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 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 : X-PLOR_NIH 2.14
REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE
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 RCSB ID CODE IS RCSB101784.
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 CHLORIDE
REMARK 210 -17, 2 MM UBIQUITIN-18, 90% H2O/
REMARK 210 10% D2O; 1.0 MM [U-100% 15N]
REMARK 210 ZNF216-A20-19, 50 UM ZINC-20, 0.1
REMARK 210 MM DSS-21, 5 MM TRIS-22, 50 MM
REMARK 210 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; 1
REMARK 210 MM [U-100% 15N] ZNF216-A20-39, 50
REMARK 210 UM ZINC-40, 0.1 MM DSS-41, 5 MM
REMARK 210 TRIS-42, 50 MM SODIUM CHLORIDE-
REMARK 210 43, 4 MM UBIQUITIN-44, 90% H2O/
REMARK 210 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-15N
REMARK 210 HSQC IPAP; 15N, 13C HALF FILTERED
REMARK 210 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 H GLU B 51 HH TYR B 59 1.35
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 1 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 35 SG 113.4 130.0
REMARK 620 4 CYS A 32 SG 113.7 105.2 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 35 ZN ZN A 63 1555 1555 2.62
LINK SG CYS A 32 ZN ZN A 63 1555 1555 2.83
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
(ATOM LINES ARE NOT SHOWN.)
END
