HEADER RNA BINDING PROTEIN 08-DEC-16 5U6L TITLE SOLUTION STRUCTURE OF THE ZINC FINGERS 3 AND 4 OF MBNL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUSCLEBLIND-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGERS 3 AND 4 (UNP RESIDUES 173-255); COMPND 5 SYNONYM: TRIPLET-EXPANSION RNA-BINDING PROTEIN; 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: MBNL1, EXP, KIAA0428, MBNL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZINC FINGERS RNA-BINDING, STRUCTURE FROM MOLMOL, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.D.PHUKAN,S.PARK,M.M.MARTINEZ-YAMOUT,M.ZEEB,H.J.DYSON,P.E.WRIGHT REVDAT 4 15-MAY-24 5U6L 1 REMARK REVDAT 3 14-JUN-23 5U6L 1 REMARK LINK REVDAT 2 30-AUG-17 5U6L 1 JRNL REVDAT 1 02-AUG-17 5U6L 0 JRNL AUTH S.PARK,P.D.PHUKAN,M.ZEEB,M.A.MARTINEZ-YAMOUT,H.J.DYSON, JRNL AUTH 2 P.E.WRIGHT JRNL TITL STRUCTURAL BASIS FOR INTERACTION OF THE TANDEM ZINC FINGER JRNL TITL 2 DOMAINS OF HUMAN MUSCLEBLIND WITH COGNATE RNA FROM HUMAN JRNL TITL 3 CARDIAC TROPONIN T. JRNL REF BIOCHEMISTRY V. 56 4154 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28718627 JRNL DOI 10.1021/ACS.BIOCHEM.7B00484 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5U6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225407. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-98% 13C; U-98% 15N] REMARK 210 ZINC FINGERS 3 AND 4 OF MBNL1, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC; 3D HNHA; REMARK 210 3D HNHB; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TALOS, NMRDRAW, NMRPIPE, REMARK 210 SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 201 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 181 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 231 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 201 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 231 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 201 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 201 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 201 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 178 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 186 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 190 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 181 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 190 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 181 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 190 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 ARG A 181 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 190 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 178 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 181 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 228 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A 181 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 231 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 186 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 190 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG A 201 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES 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 1 ASN A 198 -10.02 -159.09 REMARK 500 1 GLU A 232 -3.65 -59.28 REMARK 500 2 LEU A 176 9.60 -63.00 REMARK 500 2 ASN A 198 -16.43 -158.23 REMARK 500 2 ALA A 206 -63.53 -95.66 REMARK 500 2 ASP A 215 -1.01 -141.75 REMARK 500 2 SER A 230 11.14 -143.70 REMARK 500 3 THR A 179 -55.26 -150.10 REMARK 500 3 ASN A 198 -15.43 -158.96 REMARK 500 3 SER A 230 7.33 -152.63 REMARK 500 3 CYS A 234 172.33 -59.77 REMARK 500 4 ASN A 198 -10.80 -158.29 REMARK 500 4 THR A 209 -13.12 -38.85 REMARK 500 4 ASP A 215 -4.86 -141.57 REMARK 500 4 ARG A 228 145.76 -170.94 REMARK 500 4 SER A 230 11.27 -151.23 REMARK 500 4 CYS A 234 175.39 -59.84 REMARK 500 5 LEU A 176 -9.84 -49.55 REMARK 500 5 ASN A 198 -10.72 -159.67 REMARK 500 5 ASP A 199 -31.71 -133.58 REMARK 500 5 SER A 230 8.45 -152.35 REMARK 500 5 LYS A 233 43.83 -140.29 REMARK 500 5 CYS A 234 170.50 -57.51 REMARK 500 6 ASN A 198 -16.61 -156.57 REMARK 500 6 ASP A 199 -33.66 -134.11 REMARK 500 6 ALA A 206 -63.47 -95.63 REMARK 500 6 ASP A 215 -0.02 -142.44 REMARK 500 6 SER A 230 11.04 -149.65 REMARK 500 6 CYS A 234 171.27 -57.95 REMARK 500 6 VAL A 254 -32.69 -132.97 REMARK 500 7 ASN A 198 -9.55 -159.03 REMARK 500 7 SER A 230 10.11 -144.89 REMARK 500 8 ASN A 198 -15.92 -164.62 REMARK 500 8 ASP A 207 34.90 -75.81 REMARK 500 8 ASP A 215 2.48 -150.82 REMARK 500 8 SER A 230 19.54 -161.17 REMARK 500 9 ASN A 198 -16.77 -158.36 REMARK 500 9 SER A 230 7.55 -151.64 REMARK 500 9 CYS A 234 171.74 -59.44 REMARK 500 10 ASN A 198 -20.31 -164.44 REMARK 500 11 ASN A 198 -9.78 -160.67 REMARK 500 11 THR A 209 -12.86 -40.89 REMARK 500 12 ASN A 198 -9.78 -160.83 REMARK 500 12 ASP A 215 -4.89 -140.44 REMARK 500 12 SER A 230 11.65 -154.42 REMARK 500 13 THR A 179 -78.23 -61.58 REMARK 500 13 ASN A 198 -16.19 -158.87 REMARK 500 13 THR A 209 -12.89 -40.31 REMARK 500 13 SER A 230 10.68 -151.82 REMARK 500 14 ASN A 198 -10.48 -161.28 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG A 181 0.09 SIDE CHAIN REMARK 500 9 ARG A 181 0.09 SIDE CHAIN 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 185 SG REMARK 620 2 CYS A 193 SG 110.9 REMARK 620 3 CYS A 200 SG 106.8 109.8 REMARK 620 4 HIS A 204 NE2 107.1 108.8 113.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 221 SG REMARK 620 2 CYS A 229 SG 107.9 REMARK 620 3 CYS A 234 SG 111.2 107.0 REMARK 620 4 HIS A 238 NE2 109.4 108.9 112.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30208 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE ZINC FINGERS 3 AND 4 OF MBNL1 REMARK 900 RELATED ID: 5U6H RELATED DB: PDB REMARK 900 RELATED ID: 5U9B RELATED DB: PDB DBREF 5U6L A 173 255 UNP Q9NR56 MBNL1_HUMAN 173 255 SEQRES 1 A 83 ALA GLN LYS LEU MET ARG THR ASP ARG LEU GLU VAL CYS SEQRES 2 A 83 ARG GLU TYR GLN ARG GLY ASN CYS ASN ARG GLY GLU ASN SEQRES 3 A 83 ASP CYS ARG PHE ALA HIS PRO ALA ASP SER THR MET ILE SEQRES 4 A 83 ASP THR ASN ASP ASN THR VAL THR VAL CYS MET ASP TYR SEQRES 5 A 83 ILE LYS GLY ARG CYS SER ARG GLU LYS CYS LYS TYR PHE SEQRES 6 A 83 HIS PRO PRO ALA HIS LEU GLN ALA LYS ILE LYS ALA ALA SEQRES 7 A 83 GLN TYR GLN VAL ASN HET ZN A 301 1 HET ZN A 302 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 CYS A 185 GLY A 191 1 7 HELIX 2 AA2 ASP A 207 ILE A 211 5 5 HELIX 3 AA3 PRO A 240 GLN A 251 1 12 HELIX 4 AA4 TYR A 252 ASN A 255 5 4 SHEET 1 AA1 2 ARG A 181 GLU A 183 0 SHEET 2 AA1 2 THR A 217 THR A 219 -1 O VAL A 218 N LEU A 182 LINK SG CYS A 185 ZN ZN A 301 1555 1555 2.27 LINK SG CYS A 193 ZN ZN A 301 1555 1555 2.28 LINK SG CYS A 200 ZN ZN A 301 1555 1555 2.28 LINK NE2 HIS A 204 ZN ZN A 301 1555 1555 2.08 LINK SG CYS A 221 ZN ZN A 302 1555 1555 2.27 LINK SG CYS A 229 ZN ZN A 302 1555 1555 2.27 LINK SG CYS A 234 ZN ZN A 302 1555 1555 2.28 LINK NE2 HIS A 238 ZN ZN A 302 1555 1555 2.08 SITE 1 AC1 4 CYS A 185 CYS A 193 CYS A 200 HIS A 204 SITE 1 AC2 4 CYS A 221 CYS A 229 CYS A 234 HIS A 238 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1