HEADER RNA BINDING PROTEIN 17-AUG-20 7CSX TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL TANDEM RRM DOMAINS OF RBM45 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN 45; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEVELOPMENTALLY-REGULATED RNA-BINDING PROTEIN 1,RB-1,RNA- COMPND 5 BINDING MOTIF PROTEIN 45; COMPND 6 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: RBM45, DRB1, DRBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RNA-BINDING, RRM, ALS, FTLD, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,Z.YANG,W.WANG,M.WANG REVDAT 4 29-NOV-23 7CSX 1 REMARK REVDAT 3 31-MAR-21 7CSX 1 JRNL REVDAT 2 24-FEB-21 7CSX 1 JRNL REVDAT 1 03-FEB-21 7CSX 0 JRNL AUTH X.CHEN,Z.YANG,W.WANG,K.QIAN,M.LIU,J.WANG,M.WANG JRNL TITL STRUCTURAL BASIS FOR RNA RECOGNITION BY THE N-TERMINAL JRNL TITL 2 TANDEM RRM DOMAINS OF HUMAN RBM45. JRNL REF NUCLEIC ACIDS RES. V. 49 2946 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33577684 JRNL DOI 10.1093/NAR/GKAB075 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.630 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 44.1800 - 4.2718 0.99 1249 180 0.1715 0.2087 REMARK 3 2 4.2718 - 3.3910 1.00 1277 129 0.1765 0.2629 REMARK 3 3 3.3910 - 2.9625 1.00 1274 133 0.2197 0.2704 REMARK 3 4 2.9625 - 2.6916 1.00 1242 157 0.2645 0.2990 REMARK 3 5 2.6916 - 2.5000 0.99 1240 148 0.2554 0.3183 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.96 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7CSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300018208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 : SSRF REMARK 200 BEAMLINE : BL17U 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7056 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.95000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6JVX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM PHOSPHATE DIBASIC, 20% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 26.01150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.01725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.00575 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 109 REMARK 465 GLY A 110 REMARK 465 SER A 111 REMARK 465 ASN A 194 REMARK 465 LYS A 195 REMARK 465 ALA A 196 REMARK 465 SER A 197 REMARK 465 GLU A 198 REMARK 465 SER A 199 REMARK 465 SER A 200 REMARK 465 GLU A 201 REMARK 465 GLN A 202 REMARK 465 LEU A 203 REMARK 465 GLU A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 REMARK 465 HIS A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 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 365 O HOH A 375 2.16 REMARK 500 O HOH A 354 O HOH A 382 2.19 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 THR A 96 -112.89 61.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 385 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 386 DISTANCE = 6.80 ANGSTROMS DBREF 7CSX A 23 202 UNP Q8IUH3 RBM45_HUMAN 23 202 SEQADV 7CSX MET A 22 UNP Q8IUH3 INITIATING METHIONINE SEQADV 7CSX LEU A 203 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX GLU A 204 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 205 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 206 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 207 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 208 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 209 UNP Q8IUH3 EXPRESSION TAG SEQADV 7CSX HIS A 210 UNP Q8IUH3 EXPRESSION TAG SEQRES 1 A 189 MET PRO PRO ASN SER ARG ILE PHE LEU VAL ILE SER LYS SEQRES 2 A 189 TYR THR PRO GLU SER VAL LEU ARG GLU ARG PHE SER PRO SEQRES 3 A 189 PHE GLY ASP ILE GLN ASP ILE TRP VAL VAL ARG ASP LYS SEQRES 4 A 189 HIS THR LYS GLU SER LYS GLY ILE ALA PHE VAL LYS PHE SEQRES 5 A 189 ALA ARG SER SER GLN ALA CYS ARG ALA MET GLU GLU MET SEQRES 6 A 189 HIS GLY GLN CYS LEU GLY PRO ASN ASP THR LYS PRO ILE SEQRES 7 A 189 LYS VAL PHE ILE ALA GLN SER ARG SER SER GLY SER HIS SEQRES 8 A 189 ARG ASP VAL GLU ASP GLU GLU LEU THR ARG ILE PHE VAL SEQRES 9 A 189 MET ILE PRO LYS SER TYR THR GLU GLU ASP LEU ARG GLU SEQRES 10 A 189 LYS PHE LYS VAL TYR GLY ASP ILE GLU TYR CYS SER ILE SEQRES 11 A 189 ILE LYS ASN LYS VAL THR GLY GLU SER LYS GLY LEU GLY SEQRES 12 A 189 TYR VAL ARG TYR LEU LYS PRO SER GLN ALA ALA GLN ALA SEQRES 13 A 189 ILE GLU ASN CYS ASP ARG SER PHE ARG ALA ILE LEU ALA SEQRES 14 A 189 GLU PRO LYS ASN LYS ALA SER GLU SER SER GLU GLN LEU SEQRES 15 A 189 GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *86(H2 O) HELIX 1 AA1 PRO A 37 SER A 46 1 10 HELIX 2 AA2 PRO A 47 GLY A 49 5 3 HELIX 3 AA3 ARG A 75 HIS A 87 1 13 HELIX 4 AA4 GLY A 92 THR A 96 5 5 HELIX 5 AA5 GLU A 116 LEU A 120 5 5 HELIX 6 AA6 THR A 132 LYS A 141 1 10 HELIX 7 AA7 VAL A 142 GLY A 144 5 3 HELIX 8 AA8 LYS A 170 CYS A 181 1 12 HELIX 9 AA9 ASP A 182 ARG A 186 5 5 SHEET 1 AA1 4 ILE A 51 ARG A 58 0 SHEET 2 AA1 4 SER A 65 PHE A 73 -1 O LYS A 72 N GLN A 52 SHEET 3 AA1 4 ARG A 27 VAL A 31 -1 N ILE A 28 O VAL A 71 SHEET 4 AA1 4 LYS A 100 ILE A 103 -1 O LYS A 100 N VAL A 31 SHEET 1 AA2 4 ILE A 146 LYS A 153 0 SHEET 2 AA2 4 SER A 160 TYR A 168 -1 O LYS A 161 N ILE A 152 SHEET 3 AA2 4 ARG A 122 MET A 126 -1 N ILE A 123 O VAL A 166 SHEET 4 AA2 4 ILE A 188 LEU A 189 -1 O ILE A 188 N PHE A 124 CRYST1 62.485 62.485 52.023 90.00 90.00 90.00 P 43 4 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 0.016004 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019222 0.00000