRES 1 A 179 GLY SER HIS MET GLU MET ALA GLY ASP LEU SER ALA GLY SEQRES 2 A 179 PHE PHE MET GLU GLU LEU ASN THR TYR ARG GLN LYS GLN SEQRES 3 A 179 GLY VAL VAL LEU LYS TYR GLN GLU LEU PRO ASN SER GLY SEQRES 4 A 179 PRO PRO HIS ASP ARG ARG PHE THR PHE GLN VAL ILE ILE SEQRES 5 A 179 ASP GLY ARG GLU PHE PRO GLU GLY GLU GLY ARG SER LYS SEQRES 6 A 179 LYS GLU ALA LYS ASN ALA ALA ALA LYS LEU ALA VAL GLU SEQRES 7 A 179 ILE LEU ASN LYS GLU LYS LYS ALA VAL SER PRO LEU LEU SEQRES 8 A 179 LEU THR THR THR ASN SER SER GLU GLY LEU SER MET GLY SEQRES 9 A 179 ASN TYR ILE GLY LEU ILE ASN ARG ILE ALA GLN LYS LYS SEQRES 10 A 179 ARG LEU THR VAL ASN TYR GLU GLN CYS ALA SER GLY VAL SEQRES 11 A 179 HIS GLY PRO GLU GLY PHE HIS TYR LYS CYS LYS MET GLY SEQRES 12 A 179 GLN LYS GLU TYR SER ILE GLY THR GLY SER THR LYS GLN SEQRES 13 A 179 GLU ALA LYS GLN LEU ALA ALA LYS LEU ALA TYR LEU GLN SEQRES 14 A 179 ILE LEU SER GLU GLU THR GLY SER GLY CYS SEQRES 1 C 88 GLU ASP HIS LYS SER PHE ASP ASP VAL ILE PRO ALA LYS SEQRES 2 C 88 LYS ILE ILE ASP TRP LYS GLY ALA ASN PRO VAL THR VAL SEQRES 3 C 88 ILE ASN GLU TYR CYS GLN ILE THR ARG ARG ASP TRP SER SEQRES 4 C 88 PHE ARG ILE GLU SER VAL GLY PRO SER ASN SER PRO THR SEQRES 5 C 88 PHE TYR ALA CYS VAL ASP ILE ASP GLY ARG VAL PHE ASP SEQRES 6 C 88 LYS ALA ASP GLY LYS SER LYS ARG ASP ALA LYS ASN ASN SEQRES 7 C 88 ALA ALA LYS LEU ALA VAL ASP LYS LEU LEU HELIX 1 AA1 ASN B 15 LYS B 24 1 10 HELIX 2 AA2 PHE A 15 ARG A 23 1 9 HELIX 3 AA3 LYS A 66 LYS A 69 5 4 HELIX 4 AA4 ASN A 70 LEU A 75 1 6 HELIX 5 AA5 LEU A 109 ALA A 114 1 6 HELIX 6 AA6 THR A 154 LYS A 159 1 6 HELIX 7 AA7 GLN A 160 LEU A 171 1 12 HELIX 8 AA8 ASP C 97 ILE C 105 1 9 HELIX 9 AA9 LYS C 108 LYS C 114 1 7 HELIX 10 AB1 ILE C 122 GLN C 127 1 6 HELIX 11 AB2 SER C 166 ASP C 180 1 15 HELIX 12 AB3 LYS C 181 LEU C 183 5 3 SHEET 1 AA1 2 CYS A 126 ALA A 127 0 SHEET 2 AA1 2 PHE A 136 HIS A 137 -1 O HIS A 137 N CYS A 126 SHEET 1 AA2 2 SER C 134 PHE C 135 0 SHEET 2 AA2 2 VAL C 152 ASP C 153 -1 O ASP C 153 N SER C 134 CISPEP 1 ILE B 66 PRO B 67 0 -11.87 CISPEP 2 ILE C 137 GLU C 138 0 3.89 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