HEADER NUCLEAR PROTEIN 31-MAR-08 2VRD TITLE THE STRUCTURE OF THE ZINC FINGER FROM THE HUMAN SPLICEOSOMAL PROTEIN TITLE 2 U1C COMPND MOL_ID: 1; COMPND 2 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DOMAIN, RESIDUES 1-61; COMPND 5 SYNONYM: U1 SNRNP PROTEIN C, U1C PROTEIN, U1-C; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3B KEYWDS RNA-BINDING PROTEIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, SPLICEOSOMAL PROTEIN, KEYWDS 3 PHOSPHOPROTEIN, NUCLEAR PROTEIN, RIBONUCLEOPROTEIN, ZINC-FINGER, KEYWDS 4 ZINC FINGER, METAL-BINDING, ZINC, RSGI, NUCLEUS, U1 SNRNP, RNA- KEYWDS 5 BINDING EXPDTA SOLUTION NMR NUMMDL 47 AUTHOR Y.MUTO,D.POMERANZ-KRUMMEL,C.OUBRIDGE,H.HERNANDEZ,C.ROBINSON, AUTHOR 2 D.NEUHAUS,K.NAGAI REVDAT 3 15-MAY-24 2VRD 1 REMARK LINK REVDAT 2 24-FEB-09 2VRD 1 VERSN REVDAT 1 08-APR-08 2VRD 0 SPRSDE 08-APR-08 2VRD 1UW2 JRNL AUTH Y.MUTO,D.POMERANZ-KRUMMEL,C.OUBRIDGE,H.HERNANDEZ,C.ROBINSON, JRNL AUTH 2 D.NEUHAUS,K.NAGAI JRNL TITL THE STRUCTURE AND BIOCHEMICAL PROPERTIES OF THE HUMAN JRNL TITL 2 SPLICEOSOMAL PROTEIN U1C JRNL REF J.MOL.BIOL. V. 341 185 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15312772 JRNL DOI 10.1016/J.JMB.2004.04.078 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2VRD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1290035827. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90%WATER/10%D2O AND 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY; NOESY 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 : XWINNMR, SPARKY, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 47 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOW RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR REMARK 210 SPECTROSCOPY ON UNLABELLED U1C ZINC FINGER DOMAIN 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: 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 LYS A 3 140.53 61.27 REMARK 500 1 CYS A 25 44.81 -99.40 REMARK 500 1 TYR A 38 33.79 -99.61 REMARK 500 1 MET A 42 38.59 -152.75 REMARK 500 1 ALA A 56 53.70 -95.57 REMARK 500 1 GLN A 58 -57.83 -150.78 REMARK 500 2 LYS A 3 122.24 60.90 REMARK 500 2 CYS A 25 43.54 -100.18 REMARK 500 2 TYR A 38 35.00 -99.72 REMARK 500 2 MET A 42 -65.76 -154.95 REMARK 500 2 GLN A 45 75.23 -152.96 REMARK 500 2 ALA A 56 47.23 -97.22 REMARK 500 3 CYS A 25 51.93 -96.02 REMARK 500 3 MET A 42 -56.53 -156.29 REMARK 500 3 ALA A 56 59.39 -92.89 REMARK 500 4 CYS A 25 50.06 -97.25 REMARK 500 4 MET A 42 -62.98 -151.78 REMARK 500 4 ALA A 56 36.87 -97.87 REMARK 500 5 CYS A 25 56.00 -92.42 REMARK 500 5 MET A 42 -63.10 -149.10 REMARK 500 5 GLN A 58 -58.44 -130.40 REMARK 500 6 CYS A 25 52.12 -96.08 REMARK 500 6 GLN A 45 71.69 54.71 REMARK 500 7 LYS A 3 169.94 55.56 REMARK 500 7 CYS A 25 52.81 -94.92 REMARK 500 7 TYR A 38 31.98 -99.41 REMARK 500 7 GLU A 44 -56.66 -157.55 REMARK 500 7 GLN A 45 82.77 -164.18 REMARK 500 7 GLN A 59 42.16 -163.61 REMARK 500 8 CYS A 25 45.17 -99.26 REMARK 500 8 TYR A 38 34.42 -99.31 REMARK 500 8 GLU A 43 -60.66 -167.17 REMARK 500 8 GLU A 44 -51.52 -172.21 REMARK 500 8 GLN A 58 66.60 -113.33 REMARK 500 9 CYS A 25 53.12 -95.32 REMARK 500 9 TYR A 38 31.63 -99.01 REMARK 500 9 MET A 42 -63.63 -148.14 REMARK 500 9 ALA A 56 35.43 -98.77 REMARK 500 9 GLN A 59 -59.18 -147.24 REMARK 500 10 CYS A 25 50.32 -97.80 REMARK 500 10 TYR A 38 34.21 -99.87 REMARK 500 10 MET A 42 -64.18 -151.98 REMARK 500 10 GLN A 45 74.56 53.27 REMARK 500 11 LYS A 3 168.08 56.26 REMARK 500 11 CYS A 25 56.61 -93.25 REMARK 500 11 TYR A 38 34.88 -99.85 REMARK 500 11 MET A 42 -67.36 -142.48 REMARK 500 11 GLU A 43 38.82 -156.98 REMARK 500 11 ALA A 46 73.44 -154.83 REMARK 500 11 ALA A 56 30.21 -97.93 REMARK 500 REMARK 500 THIS ENTRY HAS 235 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 A 21 0.23 SIDE CHAIN REMARK 500 1 ARG A 28 0.28 SIDE CHAIN REMARK 500 2 ARG A 21 0.21 SIDE CHAIN REMARK 500 2 ARG A 28 0.31 SIDE CHAIN REMARK 500 3 ARG A 21 0.22 SIDE CHAIN REMARK 500 3 ARG A 28 0.25 SIDE CHAIN REMARK 500 4 ARG A 21 0.20 SIDE CHAIN REMARK 500 4 ARG A 28 0.29 SIDE CHAIN REMARK 500 5 ARG A 21 0.30 SIDE CHAIN REMARK 500 5 ARG A 28 0.26 SIDE CHAIN REMARK 500 6 ARG A 21 0.29 SIDE CHAIN REMARK 500 6 ARG A 28 0.32 SIDE CHAIN REMARK 500 7 ARG A 21 0.31 SIDE CHAIN REMARK 500 7 ARG A 28 0.31 SIDE CHAIN REMARK 500 8 ARG A 21 0.28 SIDE CHAIN REMARK 500 8 ARG A 28 0.26 SIDE CHAIN REMARK 500 9 ARG A 21 0.29 SIDE CHAIN REMARK 500 9 ARG A 28 0.23 SIDE CHAIN REMARK 500 10 ARG A 21 0.22 SIDE CHAIN REMARK 500 10 ARG A 28 0.27 SIDE CHAIN REMARK 500 11 ARG A 21 0.24 SIDE CHAIN REMARK 500 11 ARG A 28 0.28 SIDE CHAIN REMARK 500 12 ARG A 21 0.29 SIDE CHAIN REMARK 500 12 ARG A 28 0.30 SIDE CHAIN REMARK 500 13 ARG A 21 0.23 SIDE CHAIN REMARK 500 13 ARG A 28 0.31 SIDE CHAIN REMARK 500 14 ARG A 21 0.24 SIDE CHAIN REMARK 500 14 ARG A 28 0.28 SIDE CHAIN REMARK 500 15 ARG A 21 0.32 SIDE CHAIN REMARK 500 15 ARG A 28 0.23 SIDE CHAIN REMARK 500 16 ARG A 21 0.32 SIDE CHAIN REMARK 500 16 ARG A 28 0.26 SIDE CHAIN REMARK 500 17 ARG A 21 0.32 SIDE CHAIN REMARK 500 17 ARG A 28 0.30 SIDE CHAIN REMARK 500 18 ARG A 21 0.24 SIDE CHAIN REMARK 500 18 ARG A 28 0.31 SIDE CHAIN REMARK 500 19 ARG A 21 0.22 SIDE CHAIN REMARK 500 19 ARG A 28 0.24 SIDE CHAIN REMARK 500 20 ARG A 21 0.28 SIDE CHAIN REMARK 500 20 ARG A 28 0.31 SIDE CHAIN REMARK 500 21 ARG A 21 0.29 SIDE CHAIN REMARK 500 21 ARG A 28 0.25 SIDE CHAIN REMARK 500 22 ARG A 21 0.21 SIDE CHAIN REMARK 500 22 ARG A 28 0.26 SIDE CHAIN REMARK 500 23 ARG A 21 0.23 SIDE CHAIN REMARK 500 23 ARG A 28 0.29 SIDE CHAIN REMARK 500 24 ARG A 21 0.22 SIDE CHAIN REMARK 500 24 ARG A 28 0.22 SIDE CHAIN REMARK 500 25 ARG A 21 0.21 SIDE CHAIN REMARK 500 25 ARG A 28 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 94 PLANE DEVIATIONS. 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 A1062 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 111.1 REMARK 620 3 HIS A 24 NE2 108.5 109.7 REMARK 620 4 HIS A 30 NE2 112.5 106.0 108.9 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 A1062 DBREF 2VRD A 1 61 UNP P09234 RU1C_HUMAN 1 61 SEQRES 1 A 61 MET PRO LYS PHE TYR CYS ASP TYR CYS ASP THR TYR LEU SEQRES 2 A 61 THR HIS ASP SER PRO SER VAL ARG LYS THR HIS CYS SER SEQRES 3 A 61 GLY ARG LYS HIS LYS GLU ASN VAL LYS ASP TYR TYR GLN SEQRES 4 A 61 LYS TRP MET GLU GLU GLN ALA GLN SER LEU ILE ASP LYS SEQRES 5 A 61 THR THR ALA ALA PHE GLN GLN GLY LYS HET ZN A1062 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 17 CYS A 25 1 9 HELIX 2 2 ARG A 28 TYR A 38 1 11 HELIX 3 3 SER A 48 ALA A 56 1 9 LINK SG CYS A 6 ZN ZN A1062 1555 1555 2.30 LINK SG CYS A 9 ZN ZN A1062 1555 1555 2.30 LINK NE2 HIS A 24 ZN ZN A1062 1555 1555 2.00 LINK NE2 HIS A 30 ZN ZN A1062 1555 1555 2.00 SITE 1 AC1 4 CYS A 6 CYS A 9 HIS A 24 HIS A 30 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