HEADER STRUCTURAL PROTEIN 29-OCT-19 6UT2 TITLE 3D STRUCTURE OF THE LEIOMODIN/TROPOMYOSIN BINDING INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEIOMODIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARDIAC LEIOMODIN,C-LMOD,LEIOMODIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TROPOMYOSIN ALPHA-1 CHAIN CHIMERIC PEPTIDE; COMPND 8 CHAIN: B, C; COMPND 9 SYNONYM: ALPHA-TROPOMYOSIN,TROPOMYOSIN-1; COMPND 10 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: LMOD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: TPM1, C15ORF13, TMSA; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS POINTED END, THIN FILAMENTS, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.TOLKATCHEV,G.E.SMITH,G.L.HELMS,J.R.CORT,A.S.KOSTYUKOVA REVDAT 2 01-MAY-24 6UT2 1 REMARK REVDAT 1 30-SEP-20 6UT2 0 JRNL AUTH D.TOLKATCHEV,G.E.SMITH JR.,L.E.SCHULTZ,M.COLPAN,G.L.HELMS, JRNL AUTH 2 J.R.CORT,C.C.GREGORIO,A.S.KOSTYUKOVA JRNL TITL LEIOMODIN CREATES A LEAKY CAP AT THE POINTED END OF JRNL TITL 2 ACTIN-THIN FILAMENTS. JRNL REF PLOS BIOL. V. 18 00848 2020 JRNL REFN ESSN 1545-7885 JRNL PMID 32898131 JRNL DOI 10.1371/JOURNAL.PBIO.3000848 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 6UT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000243885. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.081 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] LEIOMODIN REMARK 210 PEPTIDE, 1 MM TROPOMYOSIN REMARK 210 PEPTIDE, 90% H2O/10% D2O; 0.5 MM REMARK 210 [U-13C; U-15N] TROPOMYOSIN REMARK 210 PEPTIDE, 1 MM LEIOMODIN PEPTIDE, REMARK 210 90% H2O/10% D2O; 0.3 MM [U-15N] REMARK 210 LEIOMODIN PEPTIDE, 0.6 MM REMARK 210 TROPOMYOSIN PEPTIDE, 90% H2O/10% REMARK 210 D2O; 0.3 MM [U-15N] TROPOMYOSIN REMARK 210 PEPTIDE, 0.6 MM LEIOMODIN REMARK 210 PEPTIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D HNCA; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS TALOS+, NMRVIEW NMRVIEWJ REMARK 210 VERSION 9.2.0-B4 WITH JAVA 1.8.0_ REMARK 210 92 X86_64 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 HG SER A 11 OE2 GLU A 14 1.53 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 1 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG C 32 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG C 32 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG C 24 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ARG A 7 -27.89 -140.43 REMARK 500 1 GLU B 31 -176.79 -68.36 REMARK 500 2 LEU A 10 -25.83 -153.86 REMARK 500 3 ARG A 7 -8.03 56.28 REMARK 500 4 SER A 15 48.92 -73.69 REMARK 500 5 ILE A 16 -58.74 -137.56 REMARK 500 5 ASP A 39 1.15 -63.58 REMARK 500 6 PHE A 4 -12.91 65.27 REMARK 500 7 GLU A 18 30.92 -78.82 REMARK 500 8 GLU B 31 -166.38 -71.28 REMARK 500 8 GLU C 31 -161.34 -116.65 REMARK 500 9 TYR A 6 107.20 -47.76 REMARK 500 9 ARG A 7 18.07 52.57 REMARK 500 10 THR A 3 48.97 -145.02 REMARK 500 10 SER A 15 36.42 -68.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY C 0 MET C 1 9 -149.48 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 7 TYR A 6 0.07 SIDE CHAIN REMARK 500 9 TYR B 16 0.07 SIDE CHAIN REMARK 500 9 ARG B 32 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30681 RELATED DB: BMRB REMARK 900 3D STRUCTURE OF THE LEIOMODIN/TROPOMYOSIN BINDING INTERFACE DBREF 6UT2 A 2 41 UNP Q6P5Q4 LMOD2_HUMAN 2 41 DBREF 6UT2 B 1 14 UNP P09493 TPM1_HUMAN 1 14 DBREF 6UT2 B 15 32 PDB 6UT2 6UT2 15 32 DBREF 6UT2 C 1 14 UNP P09493 TPM1_HUMAN 1 14 DBREF 6UT2 C 15 32 PDB 6UT2 6UT2 15 32 SEQADV 6UT2 GLY B 0 UNP P09493 EXPRESSION TAG SEQADV 6UT2 GLY C 0 UNP P09493 EXPRESSION TAG SEQRES 1 A 40 SER THR PHE GLY TYR ARG ARG GLY LEU SER LYS TYR GLU SEQRES 2 A 40 SER ILE ASP GLU ASP GLU LEU LEU ALA SER LEU SER ALA SEQRES 3 A 40 GLU GLU LEU LYS GLU LEU GLU ARG GLU LEU GLU ASP ILE SEQRES 4 A 40 GLU SEQRES 1 B 33 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 B 33 LEU ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 B 33 LYS LYS LEU VAL GLY GLU ARG SEQRES 1 C 33 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 C 33 LEU ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG LEU SEQRES 3 C 33 LYS LYS LEU VAL GLY GLU ARG HELIX 1 AA1 SER A 2 ARG A 7 5 6 HELIX 2 AA2 ASP A 17 LEU A 22 1 6 HELIX 3 AA3 SER A 26 GLU A 41 1 16 HELIX 4 AA4 MET B 1 VAL B 29 1 29 HELIX 5 AA5 MET C 1 VAL C 29 1 29 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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