HEADER TRANSPORT PROTEIN/SIGNALING PROTEIN 14-JUL-14 2MRO TITLE STRUCTURE OF THE COMPLEX OF UBIQUITIN AND THE UBA DOMAIN FROM DNA- TITLE 2 DAMAGE-INDUCIBLE 1 PROTEIN (DDI1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HUMAN UBIQUITIN; COMPND 5 SYNONYM: UBIQUITIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA DAMAGE-INDUCIBLE PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UBIQUITIN ASSOCIATED DOMAIN, UNP RESIDUES 389-428; COMPND 11 SYNONYM: V-SNARE-MASTER 1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 559292; SOURCE 14 STRAIN: ATCC 204508 / S288C; SOURCE 15 GENE: DDI1, VSM1, YER143W; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR: PGEX 4T2 KEYWDS DNA-DAMAGE-INDUCIBLE 1 PROTEIN, UBIQUITIN ASSOCIATED DOMAIN, DDI1, KEYWDS 2 UBA, HYDROLASE-SIGNALING PROTEIN COMPLEX, TRANSPORT PROTEIN- KEYWDS 3 SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.ZHANG,D.FUSHMAN REVDAT 4 14-JUN-23 2MRO 1 REMARK REVDAT 3 06-NOV-19 2MRO 1 REMARK SEQADV REVDAT 2 18-MAR-15 2MRO 1 JRNL REVDAT 1 04-FEB-15 2MRO 0 JRNL AUTH U.NOWICKA,D.ZHANG,O.WALKER,D.KRUTAUZ,C.A.CASTANEDA, JRNL AUTH 2 A.CHATURVEDI,T.Y.CHEN,N.REIS,M.H.GLICKMAN,D.FUSHMAN JRNL TITL DNA-DAMAGE-INDUCIBLE 1 PROTEIN (DDI1) CONTAINS AN JRNL TITL 2 UNCHARACTERISTIC UBIQUITIN-LIKE DOMAIN THAT BINDS UBIQUITIN. JRNL REF STRUCTURE V. 23 542 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25703377 JRNL DOI 10.1016/J.STR.2015.01.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, HADDOCK 2.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), ALEXANDRE BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000103971. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.2 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] UB-1, 20 MM REMARK 210 SODIUM PHOSPHATE-2, 7 % [U-99% REMARK 210 2H] D2O-3, 93 % H2O-4, 93% H2O/7% REMARK 210 D2O; 1 MM [U-100% 15N] UBA-5, REMARK 210 20 MM SODIUM PHOSPHATE-6, 7 % [U- REMARK 210 99% 2H] D2O-7, 93 % H2O-8, 93% REMARK 210 H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC 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, CARA 1.8.1, HADDOCK REMARK 210 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 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: TWO TITRATION EXPERIMENTS WERE CONDUCTED. BASICALLY REMARK 210 UNLABELED LIGAND PROTEIN WAS ADDED STEPWISE TO N15-LABELED REMARK 210 PROTEIN SOLUTION. 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: 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 HZ2 LYS A 6 OD2 ASP B 400 1.57 REMARK 500 OD2 ASP A 21 HZ2 LYS A 29 1.57 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 ASN B 416 63.56 70.09 REMARK 500 2 GLU A 34 -65.27 -92.00 REMARK 500 2 GLN A 62 -167.69 -106.33 REMARK 500 3 THR A 9 29.84 -79.26 REMARK 500 3 GLN A 62 -166.23 -114.94 REMARK 500 4 SER B 387 39.88 -143.00 REMARK 500 4 ASN B 416 62.10 68.30 REMARK 500 5 GLN A 62 -166.60 -106.14 REMARK 500 6 GLN A 62 -167.06 -101.46 REMARK 500 6 ASN B 416 60.85 61.82 REMARK 500 7 ARG A 42 94.51 -160.37 REMARK 500 7 GLN A 62 -163.24 -109.50 REMARK 500 7 ARG A 74 -63.25 -103.36 REMARK 500 7 ASN B 418 93.99 -67.80 REMARK 500 8 GLN A 62 -165.99 -107.92 REMARK 500 9 GLN A 62 -164.35 -113.24 REMARK 500 9 ASN B 416 61.10 61.96 REMARK 500 10 GLN A 62 -167.99 -110.96 REMARK 500 10 GLU A 64 -1.53 70.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 2MR9 RELATED DB: PDB REMARK 900 UBA DOMAIN OF DNA-DAMAGE-INDUCIBLE 1 PROTEIN (DDI1) DBREF 2MRO A 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 2MRO B 389 428 UNP P40087 DDI1_YEAST 389 428 SEQADV 2MRO GLY B 386 UNP P40087 EXPRESSION TAG SEQADV 2MRO SER B 387 UNP P40087 EXPRESSION TAG SEQADV 2MRO ALA B 388 UNP P40087 EXPRESSION TAG SEQADV 2MRO SER B 429 UNP P40087 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 44 GLY SER ALA THR PHE PRO GLU GLN THR ILE LYS GLN LEU SEQRES 2 B 44 MET ASP LEU GLY PHE PRO ARG ASP ALA VAL VAL LYS ALA SEQRES 3 B 44 LEU LYS GLN THR ASN GLY ASN ALA GLU PHE ALA ALA SER SEQRES 4 B 44 LEU LEU PHE GLN SER HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 THR A 55 ASN A 60 5 6 HELIX 3 3 PRO B 391 LEU B 401 1 11 HELIX 4 4 PRO B 404 GLN B 414 1 11 HELIX 5 5 ASN B 418 PHE B 427 1 10 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 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