HEADER MEMBRANE PROTEIN 19-SEP-20 7K6B TITLE SOLUTION STRUCTURE OF THE DYSFERLIN C2A DOMAIN IN ITS CALCIUM-FREE TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 15 OF DYSFERLIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DYSTROPHY-ASSOCIATED FER-1-LIKE PROTEIN,FER-1-LIKE PROTEIN COMPND 5 1; 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: DYSF, FER1L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MEMBRANE REPAIR, CALCIUM-BINDING, BETA-SANDWICH, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WANG,P.MERCIER,L.SANTAMARIA,G.S.SHAW REVDAT 2 14-JUN-23 7K6B 1 REMARK REVDAT 1 27-JAN-21 7K6B 0 JRNL AUTH Y.WANG,R.TADAYON,L.SANTAMARIA,P.MERCIER,C.J.FORRISTAL, JRNL AUTH 2 G.S.SHAW JRNL TITL CALCIUM BINDS AND RIGIDIFIES THE DYSFERLIN C2A DOMAIN IN A JRNL TITL 2 TIGHTLY COUPLED MANNER. JRNL REF BIOCHEM.J. V. 478 197 2021 JRNL REFN ESSN 1470-8728 JRNL PMID 33449082 JRNL DOI 10.1042/BCJ20200773 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.37 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN EXPLICIT WATER SOLVENT REMARK 4 REMARK 4 7K6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251607. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DSS, 25 MM MES, 150 MM REMARK 210 NACL, 5 MM EDTA, 1 MM DTT, 0.3 REMARK 210 MM [U-13C; U-15N] PROTEIN, 90% REMARK 210 H2O/10% D2O; 1 MM DSS, 25 MM MES, REMARK 210 150 MM NACL, 5 MM EDTA, 1 MM REMARK 210 DTT, 0.3 MM [U-13C; U-15N] REMARK 210 PROTEIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC NH2 ONLY; 2D 1H REMARK 210 -13C HSQC; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCO; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D C(CO)NH; 3D H(CCO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ, NMRPIPE, NMRVIEW, CYANA REMARK 210 2.1 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: 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 OE2 GLU A 73 HZ1 LYS A 85 1.55 REMARK 500 HZ3 LYS A 70 OE1 GLU A 73 1.56 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 TYR A 8 108.85 83.78 REMARK 500 1 ALA A 22 33.11 -155.35 REMARK 500 1 CYS A 24 97.29 -66.20 REMARK 500 1 PHE A 28 -80.14 -85.15 REMARK 500 1 VAL A 37 55.86 39.37 REMARK 500 1 GLU A 48 -51.69 68.39 REMARK 500 1 VAL A 68 -46.18 67.53 REMARK 500 1 VAL A 69 -65.70 -29.31 REMARK 500 1 ARG A 77 -48.54 69.81 REMARK 500 1 THR A 108 -63.22 -157.86 REMARK 500 1 GLN A 111 138.91 -36.30 REMARK 500 2 TYR A 8 115.11 81.57 REMARK 500 2 THR A 14 70.04 62.90 REMARK 500 2 THR A 17 -18.62 69.77 REMARK 500 2 PHE A 28 -90.24 -69.84 REMARK 500 2 SER A 41 82.06 62.69 REMARK 500 2 GLU A 48 -36.48 71.54 REMARK 500 2 LYS A 70 -76.90 -139.69 REMARK 500 2 LEU A 81 -72.77 68.12 REMARK 500 2 GLU A 83 47.44 -87.56 REMARK 500 2 THR A 108 -31.28 -169.07 REMARK 500 2 GLN A 111 127.36 -39.68 REMARK 500 3 TYR A 8 106.37 88.09 REMARK 500 3 THR A 17 -152.45 -103.85 REMARK 500 3 PHE A 28 -80.77 -93.83 REMARK 500 3 GLU A 48 -62.12 66.52 REMARK 500 3 LYS A 70 -152.68 -176.04 REMARK 500 3 MET A 75 -85.48 -95.41 REMARK 500 3 PHE A 80 137.06 -175.62 REMARK 500 3 LEU A 81 -73.78 69.98 REMARK 500 3 ASP A 107 -64.56 -147.05 REMARK 500 3 LYS A 109 -65.69 -93.84 REMARK 500 4 TYR A 8 94.79 76.81 REMARK 500 4 PRO A 15 48.12 -69.26 REMARK 500 4 PHE A 28 -70.13 -89.54 REMARK 500 4 ILE A 38 -43.53 -130.86 REMARK 500 4 LYS A 39 111.41 -163.23 REMARK 500 4 VAL A 42 -41.64 74.09 REMARK 500 4 PRO A 44 49.28 -78.10 REMARK 500 4 VAL A 69 31.91 -92.98 REMARK 500 4 LYS A 70 -85.93 -161.09 REMARK 500 4 GLU A 73 84.44 46.37 REMARK 500 4 THR A 108 -23.57 172.32 REMARK 500 4 GLN A 111 131.05 -36.42 REMARK 500 4 THR A 113 -15.00 -143.45 REMARK 500 5 LEU A 7 -54.28 70.41 REMARK 500 5 TYR A 8 117.39 172.47 REMARK 500 5 VAL A 12 20.36 49.59 REMARK 500 5 PHE A 28 -75.83 -82.36 REMARK 500 5 LYS A 36 -162.19 -78.60 REMARK 500 REMARK 500 THIS ENTRY HAS 245 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30798 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE DYSFERLIN C2A DOMAIN IN ITS CALCIUM-FREE REMARK 900 STATE DBREF 7K6B A 1 130 UNP O75923 DYSF_HUMAN 1 130 SEQADV 7K6B GLY A -6 UNP O75923 EXPRESSION TAG SEQADV 7K6B SER A -5 UNP O75923 EXPRESSION TAG SEQADV 7K6B GLY A -4 UNP O75923 EXPRESSION TAG SEQADV 7K6B GLY A -3 UNP O75923 EXPRESSION TAG SEQADV 7K6B GLY A -2 UNP O75923 EXPRESSION TAG SEQADV 7K6B GLY A -1 UNP O75923 EXPRESSION TAG SEQADV 7K6B GLY A 0 UNP O75923 EXPRESSION TAG SEQADV 7K6B LEU A 131 UNP O75923 EXPRESSION TAG SEQRES 1 A 138 GLY SER GLY GLY GLY GLY GLY MET LEU ARG VAL PHE ILE SEQRES 2 A 138 LEU TYR ALA GLU ASN VAL HIS THR PRO ASP THR ASP ILE SEQRES 3 A 138 SER ASP ALA TYR CYS SER ALA VAL PHE ALA GLY VAL LYS SEQRES 4 A 138 LYS ARG THR LYS VAL ILE LYS ASN SER VAL ASN PRO VAL SEQRES 5 A 138 TRP ASN GLU GLY PHE GLU TRP ASP LEU LYS GLY ILE PRO SEQRES 6 A 138 LEU ASP GLN GLY SER GLU LEU HIS VAL VAL VAL LYS ASP SEQRES 7 A 138 HIS GLU THR MET GLY ARG ASN ARG PHE LEU GLY GLU ALA SEQRES 8 A 138 LYS VAL PRO LEU ARG GLU VAL LEU ALA THR PRO SER LEU SEQRES 9 A 138 SER ALA SER PHE ASN ALA PRO LEU LEU ASP THR LYS LYS SEQRES 10 A 138 GLN PRO THR GLY ALA SER LEU VAL LEU GLN VAL SER TYR SEQRES 11 A 138 THR PRO LEU PRO GLY ALA VAL LEU HELIX 1 AA1 LEU A 88 THR A 94 1 7 SHEET 1 AA1 4 PHE A 50 ASP A 53 0 SHEET 2 AA1 4 GLY A 0 PHE A 5 -1 N LEU A 2 O TRP A 52 SHEET 3 AA1 4 VAL A 118 PRO A 125 -1 O THR A 124 N MET A 1 SHEET 4 AA1 4 SER A 98 ASN A 102 -1 N ALA A 99 O VAL A 121 SHEET 1 AA2 4 LYS A 32 LYS A 33 0 SHEET 2 AA2 4 ALA A 26 VAL A 27 -1 N ALA A 26 O LYS A 33 SHEET 3 AA2 4 GLU A 64 VAL A 67 -1 O HIS A 66 N VAL A 27 SHEET 4 AA2 4 LYS A 85 PRO A 87 -1 O VAL A 86 N LEU A 65 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