10 20 30 40 50 60 70 80 2KDI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 09-JAN-09 2KDI
TITLE SOLUTION STRUCTURE OF A UBIQUITIN/UIM FUSION PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN, VACUOLAR PROTEIN SORTING-ASSOCIATED COMPND 3 PROTEIN 27 FUSION PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UIM 1; COMPND 6 SYNONYM: GOLGI RETENTION DEFECTIVE PROTEIN 11; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SCRG_04109, SCRG_05320,VPS27, DID7, GRD11, SSV17, SOURCE 6 VPL23, VPT27, YNR006W, N2038; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGIA
KEYWDS UBIQUITIN, UBIQUITIN INTERACTING MOTIF, UIM, PROTEIN DOMAIN KEYWDS 2 INTERFACE, ENDOSOME, MEMBRANE, METAL-BINDING, KEYWDS 3 PHOSPHOPROTEIN, ZINC, ZINC-FINGER, SIGNALING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.G.SGOURAKIS,M.M.PATEL,A.E.GARCIA,G.I.MAKHATADZE, AUTHOR 2 S.A.MCCALLUM
REVDAT 2 02-MAR-10 2KDI 1 JRNL REVDAT 1 09-FEB-10 2KDI 0
JRNL AUTH N.G.SGOURAKIS,M.M.PATEL,A.E.GARCIA,G.I.MAKHATADZE, JRNL AUTH 2 S.A.MCCALLUM JRNL TITL CONFORMATIONAL DYNAMICS AND STRUCTURAL PLASTICITY JRNL TITL 2 PLAY CRITICAL ROLES IN THE UBIQUITIN RECOGNITION OF JRNL TITL 3 A UIM DOMAIN. JRNL REF J.MOL.BIOL. V. 396 1128 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20053359 JRNL DOI 10.1016/J.JMB.2009.12.052
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.M.PATEL,N.G.SGOURAKIS,W.W.STREICHER,S.A.MCCALLUM, REMARK 1 AUTH 2 A.E.GARCIA,G.I.MAKHATADZE REMARK 1 TITL FOLDING COOPERATIVITY AND DYNAMICS OF A REMARK 1 TITL 2 UBIQUITIN/UIM FUSION PROTEIN BY NMR, DSC, CD, REMARK 1 TITL 3 FLUORESCENCE EXPERIMENTS AND MD SIMULATIONS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.18 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KDI COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB100985.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.103 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.24 MM [U-100% 13C; U-100% REMARK 210 15N] UBIQUITIN/UIM FUSION REMARK 210 PROTEIN-1, 3 MM SODIUM AZIDE- REMARK 210 2, 20 MM SODIUM PHOSPHATE-3, REMARK 210 50 MM SODIUM CHLORIDE-4, 95% REMARK 210 H2O/5% D2O; 1.1 MM [U-100% REMARK 210 15N] UBIQUITIN/UIM FUSION REMARK 210 PROTEIN-5, 3 MM SODIUM AZIDE- REMARK 210 6, 20 MM SODIUM PHOSPHATE-7, REMARK 210 50 MM SODIUM CHLORIDE-8, 95% REMARK 210 H2O/5% D2O; 0.5 MM [U-100% REMARK 210 15N] UBIQUITIN/UIM FUSION REMARK 210 PROTEIN-9, 3 MM SODIUM AZIDE- REMARK 210 10, 20 MM SODIUM PHOSPHATE-11, REMARK 210 50 MM SODIUM CHLORIDE-12, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 3D HN(CO)CACB; 3D REMARK 210 HNCACB; 3D 1H-15N NOESY; 3D 1H REMARK 210 -13C NOESY; 3D HCCH-COSY; 3D REMARK 210 HNCO; 3D H(CCO)NH; 2D HN-IPAP; REMARK 210 3D 1H-15N TOCSY; 3D HCCH- REMARK 210 TOCSY; 3D (H)C(CCO)NH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY 3.111, X- REMARK 210 PLOR 2.18, TALOS REMARK 210 2003.027.13.05, PALES REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, MOLECULAR REMARK 210 DYNAMICS, ENERGY MINIMIZATION 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 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 HE21 GLN A 71 H GLU A 73 1.41 REMARK 500 O GLU A 60 H ARG A 63 1.57 REMARK 500 O PHE A 13 H LEU A 76 1.57 REMARK 500 H GLN A 11 HH22 ARG A 72 1.60 REMARK 500 HA SER A 29 H SER A 66 1.60 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 HIS A 2 23.98 -78.90 REMARK 500 1 HIS A 3 175.92 63.03 REMARK 500 1 HIS A 7 60.82 -157.60 REMARK 500 1 ILE A 45 125.19 -39.58 REMARK 500 1 GLN A 71 -150.29 -70.71 REMARK 500 1 ASP A 92 -78.79 -134.99 REMARK 500 1 GLU A 93 -43.91 -146.79 REMARK 500 1 LEU A 103 -70.22 -96.10 REMARK 500 2 HIS A 4 100.88 69.91 REMARK 500 2 VAL A 26 -169.31 -119.29 REMARK 500 2 ASP A 30 158.58 -46.10 REMARK 500 2 ILE A 45 128.89 -37.13 REMARK 500 2 GLN A 71 -156.95 53.49 REMARK 500 2 ALA A 90 -70.76 -82.45 REMARK 500 2 ASP A 92 -86.43 -88.23 REMARK 500 2 GLU A 93 -40.12 -140.63 REMARK 500 2 LEU A 103 -74.44 -89.40 REMARK 500 3 HIS A 4 -82.99 66.72 REMARK 500 3 HIS A 5 157.46 66.50 REMARK 500 3 HIS A 6 -46.02 -149.71 REMARK 500 3 HIS A 7 3.47 -167.18 REMARK 500 3 GLU A 9 -13.81 -140.69 REMARK 500 3 ASN A 69 63.76 75.08 REMARK 500 3 GLU A 73 45.41 -79.08 REMARK 500 3 ASP A 92 -103.75 -88.19 REMARK 500 3 LEU A 103 -69.66 -97.12 REMARK 500 4 HIS A 3 92.97 -68.95 REMARK 500 4 HIS A 7 13.31 -163.30 REMARK 500 4 ASP A 30 158.76 -48.19 REMARK 500 4 ILE A 45 123.89 -38.77 REMARK 500 4 ALA A 55 41.45 71.24 REMARK 500 4 ASN A 69 36.40 73.01 REMARK 500 4 SER A 86 102.69 67.60 REMARK 500 4 ASP A 92 -61.47 -135.22 REMARK 500 4 GLU A 93 -62.62 -160.43 REMARK 500 4 LEU A 96 -29.50 -39.27 REMARK 500 4 LYS A 99 -71.34 -66.54 REMARK 500 4 ALA A 100 -29.58 -38.79 REMARK 500 4 LEU A 103 -68.36 -97.19 REMARK 500 5 HIS A 5 -124.11 -79.03 REMARK 500 5 HIS A 6 104.69 65.63 REMARK 500 5 ASP A 30 153.10 -44.00 REMARK 500 5 ASN A 69 38.66 77.58 REMARK 500 5 GLN A 71 -135.09 -84.35 REMARK 500 5 GLU A 73 44.83 -84.19 REMARK 500 5 ALA A 90 -71.18 -74.68 REMARK 500 5 ASP A 92 34.90 -142.73 REMARK 500 5 GLU A 94 -82.48 156.73 REMARK 500 5 LEU A 103 -73.96 -90.24 REMARK 500 6 HIS A 2 172.95 64.06 REMARK 500 REMARK 500 THIS ENTRY HAS 228 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 51 0.27 SIDE CHAIN REMARK 500 1 ARG A 63 0.30 SIDE CHAIN REMARK 500 1 ARG A 72 0.28 SIDE CHAIN REMARK 500 1 ARG A 81 0.15 SIDE CHAIN REMARK 500 1 ARG A 83 0.30 SIDE CHAIN REMARK 500 1 ARG A 98 0.27 SIDE CHAIN REMARK 500 1 ARG A 109 0.28 SIDE CHAIN REMARK 500 2 ARG A 51 0.31 SIDE CHAIN REMARK 500 2 ARG A 63 0.30 SIDE CHAIN REMARK 500 2 ARG A 72 0.30 SIDE CHAIN REMARK 500 2 ARG A 81 0.31 SIDE CHAIN REMARK 500 2 ARG A 83 0.30 SIDE CHAIN REMARK 500 2 ARG A 98 0.31 SIDE CHAIN REMARK 500 2 ARG A 109 0.31 SIDE CHAIN REMARK 500 3 ARG A 51 0.27 SIDE CHAIN REMARK 500 3 ARG A 63 0.31 SIDE CHAIN REMARK 500 3 ARG A 72 0.31 SIDE CHAIN REMARK 500 3 ARG A 81 0.30 SIDE CHAIN REMARK 500 3 ARG A 83 0.22 SIDE CHAIN REMARK 500 3 ARG A 98 0.31 SIDE CHAIN REMARK 500 4 ARG A 51 0.31 SIDE CHAIN REMARK 500 4 ARG A 63 0.29 SIDE CHAIN REMARK 500 4 ARG A 72 0.31 SIDE CHAIN REMARK 500 4 ARG A 81 0.29 SIDE CHAIN REMARK 500 4 ARG A 83 0.26 SIDE CHAIN REMARK 500 4 ARG A 98 0.30 SIDE CHAIN REMARK 500 4 ARG A 109 0.30 SIDE CHAIN REMARK 500 5 ARG A 51 0.27 SIDE CHAIN REMARK 500 5 ARG A 63 0.29 SIDE CHAIN REMARK 500 5 ARG A 72 0.30 SIDE CHAIN REMARK 500 5 ARG A 81 0.30 SIDE CHAIN REMARK 500 5 ARG A 83 0.31 SIDE CHAIN REMARK 500 5 ARG A 98 0.31 SIDE CHAIN REMARK 500 5 ARG A 109 0.23 SIDE CHAIN REMARK 500 6 ARG A 51 0.31 SIDE CHAIN REMARK 500 6 ARG A 63 0.31 SIDE CHAIN REMARK 500 6 ARG A 72 0.30 SIDE CHAIN REMARK 500 6 ARG A 81 0.31 SIDE CHAIN REMARK 500 6 ARG A 83 0.30 SIDE CHAIN REMARK 500 6 ARG A 98 0.30 SIDE CHAIN REMARK 500 6 ARG A 109 0.29 SIDE CHAIN REMARK 500 7 ARG A 51 0.28 SIDE CHAIN REMARK 500 7 ARG A 63 0.18 SIDE CHAIN REMARK 500 7 ARG A 72 0.31 SIDE CHAIN REMARK 500 7 ARG A 81 0.30 SIDE CHAIN REMARK 500 7 ARG A 83 0.28 SIDE CHAIN REMARK 500 7 ARG A 98 0.31 SIDE CHAIN REMARK 500 7 ARG A 109 0.27 SIDE CHAIN REMARK 500 8 ARG A 51 0.26 SIDE CHAIN REMARK 500 8 ARG A 63 0.29 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 137 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16114 RELATED DB: BMRB
DBREF 2KDI A 11 85 UNP B3LRG8 B3LRG8_YEAS1 2 76 DBREF 2KDI A 92 111 UNP P40343 VPS27_YEAST 258 277
SEQADV 2KDI MET A 1 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 2 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 3 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 4 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 5 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 6 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI HIS A 7 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI GLY A 8 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI GLU A 9 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI PHE A 10 UNP B3LRG8 EXPRESSION TAG SEQADV 2KDI ALA A 14 UNP B3LRG8 VAL 5 ENGINEERED SEQADV 2KDI TRP A 54 UNP B3LRG8 PHE 45 ENGINEERED SEQADV 2KDI ARG A 72 UNP B3LRG8 LYS 63 ENGINEERED SEQADV 2KDI SER A 86 UNP B3LRG8 LINKER SEQADV 2KDI MET A 87 UNP B3LRG8 LINKER SEQADV 2KDI GLY A 88 UNP B3LRG8 LINKER SEQADV 2KDI GLY A 89 UNP B3LRG8 LINKER SEQADV 2KDI ALA A 90 UNP B3LRG8 LINKER SEQADV 2KDI ALA A 91 UNP B3LRG8 LINKER SEQADV 2KDI GLY A 112 UNP P40343 EXPRESSION TAG SEQADV 2KDI GLY A 113 UNP P40343 EXPRESSION TAG SEQADV 2KDI TYR A 114 UNP P40343 EXPRESSION TAG
SEQRES 1 A 114 MET HIS HIS HIS HIS HIS HIS GLY GLU PHE GLN ILE PHE SEQRES 2 A 114 ALA LYS THR LEU THR GLY LYS THR ILE THR LEU GLU VAL SEQRES 3 A 114 GLU SER SER ASP THR ILE ASP ASN VAL LYS SER LYS ILE SEQRES 4 A 114 GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN ARG LEU SEQRES 5 A 114 ILE TRP ALA GLY LYS GLN LEU GLU ASP GLY ARG THR LEU SEQRES 6 A 114 SER ASP TYR ASN ILE GLN ARG GLU SER THR LEU HIS LEU SEQRES 7 A 114 VAL LEU ARG LEU ARG GLY GLY SER MET GLY GLY ALA ALA SEQRES 8 A 114 ASP GLU GLU GLU LEU ILE ARG LYS ALA ILE GLU LEU SER SEQRES 9 A 114 LEU LYS GLU SER ARG ASN SER GLY GLY TYR
HELIX 1 1 THR A 31 GLY A 44 1 14 HELIX 2 2 PRO A 46 ASP A 48 5 3 HELIX 3 3 GLU A 94 LEU A 103 1 10 HELIX 4 4 LEU A 105 SER A 111 1 7 HELIX 5 5 GLY A 112 TYR A 114 5 3
SHEET 1 A 5 THR A 21 GLU A 25 0 SHEET 2 A 5 GLN A 11 THR A 16 -1 N ALA A 14 O ILE A 22 SHEET 3 A 5 THR A 75 LEU A 80 1 O LEU A 76 N PHE A 13 SHEET 4 A 5 GLN A 50 TRP A 54 -1 N ARG A 51 O VAL A 79 SHEET 5 A 5 LYS A 57 GLN A 58 -1 O LYS A 57 N TRP A 54
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