HEADER CYTOSOLIC PROTEIN 16-SEP-25 9YAK TITLE STRUCTURE OF THE GCN2 PSEUDOKINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EIF-2-ALPHA KINASE GCN2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PSEUDOKINASE DOMAIN; COMPND 5 SYNONYM: EUKARYOTIC TRANSLATION INITIATION FACTOR 2-ALPHA KINASE 4, COMPND 6 GCN2-LIKE PROTEIN; COMPND 7 EC: 2.7.11.1; COMPND 8 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: EIF2AK4, GCN2, KIAA1338; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PSEUDOKINASE, COMPLEX, HOMEOSTASIS, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,N.JURA REVDAT 1 01-JUL-26 9YAK 0 JRNL AUTH Y.LIU,J.MISRA,D.R.BHOWMIK,B.O'BOYLE,K.A.STASCHKE,N.KANNAN, JRNL AUTH 2 R.C.WEK,N.JURA JRNL TITL STRUCTURAL BASIS FOR PSEUDOKINASE-MEDIATED REGULATION OF JRNL TITL 2 GCN2 IN THE INTEGRATED STRESS RESPONSE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 98123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 41615758 JRNL DOI 10.1073/PNAS.2526598123 REMARK 2 REMARK 2 RESOLUTION. 2.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 9596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.265 REMARK 3 FREE R VALUE : 0.304 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 960 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.0600 - 5.7000 0.99 1335 148 0.2456 0.3007 REMARK 3 2 5.7000 - 4.5200 1.00 1257 140 0.2385 0.2710 REMARK 3 3 4.5200 - 3.9500 0.99 1231 136 0.2491 0.2660 REMARK 3 4 3.9500 - 3.5900 0.99 1216 136 0.2861 0.3000 REMARK 3 5 3.5900 - 3.3300 1.00 1210 135 0.3484 0.3997 REMARK 3 6 3.3300 - 3.1400 0.99 1200 132 0.3581 0.3597 REMARK 3 7 3.1400 - 2.9800 0.98 1187 133 0.4608 0.5373 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.627 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.076 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 121.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 152.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2095 REMARK 3 ANGLE : 1.135 2831 REMARK 3 CHIRALITY : 0.058 326 REMARK 3 PLANARITY : 0.008 355 REMARK 3 DIHEDRAL : 11.695 777 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 25.7400 46.9209 16.8086 REMARK 3 T TENSOR REMARK 3 T11: 0.7467 T22: 1.0902 REMARK 3 T33: 0.9230 T12: -0.0871 REMARK 3 T13: -0.0486 T23: 0.1565 REMARK 3 L TENSOR REMARK 3 L11: 1.3772 L22: 0.7110 REMARK 3 L33: 2.3819 L12: 0.2442 REMARK 3 L13: 0.1204 L23: 0.9985 REMARK 3 S TENSOR REMARK 3 S11: 0.1279 S12: 0.1177 S13: 0.3703 REMARK 3 S21: -0.0817 S22: -0.0749 S23: 0.0532 REMARK 3 S31: -0.1067 S32: -0.6112 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9YAK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 2.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0387 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9609 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 42.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.5 AND 1.6 M MAGNESIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 265 REMARK 465 MET A 321 REMARK 465 GLY A 322 REMARK 465 PRO A 323 REMARK 465 PHE A 324 REMARK 465 ARG A 463 REMARK 465 VAL A 464 REMARK 465 ARG A 465 REMARK 465 PHE A 466 REMARK 465 SER A 467 REMARK 465 ASP A 468 REMARK 465 ASN A 469 REMARK 465 ALA A 470 REMARK 465 LEU A 471 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 HIS A 400 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 403 CG CD NE CZ NH1 NH2 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 274 174.94 75.09 REMARK 500 LYS A 424 -47.48 74.46 REMARK 500 VAL A 425 74.89 -117.94 REMARK 500 SER A 445 -44.31 58.86 REMARK 500 LYS A 477 -64.54 44.56 REMARK 500 GLU A 499 -119.18 52.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YAK A 266 539 UNP Q9P2K8 E2AK4_HUMAN 266 539 SEQADV 9YAK GLY A 265 UNP Q9P2K8 EXPRESSION TAG SEQRES 1 A 275 GLY GLU ILE LEU TYR PHE ASN MET GLY SER PRO ASP GLN SEQRES 2 A 275 LEU MET VAL HIS LYS GLY LYS CYS ILE GLY SER ASP GLU SEQRES 3 A 275 GLN LEU GLY LYS LEU VAL TYR ASN ALA LEU GLU THR ALA SEQRES 4 A 275 THR GLY GLY PHE VAL LEU LEU TYR GLU TRP VAL LEU GLN SEQRES 5 A 275 TRP GLN LYS LYS MET GLY PRO PHE LEU THR SER GLN GLU SEQRES 6 A 275 LYS GLU LYS ILE ASP LYS CYS LYS LYS GLN ILE GLN GLY SEQRES 7 A 275 THR GLU THR GLU PHE ASN SER LEU VAL LYS LEU SER HIS SEQRES 8 A 275 PRO ASN VAL VAL ARG TYR LEU ALA MET ASN LEU LYS GLU SEQRES 9 A 275 GLN ASP ASP SER ILE VAL VAL ASP ILE LEU VAL GLU HIS SEQRES 10 A 275 ILE SER GLY VAL SER LEU ALA ALA HIS LEU SER HIS SER SEQRES 11 A 275 GLY PRO ILE PRO VAL HIS GLN LEU ARG ARG TYR THR ALA SEQRES 12 A 275 GLN LEU LEU SER GLY LEU ASP TYR LEU HIS SER ASN SER SEQRES 13 A 275 VAL VAL HIS LYS VAL LEU SER ALA SER ASN VAL LEU VAL SEQRES 14 A 275 ASP ALA GLU GLY THR VAL LYS ILE THR ASP TYR SER ILE SEQRES 15 A 275 SER LYS ARG LEU ALA ASP ILE CYS LYS GLU ASP VAL PHE SEQRES 16 A 275 GLU GLN THR ARG VAL ARG PHE SER ASP ASN ALA LEU PRO SEQRES 17 A 275 TYR LYS THR GLY LYS LYS GLY ASP VAL TRP ARG LEU GLY SEQRES 18 A 275 LEU LEU LEU LEU SER LEU SER GLN GLY GLN GLU CYS GLY SEQRES 19 A 275 GLU TYR PRO VAL THR ILE PRO SER ASP LEU PRO ALA ASP SEQRES 20 A 275 PHE GLN ASP PHE LEU LYS LYS CYS VAL CYS LEU ASP ASP SEQRES 21 A 275 LYS GLU ARG TRP SER PRO GLN GLN LEU LEU LYS HIS SER SEQRES 22 A 275 PHE ILE HELIX 1 AA1 THR A 326 VAL A 351 1 26 HELIX 2 AA2 LEU A 387 SER A 394 1 8 HELIX 3 AA3 PRO A 398 ASN A 419 1 22 HELIX 4 AA4 SER A 445 GLU A 456 1 12 HELIX 5 AA5 LYS A 477 GLY A 494 1 18 HELIX 6 AA6 PRO A 509 VAL A 520 1 12 HELIX 7 AA7 SER A 529 LEU A 534 1 6 SHEET 1 AA1 6 ILE A 267 PHE A 270 0 SHEET 2 AA1 6 LEU A 278 SER A 288 -1 O VAL A 280 N LEU A 268 SHEET 3 AA1 6 LYS A 294 GLU A 301 -1 O LEU A 300 N HIS A 281 SHEET 4 AA1 6 PHE A 307 GLN A 316 -1 O VAL A 308 N ALA A 299 SHEET 5 AA1 6 SER A 372 GLU A 380 -1 O VAL A 379 N LEU A 309 SHEET 6 AA1 6 TYR A 361 GLU A 368 -1 N ALA A 363 O LEU A 378 SHEET 1 AA2 3 GLY A 384 SER A 386 0 SHEET 2 AA2 3 VAL A 431 ASP A 434 -1 O VAL A 433 N VAL A 385 SHEET 3 AA2 3 VAL A 439 ILE A 441 -1 O LYS A 440 N LEU A 432 CISPEP 1 TYR A 500 PRO A 501 0 -24.76 CRYST1 118.975 118.975 62.673 90.00 90.00 90.00 P 4 2 2 8 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 0.008405 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015956 0.00000 MASTER 276 0 0 7 9 0 0 6 2057 1 0 22 END