HEADER RNA BINDING PROTEIN/RNA 30-SEP-21 7VKI TITLE ESRP1 QRRM2 IN COMPLEX WITH 12MER-RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPITHELIAL SPLICING REGULATORY PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA-BINDING MOTIF PROTEIN 35A,RNA-BINDING PROTEIN 35A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (12-MER); COMPND 8 CHAIN: B; COMPND 9 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: ESRP1, RBM35A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS QRRM DOMAIN, RNA BINDING, CIRCRNA, COMPLEX, RNA BINDING PROTEIN, RNA KEYWDS 2 BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.X.WU,D.J.PATEL REVDAT 3 06-DEC-23 7VKI 1 JRNL REVDAT 2 29-NOV-23 7VKI 1 REMARK REVDAT 1 05-OCT-22 7VKI 0 JRNL AUTH D.LIU,B.K.DREDGE,A.G.BERT,K.A.PILLMAN,J.TOUBIA,W.GUO, JRNL AUTH 2 B.J.A.DYAKOV,M.M.MIGAULT,V.M.CONN,S.J.CONN,P.A.GREGORY, JRNL AUTH 3 A.C.GINGRAS,D.PATEL,B.WU,G.J.GOODALL JRNL TITL ESRP1 CONTROLS BIOGENESIS AND FUNCTION OF A LARGE ABUNDANT JRNL TITL 2 MULTIEXON CIRCRNA. JRNL REF NUCLEIC ACIDS RES. 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 38015468 JRNL DOI 10.1093/NAR/GKAD1138 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 21026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1043 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 28.2500 - 3.1500 1.00 3232 134 0.1708 0.1845 REMARK 3 2 3.1500 - 2.5000 1.00 3069 178 0.1987 0.2324 REMARK 3 3 2.5000 - 2.1800 1.00 3063 169 0.2021 0.2172 REMARK 3 4 2.1800 - 1.9800 1.00 3071 147 0.1917 0.2072 REMARK 3 5 1.9800 - 1.8400 0.99 3041 159 0.2061 0.2188 REMARK 3 6 1.8400 - 1.7300 0.90 2728 152 0.2302 0.3055 REMARK 3 7 1.7300 - 1.6500 0.59 1779 104 0.2426 0.2588 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) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.528 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.63 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 : 0.007 979 REMARK 3 ANGLE : 0.864 1338 REMARK 3 CHIRALITY : 0.056 152 REMARK 3 PLANARITY : 0.010 164 REMARK 3 DIHEDRAL : 26.315 155 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 7VKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4290 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.333 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: 2RVJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE PH 7.0, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.42667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.85333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 28.85333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.42667 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: 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 PRO A 425 REMARK 465 THR A 426 REMARK 465 PRO A 427 REMARK 465 PRO A 428 REMARK 465 ILE A 429 REMARK 465 ILE A 430 REMARK 465 U B 0 REMARK 465 G B 4 REMARK 465 G B 5 REMARK 465 U B 6 REMARK 465 G B 7 REMARK 465 G B 8 REMARK 465 U B 9 REMARK 465 G B 10 REMARK 465 G B 11 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 HOH A 596 O HOH A 618 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VKI A 312 430 UNP Q6NXG1 ESRP1_HUMAN 312 430 DBREF 7VKI B 0 11 PDB 7VKI 7VKI 0 11 SEQRES 1 A 119 THR SER ASN GLU VAL ALA GLN PHE LEU SER LYS GLU ASN SEQRES 2 A 119 GLN VAL ILE VAL ARG MET ARG GLY LEU PRO PHE THR ALA SEQRES 3 A 119 THR ALA GLU GLU VAL VAL ALA PHE PHE GLY GLN HIS CYS SEQRES 4 A 119 PRO ILE THR GLY GLY LYS GLU GLY ILE LEU PHE VAL THR SEQRES 5 A 119 TYR PRO ASP GLY ARG PRO THR GLY ASP ALA PHE VAL LEU SEQRES 6 A 119 PHE ALA CYS GLU GLU TYR ALA GLN ASN ALA LEU ARG LYS SEQRES 7 A 119 HIS LYS ASP LEU LEU GLY LYS ARG TYR ILE GLU LEU PHE SEQRES 8 A 119 ARG SER THR ALA ALA GLU VAL GLN GLN VAL LEU ASN ARG SEQRES 9 A 119 PHE SER SER ALA PRO LEU ILE PRO LEU PRO THR PRO PRO SEQRES 10 A 119 ILE ILE SEQRES 1 B 12 U G G U G G U G G U G G FORMUL 3 HOH *128(H2 O) HELIX 1 AA1 THR A 312 LYS A 322 1 11 HELIX 2 AA2 THR A 338 GLY A 347 1 10 HELIX 3 AA3 GLY A 354 GLU A 357 5 4 HELIX 4 AA4 CYS A 379 ARG A 388 1 10 HELIX 5 AA5 THR A 405 SER A 417 1 13 SHEET 1 AA1 4 ILE A 359 THR A 363 0 SHEET 2 AA1 4 PRO A 369 PHE A 377 -1 O PHE A 374 N LEU A 360 SHEET 3 AA1 4 VAL A 326 ARG A 331 -1 N MET A 330 O ALA A 373 SHEET 4 AA1 4 GLU A 400 SER A 404 -1 O PHE A 402 N ARG A 329 SHEET 1 AA2 2 LEU A 393 LEU A 394 0 SHEET 2 AA2 2 ARG A 397 TYR A 398 -1 O ARG A 397 N LEU A 394 SSBOND 1 CYS A 379 CYS A 379 1555 5555 2.04 CRYST1 86.118 86.118 43.280 90.00 90.00 120.00 P 31 2 1 6 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 0.011612 0.006704 0.000000 0.00000 SCALE2 0.000000 0.013408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023105 0.00000