HEADER METAL BINDING PROTEIN/PEPTIDE BINDING PR29-JUN-10 2L00 TITLE SOLUTION STRUCTURE OF THE NON-COVALENT COMPLEX OF THE ZNF216 A20 TITLE 2 DOMAIN WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZFAND5 PROTEIN (ZINC FINGER PROTEIN 216 (PREDICTED), COMPND 3 ISOFORM CRA_A); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: A20; COMPND 6 SYNONYM: ZNF216-A20; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UBIQUITIN CORE DOMAIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: RCG_48158, ZFAND5, ZFP216_PREDICTED; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX-4T1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: PUBI-2, UBI1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: C41 (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PKK223-3 KEYWDS A20 DOMAIN, ZNF216, UBIQUITIN, ZINC FINGER, UBIQUITIN BINDING, METAL KEYWDS 2 BINDING PROTEIN-PEPTIDE BINDING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.P.GARNER,J.E.LONG,M.S.SEARLE,R.LAYFIELD REVDAT 2 01-MAY-24 2L00 1 REMARK SEQADV LINK REVDAT 1 20-JUL-11 2L00 0 JRNL AUTH T.P.GARNER,J.STRACHAN,J.E.LONG,R.LAYFIELD,M.S.SEARLE JRNL TITL CO-LOCALISATION OF UBIQUITIN RECEPTORS ZNF216 AND P62 IN A JRNL TITL 2 UBIQUITIN-MEDIATED TERNARY COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, X-PLOR NIH 2.14 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RIGID BODY DOCKING USING HADDOCK REMARK 3 (STANDARD PROTOCOL), FULLY FLEXIBLE DOCKING IN HADDOCK BY REMARK 3 STANDARD PROTOCOL WITH REDUCED ELECTROSTATICS REMARK 4 REMARK 4 2L00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000101784. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4 MM ZNF216-A20-1, 50 UM ZINC-2, REMARK 210 0.1 MM DSS-3, 5 MM TRIS-4, 50 MM REMARK 210 SODIUM CHLORIDE-5, 1 MM [U-100% REMARK 210 15N] UBIQUITIN-6, 90% H2O/10% REMARK 210 D2O; 1.0 MM [U-100% 15N] ZNF216- REMARK 210 A20-7, 50 UM ZINC-8, 4 MM MTSL-9, REMARK 210 5 MM TRIS-10, 50 MM SODIUM REMARK 210 CHLORIDE-11, 4 MM UBIQUITIN-12, REMARK 210 90% H2O/10% D2O; 0.8 MM [U-100% REMARK 210 13C; U-100% 15N] ZNF216-A20-13, REMARK 210 50 UM ZINC-14, 0.1 MM DSS-15, 5 REMARK 210 MM TRIS-16, 50 MM SODIUM REMARK 210 CHLORIDE-17, 2 MM UBIQUITIN-18, REMARK 210 90% H2O/10% D2O; 1.0 MM [U-100% REMARK 210 15N] ZNF216-A20-19, 50 UM ZINC- REMARK 210 20, 0.1 MM DSS-21, 5 MM TRIS-22, REMARK 210 50 MM SODIUM CHLORIDE-23, 5 % REMARK 210 POLYACRYLAMIDE GEL-24, 4 MM REMARK 210 UBIQUITIN-25, 90% H2O/10% D2O; 4 REMARK 210 MM ZNF216-A20-26, 50 UM ZINC-27, REMARK 210 0.1 MM DSS-28, 5 MM TRIS-29, 50 REMARK 210 MM SODIUM CHLORIDE-30, 5 % REMARK 210 POLYACRYLAMIDE GEL-31, 1 MM [U- REMARK 210 100% 15N] UBIQUITIN-32, 90% H2O/ REMARK 210 10% D2O; 2 MM ZNF216-A20-33, 50 REMARK 210 UM ZINC-34, 0.1 MM DSS-35, 5 MM REMARK 210 TRIS-36, 50 MM SODIUM CHLORIDE- REMARK 210 37, 1 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN-38, 90% H2O/10% D2O; REMARK 210 1 MM [U-100% 15N] ZNF216-A20-39, REMARK 210 50 UM ZINC-40, 0.1 MM DSS-41, 5 REMARK 210 MM TRIS-42, 50 MM SODIUM REMARK 210 CHLORIDE-43, 4 MM UBIQUITIN-44, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 2D 1H- REMARK 210 15N HSQC IPAP; 15N, 13C HALF REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CCPNMR 1.1.15, X REMARK 210 -PLOR NIH 2.14, HADDOCK 2.0 REMARK 210 METHOD USED : RIGID BODY DOCKING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 MET A 3 REMARK 465 ALA A 4 REMARK 465 GLN A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 ASN A 8 REMARK 465 GLN A 9 REMARK 465 THR A 10 REMARK 465 PRO A 11 REMARK 465 GLY A 47 REMARK 465 ARG A 48 REMARK 465 MET A 49 REMARK 465 SER A 50 REMARK 465 PRO A 51 REMARK 465 MET A 52 REMARK 465 GLY A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 SER A 56 REMARK 465 GLY A 57 REMARK 465 SER A 58 REMARK 465 ASN A 59 REMARK 465 SER A 60 REMARK 465 PRO A 61 REMARK 465 THR A 62 REMARK 465 ARG B 72 REMARK 465 LEU B 73 REMARK 465 ARG B 74 REMARK 465 GLY B 75 REMARK 465 GLY B 76 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 PRO A 13 78.47 -69.75 REMARK 500 1 THR A 28 -153.50 -79.14 REMARK 500 2 PRO A 13 78.45 -69.80 REMARK 500 2 THR A 28 -153.54 -79.08 REMARK 500 3 PRO A 13 78.40 -69.83 REMARK 500 3 THR A 28 -153.41 -79.04 REMARK 500 4 PRO A 13 78.46 -69.76 REMARK 500 4 THR A 28 -153.54 -79.11 REMARK 500 5 PRO A 13 78.50 -69.81 REMARK 500 5 PHE A 22 -169.65 -124.57 REMARK 500 5 THR A 28 -153.57 -79.04 REMARK 500 6 PRO A 13 78.50 -69.83 REMARK 500 6 PHE A 22 -169.79 -119.84 REMARK 500 6 THR A 28 -153.51 -79.12 REMARK 500 7 PRO A 13 78.48 -69.78 REMARK 500 7 THR A 28 -153.49 -79.04 REMARK 500 7 CYS A 32 -172.06 -68.70 REMARK 500 8 PRO A 13 78.52 -69.75 REMARK 500 8 ASN A 25 119.80 -173.00 REMARK 500 8 THR A 28 -153.46 -79.20 REMARK 500 9 PRO A 13 78.46 -69.81 REMARK 500 9 THR A 28 -153.56 -79.12 REMARK 500 9 CYS A 32 -168.58 -73.59 REMARK 500 10 PRO A 13 78.48 -69.82 REMARK 500 10 THR A 28 -153.52 -79.10 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 63 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 CYS A 20 SG 106.4 REMARK 620 3 CYS A 32 SG 113.7 105.2 REMARK 620 4 CYS A 35 SG 113.4 130.0 85.5 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 ZN A 63 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17023 RELATED DB: BMRB REMARK 900 FREE ZNF216 A20 REMARK 900 RELATED ID: 2KZY RELATED DB: PDB REMARK 900 FREE ZNF216 A20 DBREF 2L00 A 3 62 UNP B5DF11 B5DF11_RAT 1 60 DBREF 2L00 B 1 76 UNP P61864 UBIQ_YEAST 1 76 SEQADV 2L00 GLY A 1 UNP B5DF11 EXPRESSION TAG SEQADV 2L00 SER A 2 UNP B5DF11 EXPRESSION TAG SEQRES 1 A 62 GLY SER MET ALA GLN GLU THR ASN GLN THR PRO GLY PRO SEQRES 2 A 62 MET LEU CYS SER THR GLY CYS GLY PHE TYR GLY ASN PRO SEQRES 3 A 62 ARG THR ASN GLY MET CYS SER VAL CYS TYR LYS GLU HIS SEQRES 4 A 62 LEU GLN ARG GLN GLN ASN SER GLY ARG MET SER PRO MET SEQRES 5 A 62 GLY THR ALA SER GLY SER ASN SER PRO THR SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN VAL SEQRES 3 B 76 LYS SER LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 63 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 1 CYS A 32 SER A 46 1 15 HELIX 2 2 THR B 22 GLY B 35 1 14 HELIX 3 3 PRO B 37 GLN B 41 5 5 HELIX 4 4 THR B 55 TYR B 59 5 5 SHEET 1 A 5 THR B 12 GLU B 16 0 SHEET 2 A 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 A 5 THR B 66 VAL B 70 1 O LEU B 67 N LYS B 6 SHEET 4 A 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 A 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS A 16 ZN ZN A 63 1555 1555 2.30 LINK SG CYS A 20 ZN ZN A 63 1555 1555 2.44 LINK SG CYS A 32 ZN ZN A 63 1555 1555 2.83 LINK SG CYS A 35 ZN ZN A 63 1555 1555 2.62 SITE 1 AC1 5 CYS A 16 THR A 18 CYS A 20 CYS A 32 SITE 2 AC1 5 CYS A 35 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