HEADER STRUCTURAL PROTEIN 08-JAN-09 2KDG TITLE SOLUTION STRUCTURE OF THE 1ST IG DOMAIN OF MYOTILIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOTILIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THE FIRST IMMUNOGLOBULIN DOMAIN (RESIDUES 249-344); COMPND 5 SYNONYM: TITIN IMMUNOGLOBULIN DOMAIN PROTEIN, MYOFIBRILLAR TITIN-LIKE COMPND 6 IG DOMAINS PROTEIN, 57 KDA CYTOSKELETAL PROTEIN; COMPND 7 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: MYOT, TTID; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: C1-5A KEYWDS MYOTILIN, IMMONOGLOBULIN DOMAIN, ACTIN-BINDING, STRUCTURAL PROTEIN, KEYWDS 2 CELL MEMBRANE, CYTOPLASM, CYTOSKELETON, DISEASE MUTATION, KEYWDS 3 IMMUNOGLOBULIN DOMAIN, LIMB-GIRDLE MUSCULAR DYSTROPHY, MEMBRANE, KEYWDS 4 MUSCLE PROTEIN, POLYMORPHISM EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR O.HEIKKINEN,I.KILPELAINEN,P.PERMI,H.KOSKELA,J.YLANNE,O.CARPEN REVDAT 2 16-MAR-22 2KDG 1 REMARK SEQADV REVDAT 1 21-JUL-09 2KDG 0 JRNL AUTH O.HEIKKINEN,P.PERMI,H.KOSKELA,O.CARPEN,J.YLANNE, JRNL AUTH 2 I.KILPELAINEN JRNL TITL SOLUTION STRUCTURE OF THE FIRST IMMUNOGLOBULIN DOMAIN OF JRNL TITL 2 HUMAN MYOTILIN JRNL REF J.BIOMOL.NMR V. 44 107 2009 JRNL REFN ISSN 0925-2738 JRNL PMID 19418025 JRNL DOI 10.1007/S10858-009-9320-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, AMBER 8.0 REMARK 3 AUTHORS : VARIAN INC (VNMR), CASE, D.A ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BORN IMPLICIT SOLVENT MODEL REMARK 4 REMARK 4 2KDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100983. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 140 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-13C; U-15N] MYOTILIN REMARK 210 249-344-1, 20MM POTASSIUM REMARK 210 PHOSPHATE-2, 140MM SODIUM REMARK 210 CHLORIDE-3, 1MM DTT-4, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D C(CO)NH; 3D H(CCO)NH; 3D REMARK 210 HCCH-COSY; 3D IHNCA; 2D 1H-13C REMARK 210 HSQC (AROM); (HB)CB(CGCD)HD; (HB) REMARK 210 CB(CGCDCE)HE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.106, TALOS, CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: DIHEDRAL ANGLE RESTRAINTS WERE EXTRACTED FROM ALPHA AND REMARK 210 BETA CARBON CHEMICAL SHIFTS USING TALOS PROGRAM 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: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL 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 2 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 314 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 314 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 314 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 314 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 ARG A 314 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 21 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 23 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 25 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.4 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 ILE A 253 -66.14 -135.47 REMARK 500 1 ASN A 286 14.28 54.01 REMARK 500 1 HIS A 296 68.78 -108.74 REMARK 500 2 ASN A 286 10.98 55.14 REMARK 500 2 ASP A 339 77.68 -106.40 REMARK 500 3 ASN A 286 16.03 53.58 REMARK 500 3 VAL A 312 87.08 -150.08 REMARK 500 4 ASN A 286 10.99 54.54 REMARK 500 5 ASN A 286 18.86 54.07 REMARK 500 5 VAL A 312 86.82 -150.28 REMARK 500 6 ASN A 286 15.00 54.90 REMARK 500 6 VAL A 312 88.16 -151.04 REMARK 500 7 ASN A 286 10.15 55.02 REMARK 500 8 ILE A 253 -59.64 -130.83 REMARK 500 8 ASN A 286 15.69 54.47 REMARK 500 9 ASN A 286 14.71 54.93 REMARK 500 10 ASN A 286 14.95 54.87 REMARK 500 10 VAL A 312 89.51 -151.78 REMARK 500 10 LEU A 341 97.71 -67.62 REMARK 500 11 ASN A 286 15.29 55.02 REMARK 500 11 HIS A 296 74.14 -110.90 REMARK 500 12 ASN A 258 108.86 -49.61 REMARK 500 12 ASN A 286 14.05 55.26 REMARK 500 13 ASN A 286 14.18 53.42 REMARK 500 14 ILE A 253 -71.10 -76.05 REMARK 500 14 ASN A 286 11.00 54.22 REMARK 500 14 VAL A 312 89.45 -151.07 REMARK 500 14 LEU A 341 96.78 -69.37 REMARK 500 15 ILE A 253 -63.80 -105.46 REMARK 500 15 ASN A 286 16.65 54.78 REMARK 500 16 ASN A 286 12.26 55.40 REMARK 500 17 GLN A 254 102.43 -46.35 REMARK 500 17 ASN A 286 15.10 54.93 REMARK 500 17 VAL A 312 85.63 -151.16 REMARK 500 18 ASN A 286 12.46 55.76 REMARK 500 19 ASN A 286 17.35 54.18 REMARK 500 19 VAL A 312 83.69 -151.88 REMARK 500 20 ASN A 286 16.24 54.72 REMARK 500 20 VAL A 312 88.91 -151.57 REMARK 500 21 ASN A 286 14.14 54.90 REMARK 500 21 VAL A 312 70.15 -150.61 REMARK 500 22 ASN A 286 17.15 54.76 REMARK 500 23 ILE A 253 -68.27 -90.64 REMARK 500 23 ASN A 286 13.33 55.54 REMARK 500 23 VAL A 312 89.42 -151.00 REMARK 500 24 ASN A 286 14.79 54.91 REMARK 500 24 VAL A 312 87.71 -150.56 REMARK 500 25 ILE A 253 -64.08 -136.40 REMARK 500 25 SER A 274 -165.70 -128.60 REMARK 500 25 ASN A 286 6.97 54.98 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7113 RELATED DB: BMRB DBREF 2KDG A 249 344 UNP Q9UBF9 MYOTI_HUMAN 249 344 SEQADV 2KDG GLY A -4 UNP Q9UBF9 EXPRESSION TAG SEQADV 2KDG ALA A -3 UNP Q9UBF9 EXPRESSION TAG SEQADV 2KDG MET A -2 UNP Q9UBF9 EXPRESSION TAG SEQADV 2KDG GLY A -1 UNP Q9UBF9 EXPRESSION TAG SEQRES 1 A 100 GLY ALA MET GLY PRO PRO ARG PHE ILE GLN VAL PRO GLU SEQRES 2 A 100 ASN MET SER ILE ASP GLU GLY ARG PHE CYS ARG MET ASP SEQRES 3 A 100 PHE LYS VAL SER GLY LEU PRO ALA PRO ASP VAL SER TRP SEQRES 4 A 100 TYR LEU ASN GLY ARG THR VAL GLN SER ASP ASP LEU HIS SEQRES 5 A 100 LYS MET ILE VAL SER GLU LYS GLY LEU HIS SER LEU ILE SEQRES 6 A 100 PHE GLU VAL VAL ARG ALA SER ASP ALA GLY ALA TYR ALA SEQRES 7 A 100 CYS VAL ALA LYS ASN ARG ALA GLY GLU ALA THR PHE THR SEQRES 8 A 100 VAL GLN LEU ASP VAL LEU ALA LYS GLU HELIX 1 1 ARG A 314 ALA A 318 5 5 SHEET 1 A 2 GLY A -1 ARG A 251 0 SHEET 2 A 2 SER A 274 LEU A 276 -1 O LEU A 276 N GLY A -1 SHEET 1 B 5 MET A 259 ASP A 262 0 SHEET 2 B 5 GLY A 330 LEU A 341 1 O ASP A 339 N MET A 259 SHEET 3 B 5 GLY A 319 ASN A 327 -1 N ALA A 325 O ALA A 332 SHEET 4 B 5 ASP A 280 LEU A 285 -1 N TYR A 284 O ALA A 322 SHEET 5 B 5 ARG A 288 VAL A 290 -1 O ARG A 288 N LEU A 285 SHEET 1 C 3 CYS A 267 LYS A 272 0 SHEET 2 C 3 LEU A 305 PHE A 310 -1 O PHE A 310 N CYS A 267 SHEET 3 C 3 MET A 298 SER A 301 -1 N ILE A 299 O SER A 307 CISPEP 1 LEU A 276 PRO A 277 1 -2.62 CISPEP 2 LEU A 276 PRO A 277 2 -1.90 CISPEP 3 LEU A 276 PRO A 277 3 -4.42 CISPEP 4 LEU A 276 PRO A 277 4 -2.78 CISPEP 5 LEU A 276 PRO A 277 5 -6.11 CISPEP 6 LEU A 276 PRO A 277 6 -3.00 CISPEP 7 LEU A 276 PRO A 277 7 -3.94 CISPEP 8 LEU A 276 PRO A 277 8 -3.72 CISPEP 9 LEU A 276 PRO A 277 9 0.61 CISPEP 10 LEU A 276 PRO A 277 10 -1.63 CISPEP 11 LEU A 276 PRO A 277 11 -2.63 CISPEP 12 LEU A 276 PRO A 277 12 -2.21 CISPEP 13 LEU A 276 PRO A 277 13 -2.83 CISPEP 14 LEU A 276 PRO A 277 14 -3.53 CISPEP 15 LEU A 276 PRO A 277 15 -3.12 CISPEP 16 LEU A 276 PRO A 277 16 -2.98 CISPEP 17 LEU A 276 PRO A 277 17 -3.12 CISPEP 18 LEU A 276 PRO A 277 18 -2.06 CISPEP 19 LEU A 276 PRO A 277 19 -3.22 CISPEP 20 LEU A 276 PRO A 277 20 -1.13 CISPEP 21 LEU A 276 PRO A 277 21 -2.96 CISPEP 22 LEU A 276 PRO A 277 22 -2.60 CISPEP 23 LEU A 276 PRO A 277 23 -4.23 CISPEP 24 LEU A 276 PRO A 277 24 -2.15 CISPEP 25 LEU A 276 PRO A 277 25 -4.19 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