HEADER TRANSCRIPTION 04-NOV-25 9Z1S TITLE BACKBONE MODIFICATION IN THE GCN4 LEUCINE ZIPPER: BETA3-ALA AT TITLE 2 POSITION 24 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 9Z1S 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 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 7120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 706 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 28.9000 - 2.9900 1.00 1329 147 0.1955 0.2065 REMARK 3 2 2.9900 - 2.3700 1.00 1301 144 0.2084 0.2196 REMARK 3 3 2.3700 - 2.0700 0.99 1281 132 0.2006 0.2292 REMARK 3 4 2.0700 - 1.8900 0.97 1254 140 0.2207 0.2816 REMARK 3 5 1.8800 - 1.7500 0.97 1249 143 0.2703 0.3511 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) : 0.252 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.686 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.28 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 : 0.003 609 REMARK 3 ANGLE : 0.644 810 REMARK 3 CHIRALITY : 0.037 89 REMARK 3 PLANARITY : 0.006 103 REMARK 3 DIHEDRAL : 15.010 258 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 9Z1S 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_1000301863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 7123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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 (%): 44.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE PH 4.6, 0.1 M REMARK 280 SODIUM CITRATE PH 4.6, 10% W/V PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING 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 42.12950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.42900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.12950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.42900 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: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 ARG A 33 REMARK 465 NH2 A 34 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 227 O HOH B 134 4555 2.19 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 B3A A 24 ARG A 25 144.94 REMARK 500 B3A B 24 ARG B 25 146.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 B3A A 24 -18.07 REMARK 500 B3A B 24 -17.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 9Z1S A 1 33 UNP P03069 GCN4_YEAST 249 281 DBREF 9Z1S B 1 33 UNP P03069 GCN4_YEAST 249 281 SEQADV 9Z1S ACE A 0 UNP P03069 ACETYLATION SEQADV 9Z1S VAL A 2 UNP P03069 MET 250 CONFLICT SEQADV 9Z1S TRP A 17 UNP P03069 TYR 265 CONFLICT SEQADV 9Z1S NH2 A 34 UNP P03069 AMIDATION SEQADV 9Z1S ACE B 0 UNP P03069 ACETYLATION SEQADV 9Z1S VAL B 2 UNP P03069 MET 250 CONFLICT SEQADV 9Z1S TRP B 17 UNP P03069 TYR 265 CONFLICT SEQADV 9Z1S NH2 B 34 UNP P03069 AMIDATION SEQRES 1 A 35 ACE ARG VAL LYS GLN LEU GLU ASP LYS VAL GLU GLU LEU SEQRES 2 A 35 LEU SER LYS ASN TRP HIS LEU GLU ASN GLU VAL B3A 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 GLU LEU SEQRES 2 B 35 LEU SER LYS ASN TRP HIS LEU GLU ASN GLU VAL B3A ARG SEQRES 3 B 35 LEU LYS LYS LEU VAL GLY GLU ARG NH2 MODRES 9Z1S B3A A 24 ALA MODIFIED RESIDUE MODRES 9Z1S B3A B 24 ALA MODIFIED RESIDUE HET ACE A 0 3 HET B3A A 24 6 HET ACE B 0 3 HET B3A B 24 6 HET NH2 B 34 1 HET GOL A 101 6 HET ACT A 102 4 HETNAM ACE ACETYL GROUP HETNAM B3A (3S)-3-AMINOBUTANOIC ACID HETNAM NH2 AMINO GROUP HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 B3A 2(C4 H9 N O2) FORMUL 2 NH2 H2 N FORMUL 3 GOL C3 H8 O3 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *73(H2 O) HELIX 1 AA1 ARG A 1 GLU A 32 1 32 HELIX 2 AA2 ARG B 1 GLY B 31 1 31 LINK C ACE A 0 N ARG A 1 1555 1555 1.34 LINK C VAL A 23 N B3A A 24 1555 1555 1.34 LINK C B3A A 24 N ARG A 25 1555 1555 1.34 LINK C ACE B 0 N ARG B 1 1555 1555 1.34 LINK C VAL B 23 N B3A B 24 1555 1555 1.33 LINK C B3A B 24 N ARG B 25 1555 1555 1.34 LINK C ARG B 33 N NH2 B 34 1555 1555 1.33 CRYST1 84.259 30.858 27.886 90.00 102.05 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 0.011868 0.000000 0.002533 0.00000 SCALE2 0.000000 0.032407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036668 0.00000 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 215 222 CONECT 220 221 CONECT 221 220 222 223 CONECT 222 215 221 CONECT 223 221 224 CONECT 224 223 225 226 CONECT 225 224 CONECT 226 224 CONECT 292 293 294 295 CONECT 293 292 CONECT 294 292 CONECT 295 292 CONECT 509 516 CONECT 514 515 CONECT 515 514 516 517 CONECT 516 509 515 CONECT 517 515 518 CONECT 518 517 519 520 CONECT 519 518 CONECT 520 518 CONECT 587 596 CONECT 596 587 CONECT 598 599 600 CONECT 599 598 CONECT 600 598 601 602 CONECT 601 600 CONECT 602 600 603 CONECT 603 602 CONECT 604 605 606 607 CONECT 605 604 CONECT 606 604 CONECT 607 604 MASTER 253 0 7 2 0 0 0 6 641 2 36 6 END