HEADER STRUCTURAL PROTEIN 18-SEP-17 6B1G TITLE SOLUTION STRUCTURE OF TDP-43 N-TERMINAL DOMAIN DIMER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43, S48E MUTANT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NTD DOMAIN; COMPND 5 SYNONYM: TDP-43; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TAR DNA-BINDING PROTEIN 43, Y4R MUTANT; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: NTD DOMAIN; COMPND 12 SYNONYM: TDP-43; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TARDBP, TDP43; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PJ411; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJ411/TDP-43 S48E; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: TARDBP, TDP43; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PJ411; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PJ411/TDP-43 Y4R KEYWDS TDP-43, AMYOTROPHIC LATERAL SCLEROSIS, PROTEIN AGGREGATION, RNA KEYWDS 2 BINDING PROTEIN, PROTEIN SELF-ASSEMBLY, DIMERIZATION, STRUCTURAL KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.T.NAIK,A.WANG,A.CONICELLA,N.L.FAWZI REVDAT 4 01-MAY-24 6B1G 1 REMARK REVDAT 3 01-JAN-20 6B1G 1 REMARK REVDAT 2 14-MAR-18 6B1G 1 JRNL REVDAT 1 28-FEB-18 6B1G 0 JRNL AUTH A.WANG,A.E.CONICELLA,H.B.SCHMIDT,E.W.MARTIN,S.N.RHOADS, JRNL AUTH 2 A.N.REEB,A.NOURSE,D.RAMIREZ MONTERO,V.H.RYAN,R.ROHATGI, JRNL AUTH 3 F.SHEWMAKER,M.T.NAIK,T.MITTAG,Y.M.AYALA,N.L.FAWZI JRNL TITL A SINGLE N-TERMINAL PHOSPHOMIMIC DISRUPTS TDP-43 JRNL TITL 2 POLYMERIZATION, PHASE SEPARATION, AND RNA SPLICING. JRNL REF EMBO J. V. 37 2018 JRNL REFN ESSN 1460-2075 JRNL PMID 29438978 JRNL DOI 10.15252/EMBJ.201797452 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.45 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT REMARK 4 REMARK 4 6B1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230132. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-99% 13C; U-99% 15N] REMARK 210 TDP-43 NTD S48E, 2.0 MM TDP-43 REMARK 210 NTD Y4R, 20 MM HEPES, 1 MM DTT, REMARK 210 90% H2O/10% D2O; 0.7 MM [U-99% REMARK 210 13C; U-99% 15N] TDP-43 NTD Y4R, REMARK 210 2 MM TDP-43 NTD S48E, 20 MM REMARK 210 HEPES, 1 MM DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D HCCH-COSY; 3D REMARK 210 CCH-TOCSY; HBCBCGCDHD; REMARK 210 HBCBCGCDCEHE; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 FILTERED 1H-13C NOESY; 3D REMARK 210 FILTERED 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, SPARKY 3.114, TOPSPIN REMARK 210 3.5, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLY B 98 REMARK 465 HIS B 99 REMARK 465 MET B 100 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: 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 ASP A 13 -165.78 -105.31 REMARK 500 1 PRO A 64 -153.77 -64.88 REMARK 500 1 ASN A 70 -32.60 -153.24 REMARK 500 1 SER B 102 -58.72 -165.22 REMARK 500 1 PRO B 164 -168.95 -71.09 REMARK 500 1 VAL B 172 96.35 -63.45 REMARK 500 1 TYR B 173 -81.58 -155.26 REMARK 500 2 PRO A 64 -166.04 -68.47 REMARK 500 2 ASN A 70 -32.92 -170.76 REMARK 500 2 PRO A 78 -169.07 -71.87 REMARK 500 2 SER B 102 -84.74 -136.09 REMARK 500 2 THR B 108 -177.64 -170.61 REMARK 500 2 PRO B 136 57.43 -67.04 REMARK 500 2 PRO B 164 -175.22 -65.73 REMARK 500 2 VAL B 172 101.22 -58.55 REMARK 500 2 TYR B 173 -75.26 -164.00 REMARK 500 3 PRO A 64 -177.69 -68.80 REMARK 500 3 ASN A 70 -26.96 -155.53 REMARK 500 3 ASP B 113 -161.50 -101.70 REMARK 500 3 PRO B 136 57.53 -67.34 REMARK 500 3 PRO B 164 -171.47 -69.33 REMARK 500 3 VAL B 172 93.18 -59.65 REMARK 500 3 TYR B 173 -82.74 -156.27 REMARK 500 4 PRO A 46 0.97 -66.50 REMARK 500 4 PRO A 64 -176.66 -69.79 REMARK 500 4 ASN A 70 -26.70 -178.50 REMARK 500 4 SER B 102 -73.83 -140.05 REMARK 500 4 PRO B 136 45.93 -71.07 REMARK 500 4 PRO B 164 -172.86 -69.30 REMARK 500 4 VAL B 172 101.47 -58.68 REMARK 500 4 TYR B 173 -80.80 -158.80 REMARK 500 5 ASN A 70 -33.65 -161.88 REMARK 500 5 PRO A 78 -166.48 -74.21 REMARK 500 5 SER B 102 -65.66 -161.84 REMARK 500 5 PRO B 136 49.87 -71.08 REMARK 500 5 PRO B 164 -169.68 -72.17 REMARK 500 5 VAL B 172 97.88 -63.45 REMARK 500 5 TYR B 173 -80.69 -162.87 REMARK 500 6 ASP A 13 -155.88 -135.57 REMARK 500 6 PRO A 64 -167.92 -71.61 REMARK 500 6 ASN A 70 -26.76 -171.82 REMARK 500 6 SER B 102 -78.82 -123.73 REMARK 500 6 PRO B 136 43.75 -71.36 REMARK 500 6 PRO B 164 -163.07 -75.96 REMARK 500 6 VAL B 172 91.32 -63.44 REMARK 500 6 TYR B 173 -79.33 -156.35 REMARK 500 7 PRO A 64 -169.39 -69.41 REMARK 500 7 ASN A 70 -30.34 -178.17 REMARK 500 7 SER B 102 -65.75 -154.54 REMARK 500 7 ASP B 113 -157.98 -90.62 REMARK 500 REMARK 500 THIS ENTRY HAS 149 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30345 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF TDP-43 N-TERMINAL DOMAIN DIMER. DBREF 6B1G A 1 80 UNP Q13148 TADBP_HUMAN 1 80 DBREF 6B1G B 101 180 UNP Q13148 TADBP_HUMAN 1 80 SEQADV 6B1G GLY A -2 UNP Q13148 EXPRESSION TAG SEQADV 6B1G HIS A -1 UNP Q13148 EXPRESSION TAG SEQADV 6B1G MET A 0 UNP Q13148 EXPRESSION TAG SEQADV 6B1G GLU A 48 UNP Q13148 SER 48 ENGINEERED MUTATION SEQADV 6B1G GLY B 98 UNP Q13148 EXPRESSION TAG SEQADV 6B1G HIS B 99 UNP Q13148 EXPRESSION TAG SEQADV 6B1G MET B 100 UNP Q13148 EXPRESSION TAG SEQADV 6B1G ARG B 104 UNP Q13148 TYR 4 ENGINEERED MUTATION SEQRES 1 A 83 GLY HIS MET MET SER GLU TYR ILE ARG VAL THR GLU ASP SEQRES 2 A 83 GLU ASN ASP GLU PRO ILE GLU ILE PRO SER GLU ASP ASP SEQRES 3 A 83 GLY THR VAL LEU LEU SER THR VAL THR ALA GLN PHE PRO SEQRES 4 A 83 GLY ALA CYS GLY LEU ARG TYR ARG ASN PRO VAL GLU GLN SEQRES 5 A 83 CYS MET ARG GLY VAL ARG LEU VAL GLU GLY ILE LEU HIS SEQRES 6 A 83 ALA PRO ASP ALA GLY TRP GLY ASN LEU VAL TYR VAL VAL SEQRES 7 A 83 ASN TYR PRO LYS ASP SEQRES 1 B 83 GLY HIS MET MET SER GLU ARG ILE ARG VAL THR GLU ASP SEQRES 2 B 83 GLU ASN ASP GLU PRO ILE GLU ILE PRO SER GLU ASP ASP SEQRES 3 B 83 GLY THR VAL LEU LEU SER THR VAL THR ALA GLN PHE PRO SEQRES 4 B 83 GLY ALA CYS GLY LEU ARG TYR ARG ASN PRO VAL SER GLN SEQRES 5 B 83 CYS MET ARG GLY VAL ARG LEU VAL GLU GLY ILE LEU HIS SEQRES 6 B 83 ALA PRO ASP ALA GLY TRP GLY ASN LEU VAL TYR VAL VAL SEQRES 7 B 83 ASN TYR PRO LYS ASP HELIX 1 AA1 LEU A 28 PHE A 35 1 8 HELIX 2 AA2 LEU B 128 ALA B 133 1 6 SHEET 1 AA1 8 MET A 51 GLY A 53 0 SHEET 2 AA1 8 LEU A 41 ARG A 44 -1 N TYR A 43 O ARG A 52 SHEET 3 AA1 8 TYR A 73 VAL A 75 -1 O VAL A 74 N ARG A 42 SHEET 4 AA1 8 TYR A 4 THR A 8 1 N ARG A 6 O TYR A 73 SHEET 5 AA1 8 ILE A 16 PRO A 19 -1 O ILE A 16 N VAL A 7 SHEET 6 AA1 8 CYS B 150 GLY B 153 1 O GLY B 153 N GLU A 17 SHEET 7 AA1 8 LEU B 141 ASN B 145 -1 N ASN B 145 O CYS B 150 SHEET 8 AA1 8 VAL B 174 VAL B 175 -1 O VAL B 174 N ARG B 142 SHEET 1 AA2 3 THR A 25 LEU A 27 0 SHEET 2 AA2 3 ILE A 60 HIS A 62 -1 O LEU A 61 N VAL A 26 SHEET 3 AA2 3 ARG A 55 VAL A 57 -1 N ARG A 55 O HIS A 62 SHEET 1 AA3 2 GLU B 103 VAL B 107 0 SHEET 2 AA3 2 ILE B 116 SER B 120 -1 O SER B 120 N GLU B 103 SHEET 1 AA4 3 THR B 125 LEU B 127 0 SHEET 2 AA4 3 ILE B 160 HIS B 162 -1 O LEU B 161 N VAL B 126 SHEET 3 AA4 3 ARG B 155 VAL B 157 -1 N ARG B 155 O HIS B 162 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