HEADER RNA BINDING PROTEIN 10-NOV-11 2LLI TITLE LOW RESOLUTION STRUCTURE OF RNA-BINDING SUBUNIT OF THE TRAMP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AIR2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 57-180; COMPND 5 SYNONYM: ARGININE METHYLTRANSFERASE-INTERACTING RING FINGER PROTEIN COMPND 6 2; COMPND 7 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: AIR2, YDL175C; SOURCE 7 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PNOPPATA1L KEYWDS RNA SURVEILLANCE, RNA DEGRADATION, RNA BINDING, EXOSOME, RNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.HOLUB,J.LALAKOVA,H.CERNA,M.SARAZOVA,J.PASULKA,K.HRAZDILOVA, AUTHOR 2 M.S.ARCE,R.STEFL,S.VANACOVA REVDAT 3 14-JUN-23 2LLI 1 REMARK LINK REVDAT 2 11-JUL-12 2LLI 1 JRNL REVDAT 1 21-MAR-12 2LLI 0 JRNL AUTH P.HOLUB,J.LALAKOVA,H.CERNA,J.PASULKA,M.SARAZOVA, JRNL AUTH 2 K.HRAZDILOVA,M.S.ARCE,F.HOBOR,R.STEFL,S.VANACOVA JRNL TITL AIR2P IS CRITICAL FOR THE ASSEMBLY AND RNA-BINDING OF THE JRNL TITL 2 TRAMP COMPLEX AND THE KOW DOMAIN OF MTR4P IS CRUCIAL FOR JRNL TITL 3 EXOSOME ACTIVATION. JRNL REF NUCLEIC ACIDS RES. V. 40 5679 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22402490 JRNL DOI 10.1093/NAR/GKS223 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CYANA 2.1, AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000102528. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 0.5 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 UM UM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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: 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 3 CYS A 80 CB - CA - C ANGL. DEV. = 9.2 DEGREES REMARK 500 5 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 CYS A 39 CB - CA - C ANGL. DEV. = 11.3 DEGREES REMARK 500 12 CYS A 39 CB - CA - C ANGL. DEV. = 8.2 DEGREES REMARK 500 12 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 TYR A 27 CB - CG - CD2 ANGL. DEV. = -3.8 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 6 -42.13 49.73 REMARK 500 1 ASN A 9 -35.67 -161.64 REMARK 500 1 SER A 11 11.87 58.49 REMARK 500 1 LEU A 16 179.21 -57.38 REMARK 500 1 TYR A 27 11.79 -142.26 REMARK 500 1 ASP A 33 -34.87 -139.23 REMARK 500 1 ALA A 42 -152.64 -86.81 REMARK 500 1 SER A 46 -155.77 -159.37 REMARK 500 1 GLU A 50 148.48 60.26 REMARK 500 1 TYR A 54 137.64 59.90 REMARK 500 1 CYS A 58 75.93 49.80 REMARK 500 1 LYS A 64 170.10 61.94 REMARK 500 1 LYS A 71 -55.48 58.62 REMARK 500 1 LYS A 73 -51.88 56.54 REMARK 500 1 HIS A 75 177.68 54.84 REMARK 500 1 SER A 82 35.38 -72.22 REMARK 500 1 ILE A 106 13.22 -146.50 REMARK 500 1 TYR A 107 50.82 -94.31 REMARK 500 1 CYS A 111 18.43 -145.38 REMARK 500 1 PHE A 117 28.14 45.89 REMARK 500 2 LYS A 6 -165.72 41.98 REMARK 500 2 ASN A 9 -34.61 -157.57 REMARK 500 2 HIS A 15 64.92 21.62 REMARK 500 2 LEU A 16 -178.28 -62.47 REMARK 500 2 LYS A 17 -69.98 -22.72 REMARK 500 2 ILE A 24 58.95 -118.98 REMARK 500 2 CYS A 39 -75.22 -5.03 REMARK 500 2 LYS A 41 33.03 -92.52 REMARK 500 2 VAL A 51 -9.81 53.55 REMARK 500 2 THR A 68 -42.94 57.29 REMARK 500 2 HIS A 116 -154.35 -83.05 REMARK 500 2 PHE A 117 25.96 -65.05 REMARK 500 3 LYS A 6 -165.14 42.17 REMARK 500 3 ASN A 9 -48.31 -136.81 REMARK 500 3 LEU A 16 -179.40 -61.67 REMARK 500 3 LYS A 17 -71.52 -14.81 REMARK 500 3 SER A 26 -61.54 -149.20 REMARK 500 3 TYR A 27 59.16 -146.55 REMARK 500 3 LYS A 41 -84.73 -75.19 REMARK 500 3 GLN A 44 174.10 47.48 REMARK 500 3 ASP A 49 -155.96 58.45 REMARK 500 3 GLU A 50 8.27 -42.51 REMARK 500 3 SER A 72 41.29 -73.25 REMARK 500 3 CYS A 80 -99.26 49.02 REMARK 500 3 TYR A 109 -23.27 -141.00 REMARK 500 3 CYS A 111 12.36 51.65 REMARK 500 3 PHE A 117 36.25 31.62 REMARK 500 4 LYS A 6 -57.77 58.37 REMARK 500 4 ASN A 9 -42.20 -161.23 REMARK 500 4 LEU A 16 -179.40 -60.60 REMARK 500 REMARK 500 THIS ENTRY HAS 374 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 PRO A 5 LYS A 6 2 -149.15 REMARK 500 PRO A 5 LYS A 6 3 -148.98 REMARK 500 VAL A 51 GLY A 52 5 -147.58 REMARK 500 CYS A 67 THR A 68 8 136.15 REMARK 500 PRO A 5 LYS A 6 9 -146.78 REMARK 500 PRO A 5 LYS A 6 11 -149.18 REMARK 500 CYS A 67 THR A 68 13 149.64 REMARK 500 ALA A 30 THR A 31 14 135.57 REMARK 500 LYS A 71 SER A 72 15 -143.39 REMARK 500 CYS A 7 ASN A 8 18 144.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 7 SG REMARK 620 2 CYS A 10 SG 94.6 REMARK 620 3 HIS A 15 NE2 98.5 129.2 REMARK 620 4 CYS A 20 SG 102.2 121.3 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 25 SG REMARK 620 2 CYS A 28 SG 96.2 REMARK 620 3 HIS A 34 NE2 95.7 110.1 REMARK 620 4 CYS A 39 SG 133.7 116.4 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 CYS A 48 SG 103.7 REMARK 620 3 HIS A 53 NE2 119.5 118.2 REMARK 620 4 CYS A 58 SG 98.9 118.0 97.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 CYS A 70 SG 118.7 REMARK 620 3 HIS A 75 NE2 100.6 96.2 REMARK 620 4 CYS A 80 SG 104.5 128.4 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 108 SG REMARK 620 2 CYS A 111 SG 108.1 REMARK 620 3 HIS A 116 NE2 98.2 119.0 REMARK 620 4 CYS A 121 SG 97.8 127.9 100.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18049 RELATED DB: BMRB DBREF 2LLI A 1 124 UNP Q12476 AIR2_YEAST 57 180 SEQRES 1 A 124 LYS GLU ALA ALA PRO LYS CYS ASN ASN CYS SER GLN ARG SEQRES 2 A 124 GLY HIS LEU LYS LYS ASP CYS PRO HIS ILE ILE CYS SER SEQRES 3 A 124 TYR CYS GLY ALA THR ASP ASP HIS TYR SER ARG HIS CYS SEQRES 4 A 124 PRO LYS ALA ILE GLN CYS SER LYS CYS ASP GLU VAL GLY SEQRES 5 A 124 HIS TYR ARG SER GLN CYS PRO HIS LYS TRP LYS LYS VAL SEQRES 6 A 124 GLN CYS THR LEU CYS LYS SER LYS LYS HIS SER LYS GLU SEQRES 7 A 124 ARG CYS PRO SER ILE TRP ARG ALA TYR ILE LEU VAL ASP SEQRES 8 A 124 ASP ASN GLU LYS ALA LYS PRO LYS VAL LEU PRO PHE HIS SEQRES 9 A 124 THR ILE TYR CYS TYR ASN CYS GLY GLY LYS GLY HIS PHE SEQRES 10 A 124 GLY ASP ASP CYS LYS GLU LYS HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET ZN A 205 1 HETNAM ZN ZINC ION FORMUL 2 ZN 5(ZN 2+) HELIX 1 1 HIS A 38 ALA A 42 5 5 LINK SG CYS A 7 ZN ZN A 205 1555 1555 2.90 LINK SG CYS A 10 ZN ZN A 205 1555 1555 2.80 LINK NE2 HIS A 15 ZN ZN A 205 1555 1555 2.54 LINK SG CYS A 20 ZN ZN A 205 1555 1555 2.60 LINK SG CYS A 25 ZN ZN A 204 1555 1555 2.78 LINK SG CYS A 28 ZN ZN A 204 1555 1555 2.94 LINK NE2 HIS A 34 ZN ZN A 204 1555 1555 2.51 LINK SG CYS A 39 ZN ZN A 204 1555 1555 2.56 LINK SG CYS A 45 ZN ZN A 203 1555 1555 2.69 LINK SG CYS A 48 ZN ZN A 203 1555 1555 2.57 LINK NE2 HIS A 53 ZN ZN A 203 1555 1555 2.45 LINK SG CYS A 58 ZN ZN A 203 1555 1555 2.83 LINK SG CYS A 67 ZN ZN A 202 1555 1555 2.86 LINK SG CYS A 70 ZN ZN A 202 1555 1555 2.76 LINK NE2 HIS A 75 ZN ZN A 202 1555 1555 2.52 LINK SG CYS A 80 ZN ZN A 202 1555 1555 2.62 LINK SG CYS A 108 ZN ZN A 201 1555 1555 2.85 LINK SG CYS A 111 ZN ZN A 201 1555 1555 2.65 LINK NE2 HIS A 116 ZN ZN A 201 1555 1555 2.52 LINK SG CYS A 121 ZN ZN A 201 1555 1555 2.69 CISPEP 1 SER A 82 ILE A 83 16 -6.23 SITE 1 AC1 4 CYS A 108 CYS A 111 HIS A 116 CYS A 121 SITE 1 AC2 4 CYS A 67 CYS A 70 HIS A 75 CYS A 80 SITE 1 AC3 4 CYS A 45 CYS A 48 HIS A 53 CYS A 58 SITE 1 AC4 4 CYS A 25 CYS A 28 HIS A 34 CYS A 39 SITE 1 AC5 4 CYS A 7 CYS A 10 HIS A 15 CYS A 20 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