HEADER RNA BINDING PROTEIN 30-SEP-11 2LK1 TITLE SOLUTION STRUCTURE AND BINDING STUDIES OF THE RANBP2-TYPE ZINC FINGER TITLE 2 OF RBM5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RANBP2-TYPE ZINC FINGER RESIDUES 181-210; COMPND 5 SYNONYM: PROTEIN G15, PUTATIVE TUMOR SUPPRESSOR LUCA15, RNA-BINDING COMPND 6 MOTIF PROTEIN 5, RENAL CARCINOMA ANTIGEN NY-REN-9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ZINC FINGER, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.FARINA,M.PELLECCHIA REVDAT 2 27-NOV-24 2LK1 1 REMARK SEQADV LINK REVDAT 1 28-DEC-11 2LK1 0 JRNL AUTH B.FARINA,R.FATTORUSSO,M.PELLECCHIA JRNL TITL TARGETING ZINC FINGER DOMAINS WITH SMALL MOLECULES: SOLUTION JRNL TITL 2 STRUCTURE AND BINDING STUDIES OF THE RANBP2-TYPE ZINC FINGER JRNL TITL 3 OF RBM5. JRNL REF CHEMBIOCHEM V. 12 2837 2011 JRNL REFN ISSN 1439-4227 JRNL PMID 22162216 JRNL DOI 10.1002/CBIC.201100582 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN V2.1, CYANA V2.1, SYBYL REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA), TRIPOS (SYBYL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000102476. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 UM RBM5-ZF1, 150 UM ZINC REMARK 210 ION, 500 UM AQN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN V2.1, CARA V1.5,V1.8, REMARK 210 CYANA V2.1, SYBYL REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION 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 1 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 1 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.1 DEGREES REMARK 500 2 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 5 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 9 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 9 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 12 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 13 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 17 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 TRP A 5 CE2 - CD2 - CG ANGL. DEV. = -5.1 DEGREES REMARK 500 18 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 18 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 20 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.4 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 9 -59.27 -138.19 REMARK 500 1 PHE A 22 46.22 -107.03 REMARK 500 1 ARG A 23 -59.55 -152.12 REMARK 500 1 PHE A 29 42.57 -108.75 REMARK 500 2 PHE A 2 57.57 -90.64 REMARK 500 2 ASP A 4 159.85 -40.12 REMARK 500 2 LYS A 9 -59.24 -132.10 REMARK 500 2 PHE A 22 43.36 -105.98 REMARK 500 2 ARG A 23 -60.41 -142.57 REMARK 500 3 PHE A 2 44.75 -103.24 REMARK 500 3 ASP A 4 161.54 -41.18 REMARK 500 3 ASN A 8 41.06 -106.81 REMARK 500 3 LYS A 9 -59.52 -147.06 REMARK 500 3 PHE A 22 49.90 -107.25 REMARK 500 3 ARG A 23 -58.99 -155.50 REMARK 500 4 GLU A 3 74.06 63.93 REMARK 500 4 ASN A 8 42.53 -107.04 REMARK 500 4 LYS A 9 -62.77 -148.91 REMARK 500 4 PHE A 22 48.74 -108.27 REMARK 500 4 ARG A 23 -59.38 -149.10 REMARK 500 4 PHE A 29 41.61 -100.72 REMARK 500 5 ASP A 4 162.35 -47.23 REMARK 500 5 LYS A 9 -60.53 -151.37 REMARK 500 5 PHE A 22 46.58 -107.81 REMARK 500 5 ARG A 23 -59.66 -146.09 REMARK 500 5 PHE A 29 51.97 -102.92 REMARK 500 6 ASP A 4 163.34 -49.66 REMARK 500 6 ASN A 8 40.07 -106.40 REMARK 500 6 LYS A 9 -59.32 -149.28 REMARK 500 6 PHE A 22 50.84 -105.23 REMARK 500 6 ARG A 23 -58.54 -155.85 REMARK 500 6 PHE A 29 54.08 -104.11 REMARK 500 7 PHE A 22 51.66 -105.91 REMARK 500 7 ARG A 23 -57.28 -161.65 REMARK 500 8 PHE A 2 46.80 -100.47 REMARK 500 8 LYS A 9 -59.25 -138.67 REMARK 500 8 PHE A 22 43.17 -101.36 REMARK 500 8 ARG A 23 -60.76 -145.81 REMARK 500 9 PHE A 2 49.61 -91.62 REMARK 500 9 ASP A 4 161.39 -45.96 REMARK 500 9 LYS A 9 -59.66 -120.49 REMARK 500 10 PHE A 22 49.71 -107.58 REMARK 500 10 ARG A 23 -59.39 -153.80 REMARK 500 11 ASP A 4 163.45 -40.79 REMARK 500 11 LYS A 9 -66.18 -129.22 REMARK 500 11 ARG A 23 -59.80 -150.08 REMARK 500 11 PHE A 29 55.49 -107.49 REMARK 500 12 PHE A 2 58.19 -92.90 REMARK 500 12 ASP A 4 160.37 -43.62 REMARK 500 12 LYS A 9 -62.28 -138.49 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. 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 33 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 7 SG REMARK 620 2 CYS A 10 SG 116.0 REMARK 620 3 CYS A 21 SG 109.2 100.7 REMARK 620 4 CYS A 24 SG 101.9 115.9 113.5 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 AQN A 32 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 33 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17970 RELATED DB: BMRB REMARK 900 RELATED ID: 2LK1 RELATED DB: PDB DBREF 2LK1 A 1 30 UNP P52756 RBM5_HUMAN 181 210 SEQADV 2LK1 ACE A 0 UNP P52756 EXPRESSION TAG SEQADV 2LK1 NH2 A 31 UNP P52756 EXPRESSION TAG SEQRES 1 A 32 ACE LYS PHE GLU ASP TRP LEU CYS ASN LYS CYS CYS LEU SEQRES 2 A 32 ASN ASN PHE ARG LYS ARG LEU LYS CYS PHE ARG CYS GLY SEQRES 3 A 32 ALA ASP LYS PHE ASP NH2 HET ACE A 0 6 HET NH2 A 31 3 HET AQN A 32 27 HET ZN A 33 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM AQN 9,10-DIOXO-9,10-DIHYDROANTHRACENE-2-SULFONIC ACID HETNAM ZN ZINC ION FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 AQN C14 H8 O5 S FORMUL 3 ZN ZN 2+ SHEET 1 A 2 TRP A 5 LEU A 6 0 SHEET 2 A 2 ASN A 13 ASN A 14 -1 O ASN A 14 N TRP A 5 LINK C ACE A 0 N LYS A 1 1555 1555 1.34 LINK C ASP A 30 N NH2 A 31 1555 1555 1.35 LINK SG CYS A 7 ZN ZN A 33 1555 1555 2.38 LINK SG CYS A 10 ZN ZN A 33 1555 1555 2.38 LINK SG CYS A 21 ZN ZN A 33 1555 1555 2.38 LINK SG CYS A 24 ZN ZN A 33 1555 1555 2.39 SITE 1 AC1 5 ASN A 13 ASN A 14 PHE A 15 ARG A 18 SITE 2 AC1 5 PHE A 22 SITE 1 AC2 4 CYS A 7 CYS A 10 CYS A 21 CYS A 24 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 HETATM 1 C ACE A 0 -0.423 15.211 2.309 1.00 0.00 C HETATM 2 O ACE A 0 -1.368 14.911 3.054 1.00 0.00 O HETATM 3 CH3 ACE A 0 0.663 16.137 2.803 1.00 0.00 C HETATM 4 H1 ACE A 0 0.709 17.024 2.171 1.00 0.00 H HETATM 5 H2 ACE A 0 1.627 15.630 2.773 1.00 0.00 H HETATM 6 H3 ACE A 0 0.444 16.425 3.831 1.00 0.00 H