HEADER RNA BINDING PROTEIN 13-JUL-21 7FBV TITLE THE SOLUTION STRUCTURE OF THE SECOND RRM DOMAIN OF MATRIN-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIN-3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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 7FBV 1 REMARK REVDAT 3 14-JUN-23 7FBV 1 REMARK REVDAT 2 18-MAY-22 7FBV 1 JRNL REVDAT 1 16-FEB-22 7FBV 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: NULL REMARK 4 REMARK 4 7FBV 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_1300022821. 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 MM [U-99% 13C; U-99% 15N] RNA REMARK 210 BINDING PROTEIN, 90% H2O/10% 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 2.0.17, KUJIRA 0.863, REMARK 210 NMRVIEW 5.0.4, TOPSPIN 2.1, REMARK 210 TALOS 2007, NMRPIPE 2007 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 562 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 530 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 13 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 13 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 ARG A 562 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 17 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 18 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 19 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 562 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 3.9 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 ASP A 485 13.86 -144.39 REMARK 500 1 LYS A 532 13.50 57.17 REMARK 500 1 SER A 533 70.29 52.90 REMARK 500 2 ASP A 485 -5.23 -142.62 REMARK 500 2 GLU A 493 44.64 -80.14 REMARK 500 2 HIS A 505 53.76 -143.48 REMARK 500 2 LYS A 532 18.03 54.25 REMARK 500 2 SER A 533 75.80 50.73 REMARK 500 3 GLU A 481 -49.05 -147.45 REMARK 500 3 LYS A 532 9.23 57.50 REMARK 500 4 ASP A 485 33.98 -77.48 REMARK 500 4 LYS A 532 14.76 55.97 REMARK 500 4 SER A 533 76.76 52.12 REMARK 500 4 LYS A 573 -39.09 61.06 REMARK 500 4 SER A 577 -25.97 63.62 REMARK 500 4 SER A 580 -5.52 60.62 REMARK 500 4 SER A 581 -173.87 57.60 REMARK 500 5 SER A 476 47.46 -75.51 REMARK 500 5 LYS A 478 163.45 62.55 REMARK 500 5 LYS A 487 -104.36 51.04 REMARK 500 5 ASP A 489 37.87 -83.72 REMARK 500 5 LYS A 491 -17.43 59.63 REMARK 500 5 PRO A 504 -175.72 -64.81 REMARK 500 5 HIS A 505 29.86 -140.77 REMARK 500 5 LYS A 573 -30.59 63.32 REMARK 500 5 SER A 580 -1.00 -145.34 REMARK 500 6 GLN A 492 -40.44 -161.28 REMARK 500 6 LYS A 532 19.67 54.00 REMARK 500 6 SER A 533 76.45 51.65 REMARK 500 6 LYS A 573 -51.78 61.19 REMARK 500 7 LYS A 532 15.82 59.65 REMARK 500 8 ASP A 489 49.73 -72.83 REMARK 500 8 PRO A 504 -175.10 -66.48 REMARK 500 8 HIS A 505 23.87 -140.10 REMARK 500 8 SER A 506 23.20 -77.58 REMARK 500 8 LYS A 532 12.84 57.63 REMARK 500 9 SER A 476 18.59 58.74 REMARK 500 9 GLN A 490 31.04 -74.45 REMARK 500 9 LYS A 491 -65.41 60.44 REMARK 500 9 LYS A 532 7.51 57.14 REMARK 500 10 LYS A 483 163.01 63.55 REMARK 500 10 GLN A 492 171.15 60.89 REMARK 500 10 ARG A 496 34.17 -143.36 REMARK 500 10 PRO A 504 -175.28 -64.00 REMARK 500 10 LYS A 532 16.82 54.09 REMARK 500 10 SER A 533 76.79 48.54 REMARK 500 10 SER A 581 167.37 62.30 REMARK 500 11 SER A 476 179.90 60.63 REMARK 500 11 ASP A 485 16.22 59.81 REMARK 500 11 ARG A 496 46.98 -81.55 REMARK 500 REMARK 500 THIS ENTRY HAS 101 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 3 ARG A 496 0.08 SIDE CHAIN REMARK 500 9 TYR A 508 0.07 SIDE CHAIN REMARK 500 18 ARG A 496 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36431 RELATED DB: BMRB REMARK 900 THE SOLUTION STRUCTURE OF THE SECOND RRM DOMAIN OF MATRIN-3 REMARK 900 RELATED ID: P041220-05 RELATED DB: TARGETTRACK DBREF 7FBV A 478 576 UNP Q8K310 MATR3_MOUSE 478 576 SEQADV 7FBV GLY A 471 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 472 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 473 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV GLY A 474 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 475 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 476 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV GLY A 477 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 577 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV GLY A 578 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV PRO A 579 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 580 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV SER A 581 UNP Q8K310 EXPRESSION TAG SEQADV 7FBV GLY A 582 UNP Q8K310 EXPRESSION TAG SEQRES 1 A 112 GLY SER SER GLY SER SER GLY LYS LYS PRO GLU GLY LYS SEQRES 2 A 112 PRO ASP GLN LYS PHE ASP GLN LYS GLN GLU LEU GLY ARG SEQRES 3 A 112 VAL ILE HIS LEU SER ASN LEU PRO HIS SER GLY TYR SER SEQRES 4 A 112 ASP SER ALA VAL LEU LYS LEU ALA GLU PRO TYR GLY LYS SEQRES 5 A 112 ILE LYS ASN TYR ILE LEU MET ARG MET LYS SER GLN ALA SEQRES 6 A 112 PHE ILE GLU MET GLU THR ARG GLU ASP ALA MET ALA MET SEQRES 7 A 112 VAL ASP HIS CYS LEU LYS LYS ALA LEU TRP PHE GLN GLY SEQRES 8 A 112 ARG CYS VAL LYS VAL ASP LEU SER GLU LYS TYR LYS LYS SEQRES 9 A 112 LEU VAL SER GLY PRO SER SER GLY HELIX 1 AA1 SER A 509 LYS A 515 1 7 HELIX 2 AA2 THR A 541 LYS A 555 1 15 SHEET 1 AA1 4 ILE A 523 MET A 529 0 SHEET 2 AA1 4 GLN A 534 MET A 539 -1 O GLU A 538 N LYS A 524 SHEET 3 AA1 4 VAL A 497 SER A 501 -1 N ILE A 498 O ILE A 537 SHEET 4 AA1 4 LYS A 565 LEU A 568 -1 O ASP A 567 N HIS A 499 SHEET 1 AA2 2 TRP A 558 PHE A 559 0 SHEET 2 AA2 2 ARG A 562 CYS A 563 -1 O ARG A 562 N PHE A 559 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