HEADER SPLICING 04-FEB-14 2MKC TITLE COOPERATIVE STRUCTURE OF THE HETEROTRIMERIC PRE-MRNA RETENTION AND TITLE 2 SPLICING COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: U2 SNRNP COMPONENT IST3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-138; COMPND 5 SYNONYM: INCREASED SODIUM TOLERANCE PROTEIN 3, U2 SNRNP PROTEIN COMPND 6 SNU17; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PRE-MRNA LEAKAGE PROTEIN 1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 22-42; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PRE-MRNA-SPLICING FACTOR CWC26; COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: UNP RESIDUES 215-245; COMPND 17 SYNONYM: BUD SITE SELECTION PROTEIN 13, COMPLEXED WITH CEF1 PROTEIN COMPND 18 26, SYNTHETIC LETHAL WITH CLF1 PROTEIN 7; COMPND 19 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: IST3, SNU17, YIB5W, YIR005W; 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: PETM-11; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: ATCC 204508 / S288C; SOURCE 17 GENE: PML1, YLR016C, L1591; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 MOL_ID: 3; SOURCE 21 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 22 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 23 ORGANISM_TAXID: 559292; SOURCE 24 STRAIN: ATCC 204508 / S288C; SOURCE 25 GENE: BUD13, CWC26, SLC7, YGL174W, G1642; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SPLICEOSOME, SNU17P, BUD13P, PML1P, HETEROTRIMER, COOPERATIVITY, RES, KEYWDS 2 SPLICING, RRM, PROTEIN BINDING, IST3P EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.WYSOCZANSKI,C.SCHNEIDER,S.XIANG,F.MUNARI,S.TROWITZSCH,M.C.WAHL, AUTHOR 2 R.LUHRMANN,S.BECKER,M.ZWECKSTETTER REVDAT 5 15-MAY-24 2MKC 1 REMARK REVDAT 4 14-JUN-23 2MKC 1 REMARK SEQADV REVDAT 3 22-OCT-14 2MKC 1 JRNL REVDAT 2 01-OCT-14 2MKC 1 JRNL REVDAT 1 03-SEP-14 2MKC 0 JRNL AUTH P.WYSOCZANSKI,C.SCHNEIDER,S.XIANG,F.MUNARI,S.TROWITZSCH, JRNL AUTH 2 M.C.WAHL,R.LUHRMANN,S.BECKER,M.ZWECKSTETTER JRNL TITL COOPERATIVE STRUCTURE OF THE HETEROTRIMERIC PRE-MRNA JRNL TITL 2 RETENTION AND SPLICING COMPLEX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 911 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 25218446 JRNL DOI 10.1038/NSMB.2889 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, CNS 1.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT (RECOORD) REMARK 4 REMARK 4 2MKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000103717. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 25 MM SODIUM PHOSPHATE, 250 MM REMARK 210 NACL, 1 MM SODIUM AZIDE, 0.9-1.3 REMARK 210 MM [U-13C; U-15N] SNU17P, 1.1- REMARK 210 1.5 MM BUD13P, 1.4-1.9 MM PML1P, REMARK 210 90% H2O/10% D2O; 25 MM SODIUM REMARK 210 PHOSPHATE, 250 MM NACL, 1 MM REMARK 210 SODIUM AZIDE, 1.0-1.3 MM SNU17P, REMARK 210 1.2-1.5 MM BUD13P, 0.8-1.0 MM [U- REMARK 210 13C; U-15N] PML1P, 90% H2O/10% REMARK 210 D2O; 25 MM SODIUM PHOSPHATE, 250 REMARK 210 MM NACL, 1 MM SODIUM AZIDE, 1.0- REMARK 210 1.3 MM SNU17P, 0.8-1.0 MM [U-10% REMARK 210 13C; U-99% 15N] BUD13P, 1.5-1.9 REMARK 210 MM PML1P, 90% H2O/10% D2O; 25 MM REMARK 210 SODIUM PHOSPHATE, 250 MM NACL, 1 REMARK 210 MM SODIUM AZIDE, 0.9-1.3 MM [U- REMARK 210 13C; U-15N; U-2H] SNU17P, 1.1- REMARK 210 1.5 MM BUD13P, 1.4-1.9 MM PML1P, REMARK 210 90% H2O/10% D2O; 25 MM SODIUM REMARK 210 PHOSPHATE, 250 MM NACL, 1 MM REMARK 210 SODIUM AZIDE, 1.0-1.3 MM [U-13C; REMARK 210 U-15N; U-2H] SNU17P, 0.8-1.0 MM REMARK 210 [U-10% 13C; U-99% 15N] BUD13P, REMARK 210 1.5-1.9 MM PML1P, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 3D HN(CO)CA; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 NOESY FILTERED/EDITED; REMARK 210 HBCBCGCDHD; 3D CCH-TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY ARG- REMARK 210 CENTERED REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.1, NMRPIPE, REMARK 210 ANALYSIS_CCPN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 AUTHORS STATE THAT THE ISOTOPICALLY LABELLED BIOSYNTHETIC PEPTIDES REMARK 400 HAVE GS CLONING ARTIFACT AT THE N-TERMINI, WHICH WERE USED REMARK 400 PRIMARILY TO DERIVE THE DATA THAT LEAD TO THE RELEVANT PARTS OF THE REMARK 400 STRUCTURE. HOWEVER, THE NATURAL ISOTOPIC ABUNDANCE SYNTHETIC REMARK 400 PEPTIDES WERE ALSO USED FOR SOME NMR EXPERIMENTS. THEY DO NOT HAVE REMARK 400 GS CLONING ARTIFACT. INSTEAD, THEY HAVE ACETYL GROUP AT THE N- REMARK 400 TERMINUS AND AMIDE AT THE C-TERMINUS. 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 ASN A 5 10.93 -66.52 REMARK 500 1 ILE B 208 -79.08 -72.54 REMARK 500 1 MET B 209 146.58 64.83 REMARK 500 1 PHE B 212 87.11 66.55 REMARK 500 1 PRO C 307 64.88 -69.90 REMARK 500 1 SER C 317 10.40 -65.71 REMARK 500 2 GLU A 6 -70.18 -81.13 REMARK 500 2 TYR A 7 -141.78 -168.03 REMARK 500 2 ASP A 9 20.07 -69.39 REMARK 500 2 ASN A 17 70.03 66.74 REMARK 500 2 GLU A 117 -71.78 -149.58 REMARK 500 2 GLN B 204 111.08 67.61 REMARK 500 2 ILE B 208 -72.82 -85.94 REMARK 500 2 MET B 209 159.19 72.27 REMARK 500 2 ASP B 211 -70.56 -105.22 REMARK 500 2 PHE B 212 90.55 64.08 REMARK 500 2 ARG C 310 -77.42 65.17 REMARK 500 2 GLU C 329 3.61 -69.14 REMARK 500 3 ASN A 10 109.36 -57.75 REMARK 500 3 ALA A 116 -85.15 -148.29 REMARK 500 3 GLN B 204 142.74 73.01 REMARK 500 3 ILE B 208 -75.90 -64.51 REMARK 500 3 MET B 209 149.99 64.23 REMARK 500 3 PHE B 212 80.20 61.36 REMARK 500 3 SER C 325 88.66 -157.21 REMARK 500 3 ASN C 326 143.84 172.39 REMARK 500 4 ASP A 9 3.62 -65.10 REMARK 500 4 VAL A 38 -61.95 -109.63 REMARK 500 4 ASN A 71 -60.19 -95.77 REMARK 500 4 LYS A 113 75.20 167.46 REMARK 500 4 GLU A 117 -79.41 -66.55 REMARK 500 4 SER B 201 -51.13 69.81 REMARK 500 4 GLN B 204 90.77 64.47 REMARK 500 4 ILE B 208 -76.53 -104.82 REMARK 500 4 MET B 209 159.22 65.83 REMARK 500 4 ASP B 211 -52.88 -120.55 REMARK 500 4 SER C 301 -33.57 -150.24 REMARK 500 4 ASN C 309 148.15 -179.66 REMARK 500 4 GLU C 329 1.25 -61.25 REMARK 500 5 ALA A 2 -66.51 67.48 REMARK 500 5 GLU A 6 -71.79 -59.36 REMARK 500 5 ASN A 115 -25.68 -163.53 REMARK 500 5 ILE B 208 -78.62 -82.26 REMARK 500 5 MET B 209 148.82 66.87 REMARK 500 5 SER C 317 -71.63 -67.57 REMARK 500 5 ARG C 318 48.07 -89.81 REMARK 500 5 VAL C 322 106.10 -56.21 REMARK 500 6 ASN A 71 -60.60 -100.14 REMARK 500 6 ASN A 115 -39.83 72.68 REMARK 500 6 ILE B 208 -80.46 -91.76 REMARK 500 REMARK 500 THIS ENTRY HAS 182 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 1 ARG C 324 0.10 SIDE CHAIN REMARK 500 3 ARG A 80 0.10 SIDE CHAIN REMARK 500 4 ARG C 324 0.14 SIDE CHAIN REMARK 500 7 ARG C 318 0.16 SIDE CHAIN REMARK 500 9 ARG A 44 0.10 SIDE CHAIN REMARK 500 10 ARG C 310 0.10 SIDE CHAIN REMARK 500 10 ARG C 324 0.08 SIDE CHAIN REMARK 500 12 ARG A 80 0.10 SIDE CHAIN REMARK 500 12 ARG C 310 0.08 SIDE CHAIN REMARK 500 12 ARG C 324 0.07 SIDE CHAIN REMARK 500 15 ARG A 108 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19766 RELATED DB: BMRB DBREF 2MKC A 5 118 UNP P40565 IST3_YEAST 25 138 DBREF 2MKC B 202 222 UNP Q07930 PML1_YEAST 22 42 DBREF 2MKC C 302 332 UNP P46947 CWC26_YEAST 215 245 SEQADV 2MKC GLY A 1 UNP P40565 EXPRESSION TAG SEQADV 2MKC ALA A 2 UNP P40565 EXPRESSION TAG SEQADV 2MKC MET A 3 UNP P40565 EXPRESSION TAG SEQADV 2MKC GLY A 4 UNP P40565 EXPRESSION TAG SEQADV 2MKC GLY B 200 UNP Q07930 EXPRESSION TAG SEQADV 2MKC SER B 201 UNP Q07930 EXPRESSION TAG SEQADV 2MKC GLY C 300 UNP P46947 EXPRESSION TAG SEQADV 2MKC SER C 301 UNP P46947 EXPRESSION TAG SEQRES 1 A 118 GLY ALA MET GLY ASN GLU TYR LYS ASP ASN ALA TYR ILE SEQRES 2 A 118 TYR ILE GLY ASN LEU ASN ARG GLU LEU THR GLU GLY ASP SEQRES 3 A 118 ILE LEU THR VAL PHE SER GLU TYR GLY VAL PRO VAL ASP SEQRES 4 A 118 VAL ILE LEU SER ARG ASP GLU ASN THR GLY GLU SER GLN SEQRES 5 A 118 GLY PHE ALA TYR LEU LYS TYR GLU ASP GLN ARG SER THR SEQRES 6 A 118 ILE LEU ALA VAL ASP ASN LEU ASN GLY PHE LYS ILE GLY SEQRES 7 A 118 GLY ARG ALA LEU LYS ILE ASP HIS THR PHE TYR ARG PRO SEQRES 8 A 118 LYS ARG SER LEU GLN LYS TYR TYR GLU ALA VAL LYS GLU SEQRES 9 A 118 GLU LEU ASP ARG ASP ILE VAL SER LYS ASN ASN ALA GLU SEQRES 10 A 118 LYS SEQRES 1 B 23 GLY SER LYS SER GLN TYR ILE ASP ILE MET PRO ASP PHE SEQRES 2 B 23 SER PRO SER GLY LEU LEU GLU LEU GLU SER SEQRES 1 C 33 GLY SER TYR ASP LYS PRO ALA PRO GLU ASN ARG PHE ALA SEQRES 2 C 33 ILE MET PRO GLY SER ARG TRP ASP GLY VAL HIS ARG SER SEQRES 3 C 33 ASN GLY PHE GLU GLU LYS TRP HELIX 1 1 THR A 23 SER A 32 1 10 HELIX 2 2 GLU A 33 GLY A 35 5 3 HELIX 3 3 ASP A 61 LEU A 72 1 12 HELIX 4 4 LEU A 95 VAL A 111 1 17 HELIX 5 5 LEU B 217 SER B 222 1 6 SHEET 1 A 4 PRO A 37 ARG A 44 0 SHEET 2 A 4 SER A 51 TYR A 59 -1 O GLN A 52 N SER A 43 SHEET 3 A 4 TYR A 12 GLY A 16 -1 N ILE A 15 O ALA A 55 SHEET 4 A 4 LYS A 83 ASP A 85 -1 O ASP A 85 N TYR A 14 SHEET 1 B 2 LYS A 76 ILE A 77 0 SHEET 2 B 2 ARG A 80 ALA A 81 -1 O ARG A 80 N ILE A 77 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