HEADER RNA BINDING PROTEIN 23-FEB-15 2MZT TITLE NMR STRUCTURE OF THE RRM3 DOMAIN OF HRB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN HRB1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD RRM DOMAIN (UNP RESIDUES 357-454); COMPND 5 SYNONYM: PROTEIN TOM34; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: HRB1, N2009, TOM34, YNL004W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS RRM, RNA BINDING DOMAIN, HRB1, THO/TREX, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.MARTINEZ-LUMBRERAS,B.SERAPHIN,J.PEREZ-CANADILLAS REVDAT 4 14-JUN-23 2MZT 1 REMARK SEQADV REVDAT 3 27-JAN-16 2MZT 1 JRNL REVDAT 2 09-DEC-15 2MZT 1 JRNL REVDAT 1 02-DEC-15 2MZT 0 JRNL AUTH S.MARTINEZ-LUMBRERAS,V.TAVERNITI,S.ZORRILLA,B.SERAPHIN, JRNL AUTH 2 J.M.PEREZ-CANADILLAS JRNL TITL GBP2 INTERACTS WITH THO/TREX THROUGH A NOVEL TYPE OF RRM JRNL TITL 2 DOMAIN. JRNL REF NUCLEIC ACIDS RES. V. 44 437 2016 JRNL REFN ISSN 0305-1048 JRNL PMID 26602689 JRNL DOI 10.1093/NAR/GKV1303 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 2MZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000104242. 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 : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM PROTEIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 0.1 MM DTT, 90% H2O/10% D2O; REMARK 210 0.8 MM PROTEIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 0.1 MM DTT, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY 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, TOPSPIN, CCPNMR ANALYSIS, REMARK 210 NMRPIPE REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 7 TYR A 450 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 TYR A 450 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 12 ARG A 435 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 18 ARG A 362 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 LYS A 401 115.15 -179.75 REMARK 500 1 ASP A 410 -94.50 -89.85 REMARK 500 1 LYS A 412 -70.68 -146.08 REMARK 500 1 ASN A 438 0.49 -175.83 REMARK 500 2 SER A 356 157.01 73.37 REMARK 500 2 LYS A 401 128.06 171.38 REMARK 500 2 ASP A 410 -89.51 -88.07 REMARK 500 2 LYS A 412 -67.17 -151.83 REMARK 500 2 ASN A 437 35.03 -78.04 REMARK 500 2 ASN A 438 -30.51 175.18 REMARK 500 3 ASN A 367 -22.53 66.33 REMARK 500 3 LYS A 401 118.28 179.86 REMARK 500 3 ASP A 410 -93.84 -89.97 REMARK 500 3 LYS A 412 -71.76 -147.74 REMARK 500 3 ASN A 437 4.77 -69.17 REMARK 500 3 ASN A 438 0.71 -151.65 REMARK 500 4 ASP A 410 -99.84 -91.68 REMARK 500 4 LYS A 412 -76.29 -139.25 REMARK 500 4 ASN A 437 38.69 -80.02 REMARK 500 4 ASN A 438 -31.47 174.28 REMARK 500 5 ASN A 367 -19.64 67.85 REMARK 500 5 ASP A 410 -90.82 -86.14 REMARK 500 5 LYS A 412 -64.47 -136.83 REMARK 500 5 ASN A 438 0.96 -151.61 REMARK 500 6 SER A 356 159.00 75.47 REMARK 500 6 ASP A 410 -98.09 -89.35 REMARK 500 6 LYS A 412 -77.13 -147.89 REMARK 500 6 ASN A 437 35.60 -79.94 REMARK 500 6 ASN A 438 -28.40 175.20 REMARK 500 6 ASP A 445 99.88 -68.95 REMARK 500 7 ASP A 410 -49.65 -145.76 REMARK 500 7 LYS A 412 -62.68 165.43 REMARK 500 7 ASN A 437 25.95 -74.71 REMARK 500 7 ASN A 438 0.32 177.86 REMARK 500 8 ARG A 376 13.46 -62.55 REMARK 500 8 LYS A 401 146.28 -172.20 REMARK 500 8 ASP A 410 -87.00 -85.26 REMARK 500 8 LYS A 412 -67.24 -142.08 REMARK 500 8 ASN A 437 24.51 -74.47 REMARK 500 8 ASN A 438 0.54 -177.14 REMARK 500 9 VAL A 357 142.56 72.13 REMARK 500 9 ASP A 410 -95.16 -84.14 REMARK 500 9 LYS A 412 -66.34 -151.95 REMARK 500 9 ARG A 435 -54.55 -122.56 REMARK 500 9 ASN A 437 29.67 -74.73 REMARK 500 9 ASN A 438 0.18 176.41 REMARK 500 10 ASN A 358 -45.94 -170.40 REMARK 500 10 GLU A 359 -45.78 71.89 REMARK 500 10 ASN A 367 -8.35 63.64 REMARK 500 10 LYS A 401 133.87 -177.78 REMARK 500 REMARK 500 THIS ENTRY HAS 112 RAMACHANDRAN OUTLIERS. 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 ASN A 437 ASN A 438 1 -140.12 REMARK 500 ASN A 437 ASN A 438 9 -147.91 REMARK 500 ASN A 437 ASN A 438 11 -144.28 REMARK 500 ASN A 437 ASN A 438 12 -144.89 REMARK 500 ASN A 437 ASN A 438 13 -145.14 REMARK 500 ASN A 437 ASN A 438 17 -145.94 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 9 TYR A 379 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25499 RELATED DB: BMRB REMARK 900 RELATED ID: 2MZQ RELATED DB: PDB REMARK 900 RELATED ID: 2MZR RELATED DB: PDB REMARK 900 RELATED ID: 2MZS RELATED DB: PDB DBREF 2MZT A 357 454 UNP P38922 HRB1_YEAST 357 454 SEQADV 2MZT GLY A 355 UNP P38922 EXPRESSION TAG SEQADV 2MZT SER A 356 UNP P38922 EXPRESSION TAG SEQRES 1 A 100 GLY SER VAL ASN GLU GLU ALA ARG LYS PHE THR GLU ASN SEQRES 2 A 100 VAL VAL GLY GLY GLY GLU ARG ASN ARG LEU ILE TYR CYS SEQRES 3 A 100 SER ASN LEU PRO PHE SER THR ALA LYS SER ASP LEU TYR SEQRES 4 A 100 ASP LEU PHE GLU THR ILE GLY LYS VAL ASN ASN ALA GLU SEQRES 5 A 100 LEU ARG TYR ASP SER LYS GLY ALA PRO THR GLY ILE ALA SEQRES 6 A 100 VAL VAL GLU TYR ASP ASN VAL ASP ASP ALA ASP VAL CYS SEQRES 7 A 100 ILE GLU ARG LEU ASN ASN TYR ASN TYR GLY GLY CYS ASP SEQRES 8 A 100 LEU ASP ILE SER TYR ALA LYS ARG LEU HELIX 1 1 ASN A 358 PHE A 364 1 7 HELIX 2 2 ALA A 388 GLU A 397 1 10 HELIX 3 3 ASN A 425 LEU A 436 1 12 SHEET 1 A 5 VAL A 368 GLY A 370 0 SHEET 2 A 5 ASP A 447 ARG A 453 -1 O LYS A 452 N VAL A 369 SHEET 3 A 5 LEU A 377 SER A 381 -1 N SER A 381 O ASP A 447 SHEET 4 A 5 PRO A 415 TYR A 423 -1 O VAL A 421 N ILE A 378 SHEET 5 A 5 VAL A 402 TYR A 409 -1 N ASN A 404 O GLU A 422 SHEET 1 B 2 ASN A 440 TYR A 441 0 SHEET 2 B 2 CYS A 444 ASP A 445 -1 O CYS A 444 N TYR A 441 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