HEADER RNA BINDING PROTEIN 20-SEP-22 8GXL TITLE HUMAN SUGP1 433-577 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURP AND G-PATCH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNA-BINDING PROTEIN RBP,SPLICING FACTOR 4; COMPND 5 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: SUGP1, SF4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRE-MRNA SPLICING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.XU,L.TONG REVDAT 1 14-DEC-22 8GXL 0 JRNL AUTH J.ZHANG,J.HUANG,K.XU,P.XING,Y.HUANG,Z.LIU,L.TONG,J.L.MANLEY JRNL TITL DHX15 IS INVOLVED IN SUGP1-MEDIATED RNA MISSPLICING BY JRNL TITL 2 MUTANT SF3B1 IN CANCER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 12119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 36459648 JRNL DOI 10.1073/PNAS.2216712119 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1388 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 51.6600 - 5.1700 1.00 1267 146 0.1902 0.2393 REMARK 3 2 5.1700 - 4.1000 1.00 1285 128 0.1636 0.2104 REMARK 3 3 4.1000 - 3.5800 1.00 1250 135 0.1787 0.2321 REMARK 3 4 3.5800 - 3.2600 1.00 1271 144 0.1982 0.2679 REMARK 3 5 3.2600 - 3.0200 1.00 1256 132 0.2180 0.2837 REMARK 3 6 3.0200 - 2.8500 1.00 1256 144 0.2395 0.3238 REMARK 3 7 2.8400 - 2.7000 1.00 1265 144 0.2251 0.2889 REMARK 3 8 2.7000 - 2.5800 1.00 1238 137 0.2313 0.3062 REMARK 3 9 2.5800 - 2.4900 1.00 1266 137 0.2332 0.3436 REMARK 3 10 2.4800 - 2.4000 1.00 1260 141 0.2707 0.4025 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) : 0.376 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.424 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.37 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 : 0.008 2098 REMARK 3 ANGLE : 0.935 2791 REMARK 3 CHIRALITY : 0.039 275 REMARK 3 PLANARITY : 0.005 356 REMARK 3 DIHEDRAL : 5.200 253 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 8GXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-19 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14002 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 51.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: SAD REMARK 200 SOFTWARE USED: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM TARTRATE DIBASIC, PH REMARK 280 7.0, AND 20% (W/V) POLYETHYLENE GLYCOL 3350., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 59.46800 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 118.93600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.20200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 148.67000 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 29.73400 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: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15130 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 GLY A 433 REMARK 465 VAL A 434 REMARK 465 THR A 435 REMARK 465 GLN A 478 REMARK 465 HIS A 479 REMARK 465 GLN A 480 REMARK 465 HIS A 481 REMARK 465 GLY A 482 REMARK 465 TYR A 483 REMARK 465 ASP A 484 REMARK 465 SER A 485 REMARK 465 ASP A 486 REMARK 465 GLU A 487 REMARK 465 GLU A 488 REMARK 465 VAL A 489 REMARK 465 ASP A 490 REMARK 465 SER A 491 REMARK 465 GLU A 492 REMARK 465 LEU A 493 REMARK 465 GLY A 494 REMARK 465 GLY A 519 REMARK 465 ARG A 520 REMARK 465 GLY A 521 REMARK 465 LYS A 522 REMARK 465 LYS A 576 REMARK 465 GLU A 577 REMARK 465 GLY B 433 REMARK 465 HIS B 479 REMARK 465 GLN B 480 REMARK 465 HIS B 481 REMARK 465 GLY B 482 REMARK 465 TYR B 483 REMARK 465 ASP B 484 REMARK 465 SER B 485 REMARK 465 ASP B 486 REMARK 465 GLU B 487 REMARK 465 GLU B 488 REMARK 465 VAL B 489 REMARK 465 ASP B 490 REMARK 465 SER B 491 REMARK 465 GLU B 492 REMARK 465 LEU B 493 REMARK 465 ARG B 520 REMARK 465 GLY B 521 REMARK 465 LYS B 522 REMARK 465 HIS B 523 REMARK 465 PHE B 524 REMARK 465 LYS B 576 REMARK 465 GLU B 577 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 LYS A 517 1.20 -58.72 REMARK 500 GLU B 546 2.84 -68.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GXL A 433 577 UNP Q8IWZ8 SUGP1_HUMAN 433 577 DBREF 8GXL B 433 577 UNP Q8IWZ8 SUGP1_HUMAN 433 577 SEQRES 1 A 145 GLY VAL THR GLU LEU SER ASP ALA GLN LYS LYS GLN LEU SEQRES 2 A 145 LYS GLU GLN GLN GLU MET GLN GLN MET TYR ASP MET ILE SEQRES 3 A 145 MET GLN HIS LYS ARG ALA MET GLN ASP MET GLN LEU LEU SEQRES 4 A 145 TRP GLU LYS ALA VAL GLN GLN HIS GLN HIS GLY TYR ASP SEQRES 5 A 145 SER ASP GLU GLU VAL ASP SER GLU LEU GLY THR TRP GLU SEQRES 6 A 145 HIS GLN LEU ARG ARG MET GLU MET ASP LYS THR ARG GLU SEQRES 7 A 145 TRP ALA GLU GLN LEU THR LYS MET GLY ARG GLY LYS HIS SEQRES 8 A 145 PHE ILE GLY ASP PHE LEU PRO PRO ASP GLU LEU GLU LYS SEQRES 9 A 145 PHE MET GLU THR PHE LYS ALA LEU LYS GLU GLY ARG GLU SEQRES 10 A 145 PRO ASP TYR SER GLU TYR LYS GLU PHE LYS LEU THR VAL SEQRES 11 A 145 GLU ASN ILE GLY TYR GLN MET LEU MET LYS MET GLY TRP SEQRES 12 A 145 LYS GLU SEQRES 1 B 145 GLY VAL THR GLU LEU SER ASP ALA GLN LYS LYS GLN LEU SEQRES 2 B 145 LYS GLU GLN GLN GLU MET GLN GLN MET TYR ASP MET ILE SEQRES 3 B 145 MET GLN HIS LYS ARG ALA MET GLN ASP MET GLN LEU LEU SEQRES 4 B 145 TRP GLU LYS ALA VAL GLN GLN HIS GLN HIS GLY TYR ASP SEQRES 5 B 145 SER ASP GLU GLU VAL ASP SER GLU LEU GLY THR TRP GLU SEQRES 6 B 145 HIS GLN LEU ARG ARG MET GLU MET ASP LYS THR ARG GLU SEQRES 7 B 145 TRP ALA GLU GLN LEU THR LYS MET GLY ARG GLY LYS HIS SEQRES 8 B 145 PHE ILE GLY ASP PHE LEU PRO PRO ASP GLU LEU GLU LYS SEQRES 9 B 145 PHE MET GLU THR PHE LYS ALA LEU LYS GLU GLY ARG GLU SEQRES 10 B 145 PRO ASP TYR SER GLU TYR LYS GLU PHE LYS LEU THR VAL SEQRES 11 B 145 GLU ASN ILE GLY TYR GLN MET LEU MET LYS MET GLY TRP SEQRES 12 B 145 LYS GLU FORMUL 3 HOH *53(H2 O) HELIX 1 AA1 SER A 438 VAL A 476 1 39 HELIX 2 AA2 TRP A 496 LYS A 517 1 22 HELIX 3 AA3 PRO A 530 GLU A 546 1 17 HELIX 4 AA4 ASP A 551 TRP A 575 1 25 HELIX 5 AA5 SER B 438 GLN B 477 1 40 HELIX 6 AA6 THR B 495 GLY B 519 1 25 HELIX 7 AA7 PRO B 530 GLU B 546 1 17 HELIX 8 AA8 ASP B 551 GLY B 574 1 24 CRYST1 59.657 59.657 178.404 90.00 90.00 120.00 P 61 12 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 0.016762 0.009678 0.000000 0.00000 SCALE2 0.000000 0.019356 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005605 0.00000