HEADER RNA BINDING PROTEIN 12-JUL-21 7FBR TITLE SOLUTION STRUCTURE OF THE FIRST RNA BINDING DOMAIN OF MATRIN-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIN-3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MATR3; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE GATEWAY CLONING VECTOR N-TERM 8XHIS SOURCE 7 EGFP PCELLFREE_G03; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1508207 KEYWDS RRM, ALS/FTD, NUCLEAR MATRIX PROTEIN, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.MUTO,N.KOBAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 15-MAY-24 7FBR 1 REMARK REVDAT 3 14-JUN-23 7FBR 1 REMARK REVDAT 2 18-MAY-22 7FBR 1 JRNL REVDAT 1 16-FEB-22 7FBR 0 JRNL AUTH F.HE,K.KUWASAKO,M.TAKIZAWA,M.TAKAHASHI,K.TSUDA,T.NAGATA, JRNL AUTH 2 S.WATANABE,A.TANAKA,N.KOBAYASHI,T.KIGAWA,P.GUNTERT, JRNL AUTH 3 M.SHIROUZU,S.YOKOYAMA,Y.MUTO JRNL TITL 1 H, 13 C AND 15 N RESONANCE ASSIGNMENTS AND SOLUTION JRNL TITL 2 STRUCTURES OF THE TWO RRM DOMAINS OF MATRIN-3. JRNL REF BIOMOL.NMR ASSIGN. V. 16 41 2022 JRNL REFN ESSN 1874-270X JRNL PMID 34783967 JRNL DOI 10.1007/S12104-021-10057-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 2063 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINS, 41 MAIN CHAIN DIHEDRAL ANGLE REMARK 3 CONSTRAINTS BASED ON TALOS PROGRAM AND 7 SIDE CHAIN DIHEDRAL REMARK 3 CONSTRAINTS BASED ON NOE PATTERN. REMARK 4 REMARK 4 7FBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023039. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 RNA BINDING PROTEIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C,15N-SEPARATED_NOESY REMARK 210 SPECTRA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, KUJIRA 0.863, NMRVIEW REMARK 210 5.0.4, TOPSPIN 2.1, TALOS 2007, REMARK 210 NMRPIPE 2007 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 FAVORABLE NON REMARK 210 -BOND 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 407 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 476 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 476 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 11 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 467 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 13 ARG A 476 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 476 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 16 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 476 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 19 ARG A 393 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 19 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 407 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. 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 SER A 384 168.13 61.87 REMARK 500 1 SER A 387 -115.53 52.51 REMARK 500 1 SER A 388 18.37 59.64 REMARK 500 1 ARG A 397 163.32 61.53 REMARK 500 1 ARG A 398 20.47 -141.01 REMARK 500 1 LYS A 475 -140.66 -125.21 REMARK 500 1 SER A 482 -116.93 53.16 REMARK 500 2 ARG A 397 148.52 65.05 REMARK 500 2 LYS A 475 -150.04 -120.80 REMARK 500 3 ARG A 397 173.32 58.96 REMARK 500 3 SER A 483 40.09 -79.52 REMARK 500 4 LYS A 391 -8.27 62.41 REMARK 500 4 ARG A 397 157.42 63.81 REMARK 500 4 ARG A 398 29.26 -140.40 REMARK 500 4 TYR A 474 97.83 -69.74 REMARK 500 5 SER A 384 169.54 61.96 REMARK 500 5 ARG A 397 172.79 60.67 REMARK 500 6 ARG A 397 145.00 65.27 REMARK 500 6 LYS A 475 -116.50 46.57 REMARK 500 6 SER A 482 -174.33 58.75 REMARK 500 7 GLN A 390 -16.93 62.00 REMARK 500 7 ARG A 397 173.57 58.27 REMARK 500 8 ARG A 476 143.63 67.09 REMARK 500 9 SER A 387 -52.21 64.68 REMARK 500 9 GLU A 395 47.30 -97.26 REMARK 500 9 ARG A 397 162.25 60.15 REMARK 500 9 TYR A 474 42.53 -78.73 REMARK 500 9 LYS A 478 161.12 61.75 REMARK 500 10 VAL A 394 31.76 -76.62 REMARK 500 10 GLU A 395 4.54 58.93 REMARK 500 10 ARG A 397 140.71 60.80 REMARK 500 10 LYS A 478 178.23 58.10 REMARK 500 11 SER A 385 -49.89 63.46 REMARK 500 11 SER A 387 36.63 -77.84 REMARK 500 11 LYS A 475 -131.38 -107.05 REMARK 500 11 SER A 482 -162.40 57.00 REMARK 500 12 ARG A 397 149.21 65.85 REMARK 500 12 GLN A 472 17.17 54.83 REMARK 500 12 SER A 479 17.92 59.47 REMARK 500 13 LYS A 391 -41.98 -155.33 REMARK 500 13 ARG A 397 156.23 67.22 REMARK 500 13 ARG A 398 27.63 -142.63 REMARK 500 14 SER A 384 -174.90 59.56 REMARK 500 14 ARG A 397 153.47 63.24 REMARK 500 14 ARG A 398 24.76 -145.08 REMARK 500 15 SER A 384 152.30 63.69 REMARK 500 15 SER A 387 18.86 55.15 REMARK 500 15 ARG A 397 158.92 64.66 REMARK 500 15 LYS A 475 -150.93 -130.76 REMARK 500 16 ARG A 397 152.20 63.93 REMARK 500 REMARK 500 THIS ENTRY HAS 62 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 5 ARG A 397 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36430 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE FIRST RNA BINDING DOMAIN OF MATRIN-3 REMARK 900 RELATED ID: 040809-03 RELATED DB: TARGETTRACK DBREF 7FBR A 390 478 UNP Q8K310 MATR3_MOUSE 390 478 SEQADV 7FBR GLY A 383 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 384 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 385 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR GLY A 386 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 387 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 388 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR GLY A 389 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR ARG A 397 UNP Q8K310 SER 397 ENGINEERED MUTATION SEQADV 7FBR SER A 479 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR GLY A 480 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR PRO A 481 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 482 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR SER A 483 UNP Q8K310 EXPRESSION TAG SEQADV 7FBR GLY A 484 UNP Q8K310 EXPRESSION TAG SEQRES 1 A 102 GLY SER SER GLY SER SER GLY GLN LYS GLY ARG VAL GLU SEQRES 2 A 102 THR ARG ARG VAL VAL HIS ILE MET ASP PHE GLN ARG GLY SEQRES 3 A 102 LYS ASN LEU ARG TYR GLN LEU LEU GLN LEU VAL GLU PRO SEQRES 4 A 102 PHE GLY VAL ILE SER ASN HIS LEU ILE LEU ASN LYS ILE SEQRES 5 A 102 ASN GLU ALA PHE ILE GLU MET ALA THR THR GLU ASP ALA SEQRES 6 A 102 GLN ALA ALA VAL ASP TYR TYR THR THR THR PRO ALA LEU SEQRES 7 A 102 VAL PHE GLY LYS PRO VAL ARG VAL HIS LEU SER GLN LYS SEQRES 8 A 102 TYR LYS ARG ILE LYS SER GLY PRO SER SER GLY HELIX 1 AA1 ASN A 410 GLN A 417 1 8 HELIX 2 AA2 LEU A 418 GLY A 423 5 6 HELIX 3 AA3 THR A 443 THR A 455 1 13 SHEET 1 AA1 5 ILE A 425 ILE A 430 0 SHEET 2 AA1 5 GLU A 436 MET A 441 -1 O PHE A 438 N LEU A 429 SHEET 3 AA1 5 VAL A 399 MET A 403 -1 N VAL A 400 O ILE A 439 SHEET 4 AA1 5 LYS A 464 LEU A 470 -1 O HIS A 469 N HIS A 401 SHEET 5 AA1 5 ALA A 459 VAL A 461 -1 N VAL A 461 O LYS A 464 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