HEADER TRANSFERASE/VIRAL PROTEIN 07-APR-23 8IZN TITLE STRUCTURAL STUDY OF INTERFERON-INDUCED, DOUBLE-STRANDED RNA-ACTIVATED TITLE 2 PROTEIN KINASE (PKR) AND NON-STRUCTURAL PROTEIN 1 (NS1) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON-INDUCED, DOUBLE-STRANDED RNA-ACTIVATED PROTEIN COMPND 3 KINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: EUKARYOTIC TRANSLATION INITIATION FACTOR 2-ALPHA KINASE 2, COMPND 6 EIF-2A PROTEIN KINASE 2,INTERFERON-INDUCIBLE RNA-DEPENDENT PROTEIN COMPND 7 KINASE,P1/EIF-2A PROTEIN KINASE,PROTEIN KINASE RNA-ACTIVATED,PKR, COMPND 8 PROTEIN KINASE R,TYROSINE-PROTEIN KINASE EIF2AK2,P68 KINASE; COMPND 9 EC: 2.7.11.1,2.7.10.2; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: NON-STRUCTURAL PROTEIN 1; COMPND 13 CHAIN: B; COMPND 14 SYNONYM: NS1,NS1A; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: EIF2AK2, PKR, PRKR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (STRAIN A/MEMPHIS/102/1972 SOURCE 10 H3N2); SOURCE 11 ORGANISM_TAXID: 385640; SOURCE 12 GENE: NS; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PKR, NS1, PKR AND NS1 COMPLEX, VIRUS, TRANSFERASE-VIRAL PROTEIN KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.W.HAN,H.J.KIM REVDAT 1 10-APR-24 8IZN 0 JRNL AUTH C.W.HAN JRNL TITL STRUCTURE OF PKR AND NS1 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 6.67 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) : 6.670 REMARK 3 NUMBER OF PARTICLES : 49802 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 8IZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036892. 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 : PKR AND NS1 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.80 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 PHE B 166 CG CD1 CD2 CE1 CE2 CZ 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 ASN A 111 NH1 ARG A 118 2.11 REMARK 500 OG1 THR B 151 N GLY B 154 2.15 REMARK 500 O LEU B 198 N TRP B 203 2.17 REMARK 500 O MET B 106 N GLN B 121 2.19 REMARK 500 O GLN A 160 N ALA A 163 2.19 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 ILE A 170 CG1 - CB - CG2 ANGL. DEV. = 16.3 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 SER A 2 115.29 -163.56 REMARK 500 ALA A 12 174.69 175.24 REMARK 500 PHE A 14 -56.78 -121.13 REMARK 500 MET A 16 -38.34 -135.31 REMARK 500 PHE A 48 94.00 -67.99 REMARK 500 PHE A 57 72.68 -110.72 REMARK 500 LYS A 65 -160.31 -160.20 REMARK 500 LYS A 85 155.90 -49.29 REMARK 500 PRO A 89 -165.77 -74.68 REMARK 500 LEU A 90 -37.30 -36.10 REMARK 500 SER A 98 128.21 -35.67 REMARK 500 GLU A 99 -163.72 -78.82 REMARK 500 LEU A 101 69.54 62.81 REMARK 500 GLN A 115 -8.45 -55.62 REMARK 500 LYS A 117 20.57 -142.98 REMARK 500 GLU A 134 -38.10 -37.52 REMARK 500 GLN A 144 12.41 -141.71 REMARK 500 SER A 153 -60.68 -98.55 REMARK 500 THR A 175 -179.29 -69.27 REMARK 500 ASP B 125 44.55 70.35 REMARK 500 THR B 143 -174.37 -170.84 REMARK 500 ILE B 145 -65.76 -124.15 REMARK 500 ASP B 189 -3.53 73.54 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 ALA A 12 GLY A 13 148.74 REMARK 500 LYS A 31 TYR A 32 -134.51 REMARK 500 GLU A 67 ALA A 68 -148.10 REMARK 500 SER A 97 SER A 98 -148.58 REMARK 500 LYS A 141 MET A 142 141.63 REMARK 500 GLN A 160 LEU A 161 -149.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35866 RELATED DB: EMDB REMARK 900 PKR AND NS1 COMPLEX DBREF 8IZN A 6 175 UNP P19525 E2AK2_HUMAN 1 170 DBREF 8IZN B 84 205 UNP Q463W9 NS1_I72A3 84 205 SEQADV 8IZN GLY A 1 UNP P19525 EXPRESSION TAG SEQADV 8IZN SER A 2 UNP P19525 EXPRESSION TAG SEQADV 8IZN HIS A 3 UNP P19525 EXPRESSION TAG SEQADV 8IZN MET A 4 UNP P19525 EXPRESSION TAG SEQADV 8IZN GLU A 5 UNP P19525 EXPRESSION TAG SEQADV 8IZN GLY A 176 UNP P19525 EXPRESSION TAG SEQADV 8IZN SER A 177 UNP P19525 EXPRESSION TAG SEQADV 8IZN GLY A 178 UNP P19525 EXPRESSION TAG SEQADV 8IZN CYS A 179 UNP P19525 EXPRESSION TAG 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 B 122 THR PRO ALA SER ARG TYR ILE THR ASP MET THR ILE GLU SEQRES 2 B 122 GLU LEU SER ARG ASP TRP PHE MET LEU MET PRO LYS GLN SEQRES 3 B 122 LYS VAL GLU GLY PRO LEU CYS ILE ARG ILE ASP GLN ALA SEQRES 4 B 122 ILE MET ASP LYS ASN ILE MET LEU LYS ALA ASN PHE SER SEQRES 5 B 122 VAL ILE PHE ASP ARG LEU GLU THR LEU ILE LEU LEU ARG SEQRES 6 B 122 ALA PHE THR GLU GLU GLY ALA ILE VAL GLY GLU ILE SER SEQRES 7 B 122 PRO LEU PRO SER PHE PRO GLY HIS THR ILE GLU ASP VAL SEQRES 8 B 122 LYS ASN ALA ILE GLY VAL LEU ILE GLY GLY LEU GLU TRP SEQRES 9 B 122 ASN ASP ASN THR VAL ARG VAL SER LYS THR LEU GLN ARG SEQRES 10 B 122 PHE ALA TRP GLY SER HELIX 1 AA1 THR A 21 LYS A 25 5 5 HELIX 2 AA2 ALA A 68 ALA A 73 5 6 HELIX 3 AA3 LEU A 109 ALA A 114 1 6 HELIX 4 AA4 GLN A 115 LYS A 117 5 3 HELIX 5 AA5 THR A 154 LYS A 159 1 6 HELIX 6 AA6 GLN A 160 LEU A 168 1 9 HELIX 7 AA7 THR B 170 LEU B 181 1 12 HELIX 8 AA8 ILE B 182 GLY B 183 5 2 HELIX 9 AA9 GLY B 184 ASP B 189 5 6 HELIX 10 AB1 LYS B 196 ALA B 202 1 7 SHEET 1 AA1 2 LEU A 35 PRO A 36 0 SHEET 2 AA1 2 PHE A 46 THR A 47 -1 O THR A 47 N LEU A 35 SHEET 1 AA2 2 PHE A 136 LYS A 139 0 SHEET 2 AA2 2 ILE A 149 GLY A 152 -1 O GLY A 150 N TYR A 138 SHEET 1 AA3 3 TYR B 89 THR B 91 0 SHEET 2 AA3 3 ASN B 133 ILE B 137 -1 O PHE B 134 N ILE B 90 SHEET 3 AA3 3 ARG B 140 THR B 143 -1 O ARG B 140 N ILE B 137 SHEET 1 AA4 2 PRO B 107 LYS B 108 0 SHEET 2 AA4 2 ILE B 119 ASP B 120 -1 O ILE B 119 N LYS B 108 SHEET 1 AA5 2 LEU B 115 CYS B 116 0 SHEET 2 AA5 2 SER B 161 PRO B 162 -1 O SER B 161 N CYS B 116 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