HEADER PROTEIN BINDING 10-DEC-21 7QGS TITLE CRYSTAL STRUCTURE OF P300 CH1 DOMAIN IN COMPLEX WITH CITIF (A CITED2- TITLE 2 HIF-1ALPHA HYBRID) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CBP/P300-INTERACTING TRANSACTIVATOR 2,HYPOXIA-INDUCIBLE COMPND 3 FACTOR 1-ALPHA; COMPND 4 CHAIN: B; COMPND 5 SYNONYM: MSG-RELATED PROTEIN 1,MRG-1,P35SRJ,HIF-1-ALPHA,HIF1-ALPHA, COMPND 6 ARNT-INTERACTING PROTEIN,BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP1, COMPND 7 CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78,BHLHE78,MEMBER OF PAS COMPND 8 PROTEIN 1,PAS DOMAIN-CONTAINING PROTEIN 8; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE ACETYLTRANSFERASE; COMPND 12 CHAIN: A; COMPND 13 EC: 2.3.1.48; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: EP300; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYPOXIA, TRANSCRIPTION FACTOR, INTRINSICALLY DISORDERED PROTEIN, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.HEGEDUS,A.J.WILSON,T.A.EDWARDS REVDAT 3 31-JAN-24 7QGS 1 REMARK REVDAT 2 15-JUN-22 7QGS 1 JRNL REVDAT 1 11-MAY-22 7QGS 0 JRNL AUTH F.HOBOR,Z.HEGEDUS,A.A.IBARRA,V.L.PETROVICZ,G.J.BARTLETT, JRNL AUTH 2 R.B.SESSIONS,A.J.WILSON,T.A.EDWARDS JRNL TITL UNDERSTANDING P300-TRANSCRIPTION FACTOR INTERACTIONS USING JRNL TITL 2 SEQUENCE VARIATION AND HYBRIDIZATION. JRNL REF RSC CHEM BIOL V. 3 592 2022 JRNL REFN ESSN 2633-0679 JRNL PMID 35656479 JRNL DOI 10.1039/D2CB00026A REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7677 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 398 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 38.6600 - 2.8800 1.00 2472 141 0.1922 0.2161 REMARK 3 2 2.8800 - 2.2900 1.00 2426 130 0.2996 0.3398 REMARK 3 3 2.2900 - 2.0000 0.98 2381 127 0.3047 0.3001 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.098 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.04 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 : 0.016 1181 REMARK 3 ANGLE : 1.545 1591 REMARK 3 CHIRALITY : 0.071 180 REMARK 3 PLANARITY : 0.009 212 REMARK 3 DIHEDRAL : 16.264 159 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 7QGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28367 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS, DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7708 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.74400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 7LVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 6.5, PEG 6K 35%, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.29950 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: B, 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 B 1 REMARK 465 PRO B 2 REMARK 465 GLY B 3 REMARK 465 GLY A 325 REMARK 465 PRO A 326 REMARK 465 ILE A 327 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 GLN A 383 OG1 THR A 407 2656 1.98 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 ALA B 36 66.67 -155.23 REMARK 500 ASN B 43 74.48 -109.41 REMARK 500 LEU B 45 140.09 -39.37 REMARK 500 LEU B 54 0.04 -67.92 REMARK 500 VAL A 361 -71.66 -70.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 351 SG REMARK 620 2 CYS A 364 SG 105.8 REMARK 620 3 CYS A 369 SG 111.7 118.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 378 NE2 REMARK 620 2 CYS A 382 SG 107.2 REMARK 620 3 CYS A 388 SG 109.0 136.9 REMARK 620 4 CYS A 393 SG 101.8 101.7 93.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 402 NE2 REMARK 620 2 CYS A 406 SG 104.5 REMARK 620 3 CYS A 411 SG 99.6 104.9 REMARK 620 4 CYS A 414 SG 110.2 121.4 113.7 REMARK 620 N 1 2 3 DBREF 7QGS B 5 23 UNP Q99967 CITE2_HUMAN 224 242 DBREF 7QGS B 24 58 UNP Q16665 HIF1A_HUMAN 792 826 DBREF 7QGS A 330 420 UNP Q7Z6C1 Q7Z6C1_HUMAN 330 420 SEQADV 7QGS GLY B 1 UNP Q99967 EXPRESSION TAG SEQADV 7QGS PRO B 2 UNP Q99967 EXPRESSION TAG SEQADV 7QGS GLY B 3 UNP Q99967 EXPRESSION TAG SEQADV 7QGS SER B 4 UNP Q99967 EXPRESSION TAG SEQADV 7QGS GLY A 325 UNP Q7Z6C1 EXPRESSION TAG SEQADV 7QGS PRO A 326 UNP Q7Z6C1 EXPRESSION TAG SEQADV 7QGS ILE A 327 UNP Q7Z6C1 EXPRESSION TAG SEQADV 7QGS GLY A 328 UNP Q7Z6C1 EXPRESSION TAG SEQADV 7QGS SER A 329 UNP Q7Z6C1 EXPRESSION TAG SEQRES 1 B 58 GLY PRO GLY SER ASP GLU GLU VAL LEU MET SER LEU VAL SEQRES 2 B 58 ILE GLU MET GLY LEU ASP ARG ILE LYS GLU LEU PRO GLN SEQRES 3 B 58 LEU THR SER TYR ASP CYS GLU VAL ASN ALA PRO ILE GLN SEQRES 4 B 58 GLY SER ARG ASN LEU LEU GLN GLY GLU GLU LEU LEU ARG SEQRES 5 B 58 ALA LEU ASP GLN VAL ASN SEQRES 1 A 96 GLY PRO ILE GLY SER ALA ASP PRO GLU LYS ARG LYS LEU SEQRES 2 A 96 ILE GLN GLN GLN LEU VAL LEU LEU LEU HIS ALA HIS LYS SEQRES 3 A 96 CYS GLN ARG ARG GLU GLN ALA ASN GLY GLU VAL ARG GLN SEQRES 4 A 96 CYS ASN LEU PRO HIS CYS ARG THR MET LYS ASN VAL LEU SEQRES 5 A 96 ASN HIS MET THR HIS CYS GLN SER GLY LYS SER CYS GLN SEQRES 6 A 96 VAL ALA HIS CYS ALA SER SER ARG GLN ILE ILE SER HIS SEQRES 7 A 96 TRP LYS ASN CYS THR ARG HIS ASP CYS PRO VAL CYS LEU SEQRES 8 A 96 PRO LEU LYS ASN ALA HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HETNAM ZN ZINC ION FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *41(H2 O) HELIX 1 AA1 ASP B 5 MET B 16 1 12 HELIX 2 AA2 THR B 28 ALA B 36 1 9 HELIX 3 AA3 GLU B 48 LEU B 54 1 7 HELIX 4 AA4 ASP A 331 ASN A 358 1 28 HELIX 5 AA5 HIS A 368 CYS A 382 1 15 HELIX 6 AA6 SER A 384 CYS A 388 5 5 HELIX 7 AA7 HIS A 392 CYS A 406 1 15 HELIX 8 AA8 CYS A 414 ASN A 419 1 6 LINK SG CYS A 351 ZN ZN A 501 1555 1555 2.39 LINK SG CYS A 364 ZN ZN A 501 1555 1555 2.35 LINK SG CYS A 369 ZN ZN A 501 1555 1555 2.31 LINK NE2 HIS A 378 ZN ZN A 502 1555 1555 2.32 LINK SG CYS A 382 ZN ZN A 502 1555 1555 2.32 LINK SG CYS A 388 ZN ZN A 502 1555 1555 2.02 LINK SG CYS A 393 ZN ZN A 502 1555 1555 2.82 LINK NE2 HIS A 402 ZN ZN A 503 1555 1555 2.26 LINK SG CYS A 406 ZN ZN A 503 1555 1555 2.28 LINK SG CYS A 411 ZN ZN A 503 1555 1555 2.28 LINK SG CYS A 414 ZN ZN A 503 1555 1555 2.52 CRYST1 30.505 48.599 39.825 90.00 103.87 90.00 P 1 21 1 2 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 0.032782 0.000000 0.008093 0.00000 SCALE2 0.000000 0.020577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025864 0.00000