HEADER LIGASE 31-JAN-12 2RSF TITLE COMPLEX STRUCTURE OF WWE IN RNF146 WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF146; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WWE DOMAIN, UNP RESIDUES 83-179; COMPND 5 SYNONYM: RING FINGER PROTEIN 146; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RNF146; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: P111111 KEYWDS WWE DOMAIN, RNF146, UBIQUITIN E3 LIGASE, LIGASE, STRUCTURAL GENOMICS, KEYWDS 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 15-MAY-24 2RSF 1 REMARK REVDAT 2 14-JUN-23 2RSF 1 REMARK SEQADV REVDAT 1 06-MAR-13 2RSF 0 JRNL AUTH F.HE,M.INOUE,T.KIGAWA,T.TERADA,Y.MUTO,S.YOKOYAMA JRNL TITL COMPLEX STRUCTURE OF WWE DOMAIN IN RNF146 WITH ATP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RSF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000150228. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 ENTITY_1-1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C 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 : NMRPIPE, NMRVIEW, KUJIRA, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 1 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 1 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 2 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 3 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 4 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 5 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 5 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 6 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 6 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 8 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 8 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 9 ARG A 46 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 9 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 10 PRO A 1 CA - N - CD ANGL. DEV. = -8.7 DEGREES REMARK 500 10 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 12 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 12 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -8.4 DEGREES REMARK 500 13 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 14 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 15 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 66 ANGLE DEVIATIONS. 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 THR A 13 -178.05 -171.49 REMARK 500 1 ASN A 27 -45.81 -132.84 REMARK 500 1 ILE A 66 -151.62 -122.18 REMARK 500 1 MET A 78 70.15 56.21 REMARK 500 1 ILE A 99 127.51 75.61 REMARK 500 2 ASN A 27 -62.73 -90.11 REMARK 500 2 TYR A 30 148.74 -172.69 REMARK 500 2 ILE A 66 -150.72 -124.92 REMARK 500 2 HIS A 86 -32.94 -135.98 REMARK 500 2 ILE A 99 128.63 74.30 REMARK 500 3 ASN A 27 -66.67 -100.25 REMARK 500 3 ASN A 38 -10.73 -144.74 REMARK 500 3 ILE A 66 -152.26 -119.20 REMARK 500 3 ILE A 99 128.43 73.22 REMARK 500 3 SER A 105 136.74 71.77 REMARK 500 4 ASN A 27 -85.10 -80.53 REMARK 500 4 TYR A 30 149.38 -171.15 REMARK 500 4 ASN A 61 147.09 -171.39 REMARK 500 4 ILE A 66 -152.66 -122.93 REMARK 500 4 ILE A 99 127.73 75.40 REMARK 500 5 SER A 2 26.16 -78.67 REMARK 500 5 SER A 5 -33.10 -153.33 REMARK 500 5 THR A 13 -176.65 -175.23 REMARK 500 5 ILE A 66 -151.99 -123.99 REMARK 500 5 ILE A 99 126.80 76.45 REMARK 500 6 SER A 2 -82.98 -164.34 REMARK 500 6 ASN A 27 -31.82 -163.38 REMARK 500 6 ILE A 66 -153.70 -121.58 REMARK 500 6 ILE A 99 127.76 72.30 REMARK 500 6 SER A 108 -173.72 -170.06 REMARK 500 7 ASN A 27 -31.42 -164.18 REMARK 500 7 ILE A 66 -150.93 -119.35 REMARK 500 7 ILE A 99 128.64 72.92 REMARK 500 8 SER A 6 23.28 -73.37 REMARK 500 8 ASN A 27 -34.61 -146.16 REMARK 500 8 ILE A 66 -152.82 -119.59 REMARK 500 8 ILE A 99 127.69 75.91 REMARK 500 9 ASN A 27 -30.81 -164.30 REMARK 500 9 ILE A 66 -152.52 -120.76 REMARK 500 9 ILE A 99 127.12 73.34 REMARK 500 10 SER A 5 -39.23 -161.04 REMARK 500 10 ASN A 27 -34.25 -151.19 REMARK 500 10 ILE A 66 -150.14 -118.12 REMARK 500 10 ILE A 99 129.01 75.11 REMARK 500 11 SER A 5 -35.09 -140.30 REMARK 500 11 ASN A 27 -25.32 -161.86 REMARK 500 11 ASN A 61 145.37 -170.69 REMARK 500 11 ILE A 66 -153.05 -120.62 REMARK 500 11 HIS A 86 -33.49 -149.06 REMARK 500 11 ILE A 99 129.74 73.58 REMARK 500 REMARK 500 THIS ENTRY HAS 90 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 49 0.09 SIDE CHAIN REMARK 500 5 ARG A 49 0.09 SIDE CHAIN REMARK 500 12 ARG A 49 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UJR RELATED DB: PDB REMARK 900 FREE STATE STRUCTURE REMARK 900 RELATED ID: 11472 RELATED DB: BMRB DBREF 2RSF A 8 104 UNP Q9CZW6 RN146_MOUSE 83 179 SEQADV 2RSF PRO A 1 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 2 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 3 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF GLY A 4 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 5 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 6 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF GLY A 7 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 105 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF GLY A 106 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF PRO A 107 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 108 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF SER A 109 UNP Q9CZW6 EXPRESSION TAG SEQADV 2RSF GLY A 110 UNP Q9CZW6 EXPRESSION TAG SEQRES 1 A 110 PRO SER SER GLY SER SER GLY PHE LEU ASP LYS PRO THR SEQRES 2 A 110 LEU LEU SER PRO GLU GLU LEU LYS ALA ALA SER ARG GLY SEQRES 3 A 110 ASN GLY GLU TYR ALA TRP TYR TYR GLU GLY ARG ASN GLY SEQRES 4 A 110 TRP TRP GLN TYR ASP GLU ARG THR SER ARG GLU LEU GLU SEQRES 5 A 110 ASP ALA PHE SER LYS GLY LYS LYS ASN THR GLU MET LEU SEQRES 6 A 110 ILE ALA GLY PHE LEU TYR VAL ALA ASP LEU GLU ASN MET SEQRES 7 A 110 VAL GLN TYR ARG ARG ASN GLU HIS GLY ARG ARG ARG LYS SEQRES 8 A 110 ILE LYS ARG ASP ILE ILE ASP ILE PRO LYS LYS GLY VAL SEQRES 9 A 110 SER GLY PRO SER SER GLY HET ATP A 201 43 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 HELIX 1 1 SER A 3 GLY A 7 5 5 HELIX 2 2 SER A 16 GLY A 26 1 11 HELIX 3 3 ASP A 44 GLY A 58 1 15 HELIX 4 4 PRO A 100 VAL A 104 5 5 SHEET 1 A 6 TRP A 40 GLN A 42 0 SHEET 2 A 6 ALA A 31 GLU A 35 -1 N TYR A 34 O TRP A 41 SHEET 3 A 6 ARG A 90 ASP A 95 -1 O ASP A 95 N ALA A 31 SHEET 4 A 6 VAL A 79 ARG A 82 -1 N GLN A 80 O ARG A 90 SHEET 5 A 6 LEU A 70 ASP A 74 -1 N VAL A 72 O TYR A 81 SHEET 6 A 6 ASN A 61 LEU A 65 -1 N MET A 64 O TYR A 71 SITE 1 AC1 8 TYR A 34 TYR A 43 ILE A 66 TYR A 71 SITE 2 AC1 8 GLN A 80 ARG A 82 ARG A 88 ARG A 90 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