HEADER TRANSCRIPTION 04-NOV-25 9Z1Q TITLE BACKBONE MODIFICATION IN THE GCN4 LEUCINE ZIPPER: CALPHA-METHYL-GLU AT TITLE 2 POSITION 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL TRANSCRIPTION FACTOR GCN4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LEUCINE ZIPPER DOMAIN; COMPND 5 SYNONYM: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN,GENERAL CONTROL COMPND 6 PROTEIN GCN4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 5 ORGANISM_TAXID: 4932 KEYWDS COILED COIL, BACKBONE MODIFICATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.E.PAGE,Y.LIN,W.S.HORNE REVDAT 1 18-MAR-26 9Z1Q 0 JRNL AUTH G.E.PAGE,Y.LIN,W.S.HORNE JRNL TITL MANIPULATING THE UNFOLDED STATE OF A FOLDED PROTEIN THROUGH JRNL TITL 2 SITE-SPECIFIC BACKBONE MODIFICATION. JRNL REF BIOCHEMISTRY 2026 JRNL REFN ISSN 0006-2960 JRNL PMID 41773780 JRNL DOI 10.1021/ACS.BIOCHEM.5C00687 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 75 861 2019 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 6143 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 615 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 28.4900 - 2.8600 1.00 1424 158 0.1794 0.2014 REMARK 3 2 2.8600 - 2.2700 1.00 1377 153 0.1740 0.1692 REMARK 3 3 2.2700 - 1.9800 1.00 1388 154 0.1610 0.1935 REMARK 3 4 1.9800 - 1.8000 0.99 1339 150 0.1909 0.2353 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) : 0.172 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.663 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.63 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 : 0.004 592 REMARK 3 ANGLE : 0.604 803 REMARK 3 CHIRALITY : 0.035 88 REMARK 3 PLANARITY : 0.006 104 REMARK 3 DIHEDRAL : 13.454 249 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9Z1Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1000301764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-25 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS 3.0 MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 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 : 4.300 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 (%): 39.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M SODIUM ACETATE PH 4.6, 0.1 M REMARK 280 SODIUM CITRATE PH 4.6, 5% W/V PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 1.000000 0.000000 0.000000 39.57800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.57800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.28500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 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 GLU A 32 REMARK 465 ARG A 33 REMARK 465 NH2 A 34 DBREF 9Z1Q A 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 9Z1Q B 1 33 UNP P03069 GCN4_YEAST 249 281 SEQADV 9Z1Q ACE A 0 UNP P03069 ACETYLATION SEQADV 9Z1Q VAL A 2 UNP P03069 MET 250 CONFLICT SEQADV 9Z1Q TRP A 17 UNP P03069 TYR 265 CONFLICT SEQADV 9Z1Q NH2 A 34 UNP P03069 AMIDATION SEQADV 9Z1Q ACE B 0 UNP P03069 ACETYLATION SEQADV 9Z1Q VAL B 2 UNP P03069 MET 250 CONFLICT SEQADV 9Z1Q TRP B 17 UNP P03069 TYR 265 CONFLICT SEQADV 9Z1Q NH2 B 34 UNP P03069 AMIDATION SEQRES 1 A 35 ACE ARG VAL LYS GLN LEU GLU ASP LYS VAL GLU GAM LEU SEQRES 2 A 35 LEU SER LYS ASN TRP HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 A 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 SEQRES 1 B 35 ACE ARG VAL LYS GLN LEU GLU ASP LYS VAL GLU GAM LEU SEQRES 2 B 35 LEU SER LYS ASN TRP HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 3 B 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 MODRES 9Z1Q GAM A 11 GLU MODIFIED RESIDUE MODRES 9Z1Q GAM B 11 GLU MODIFIED RESIDUE HET ACE A 0 3 HET GAM A 11 10 HET ACE B 0 3 HET GAM B 11 10 HET NH2 B 34 1 HETNAM ACE ACETYL GROUP HETNAM GAM ALPHA-METHYL-L-GLUTAMIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 GAM 2(C6 H11 N O4) FORMUL 2 NH2 H2 N FORMUL 3 HOH *73(H2 O) HELIX 1 AA1 ARG A 1 LYS A 28 1 28 HELIX 2 AA2 ARG B 1 GLY B 31 1 31 LINK C ACE A 0 N ARG A 1 1555 1555 1.33 LINK C GLU A 10 N GAM A 11 1555 1555 1.33 LINK C GAM A 11 N LEU A 12 1555 1555 1.33 LINK C ACE B 0 N ARG B 1 1555 1555 1.33 LINK C GLU B 10 N GAM B 11 1555 1555 1.33 LINK C GAM B 11 N LEU B 12 1555 1555 1.33 LINK C ARG B 33 N NH2 B 34 1555 1555 1.33 CRYST1 79.156 30.570 27.396 90.00 96.45 90.00 C 1 2 1 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 0.012633 0.000000 0.001428 0.00000 SCALE2 0.000000 0.032712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036734 0.00000 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 83 99 CONECT 90 98 CONECT 91 92 98 CONECT 92 91 93 CONECT 93 92 94 95 CONECT 94 93 CONECT 95 93 CONECT 96 97 98 100 CONECT 97 96 CONECT 98 90 91 96 99 CONECT 99 83 98 CONECT 100 96 CONECT 280 281 282 283 CONECT 281 280 CONECT 282 280 CONECT 283 280 CONECT 362 378 CONECT 369 377 CONECT 370 371 377 CONECT 371 370 372 CONECT 372 371 373 374 CONECT 373 372 CONECT 374 372 CONECT 375 376 377 379 CONECT 376 375 CONECT 377 369 370 375 378 CONECT 378 362 377 CONECT 379 375 CONECT 573 582 CONECT 582 573 MASTER 221 0 5 2 0 0 0 6 622 2 34 6 END