HEADER ENDOCYTOSIS/SIGNALING PROTEIN 20-FEB-06 2G3Q TITLE SOLUTION STRUCTURE OF EDE1 UBA-UBIQUITIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YBL047C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EDE1 UBA, RESIDUES 1339-1381; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: EDE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS ENDOCYTOSIS, MONOUBIQUITIN SIGNALING, SOLUTION STRUCTURE, UBA DOMAIN, KEYWDS 2 UBIQUITIN-BINDING MOTIF, ENDOCYTOSIS-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.A.SWANSON,L.HICKE,I.RADHAKRISHNAN REVDAT 3 09-MAR-22 2G3Q 1 REMARK REVDAT 2 24-FEB-09 2G3Q 1 VERSN REVDAT 1 09-MAY-06 2G3Q 0 JRNL AUTH K.A.SWANSON,L.HICKE,I.RADHAKRISHNAN JRNL TITL STRUCTURAL BASIS FOR MONOUBIQUITIN RECOGNITION BY THE EDE1 JRNL TITL 2 UBA DOMAIN. JRNL REF J.MOL.BIOL. V. 358 713 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16563434 JRNL DOI 10.1016/J.JMB.2006.02.059 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, ARIA 1.2 REMARK 3 AUTHORS : BRUNGER ET AL. (CNS), LINGE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 2489 DISTANCE RESTRAINTS, INCLUDING 2489 NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS [2069 UNAMBIGUOUS AND 420 AMBIGUOUS RESTRAINTS], 74 REMARK 3 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 161 TORSION ANGLE REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 2G3Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036649. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM 15N,13C-LABELED EDE1 UBA; REMARK 210 1MM UBIQUITIN; 20MM PHOSPHATE REMARK 210 BUFFER (PH 6.0), 2MM DTT, 0.2% REMARK 210 NAN3, 90% H2O, 10% D2O; 1MM 15N, REMARK 210 13C-LABELED EDE1 UBA; 1MM REMARK 210 UBIQUITIN; 20MM PHOSPHATE BUFFER REMARK 210 (PH 6.0), 2MM DTT, 0.2% NAN3, REMARK 210 100% D2O; 1MM EDE1 UBA; 1MM 15N, REMARK 210 13C-LABELED UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER (PH 6.0), 2MM REMARK 210 DTT, 0.2% NAN3, 90% H2O, 10% D2O; REMARK 210 1MM EDE1 UBA; 1MM 15N,13C- REMARK 210 LABELED UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER (PH 6.0), 2MM REMARK 210 DTT, 0.2% NAN3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C-SEPARATED_12C-EDITED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMERS ARE THE REMARK 210 20 STRUCTURES WITH THE LOWEST REMARK 210 RESTRAINT ENERGIES, RESTRAINT REMARK 210 VIOLATIONS, AND RMS DEVIATIONS REMARK 210 FROM IDEAL COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ADDITIONAL EXPERIMENTS: 2D DOUBLE HALF FILTERED NOESY WAS REMARK 210 PERFORMED FOR BOTH D2O AND H2O SAMPLES 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 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 ASN A1367 52.29 93.07 REMARK 500 1 ASP A1379 -64.18 -93.34 REMARK 500 1 GLU B 34 -61.94 -104.08 REMARK 500 1 ILE B 61 106.31 -56.61 REMARK 500 1 GLN B 62 -167.52 -74.65 REMARK 500 1 LEU B 73 163.19 64.61 REMARK 500 2 CYS A1366 -9.95 -58.77 REMARK 500 2 ASN A1367 53.03 93.16 REMARK 500 2 TRP A1368 81.66 39.35 REMARK 500 2 LEU A1370 -74.77 -62.66 REMARK 500 2 ASP A1379 -68.06 -94.12 REMARK 500 2 SER A1380 83.44 33.53 REMARK 500 2 VAL B 17 -162.24 -108.11 REMARK 500 2 GLU B 34 -65.57 -102.77 REMARK 500 2 GLN B 40 -47.27 -134.33 REMARK 500 2 ASN B 60 89.94 56.40 REMARK 500 2 LEU B 73 -177.32 60.13 REMARK 500 2 ARG B 74 96.97 59.13 REMARK 500 3 ASN A1367 52.83 95.03 REMARK 500 3 TRP A1368 72.21 37.07 REMARK 500 3 LEU A1370 -76.10 -53.62 REMARK 500 3 ASP A1379 -64.98 -92.94 REMARK 500 3 SER A1380 170.11 -55.48 REMARK 500 3 LYS B 33 -66.69 -104.36 REMARK 500 3 GLU B 34 -75.41 -92.39 REMARK 500 3 ALA B 46 19.84 59.01 REMARK 500 3 ASN B 60 93.41 57.58 REMARK 500 3 LEU B 73 109.62 61.80 REMARK 500 4 MET A1352 -65.66 -128.67 REMARK 500 4 CYS A1366 -8.94 -58.07 REMARK 500 4 ASN A1367 55.54 91.64 REMARK 500 4 TRP A1368 82.00 36.68 REMARK 500 4 LEU A1370 -73.41 -57.31 REMARK 500 4 ASP A1379 -62.51 -91.06 REMARK 500 4 SER A1380 170.80 -58.47 REMARK 500 4 LYS B 33 -63.05 -97.76 REMARK 500 4 GLU B 34 -73.93 -94.79 REMARK 500 4 GLN B 40 -47.86 -130.98 REMARK 500 4 ASN B 60 93.02 56.75 REMARK 500 4 LEU B 73 -83.52 63.42 REMARK 500 5 PRO A1341 -66.07 -93.41 REMARK 500 5 ASN A1367 54.67 96.25 REMARK 500 5 TRP A1368 59.34 39.51 REMARK 500 5 ASP A1379 -65.68 -92.05 REMARK 500 5 VAL B 17 -168.65 -128.32 REMARK 500 5 LYS B 33 -68.06 -93.91 REMARK 500 5 GLU B 34 -63.61 -94.41 REMARK 500 5 ALA B 46 18.56 58.70 REMARK 500 5 ASN B 60 15.59 59.88 REMARK 500 5 LEU B 71 -146.61 98.25 REMARK 500 REMARK 500 THIS ENTRY HAS 188 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DBREF 2G3Q A 1339 1381 UNP P34216 YBE7_YEAST 1339 1381 DBREF 2G3Q B 1 76 UNP P61864 UBIQ_YEAST 1 76 SEQRES 1 A 43 THR THR PRO LYS SER LEU ALA VAL GLU GLU LEU SER GLY SEQRES 2 A 43 MET GLY PHE THR GLU GLU GLU ALA HIS ASN ALA LEU GLU SEQRES 3 A 43 LYS CYS ASN TRP ASP LEU GLU ALA ALA THR ASN PHE LEU SEQRES 4 A 43 LEU ASP SER ALA 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 HELIX 1 1 PRO A 1341 SER A 1350 1 10 HELIX 2 2 GLU A 1356 CYS A 1366 1 11 HELIX 3 3 LEU A 1370 LEU A 1378 1 9 HELIX 4 4 ILE B 23 LYS B 33 1 11 HELIX 5 5 SER B 57 TYR B 59 5 3 SHEET 1 A 5 LYS B 11 GLU B 16 0 SHEET 2 A 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 A 5 THR B 66 VAL B 70 1 O LEU B 69 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 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