HEADER LIGASE/SIGNALING PROTEIN 22-APR-05 1ZGU TITLE SOLUTION STRUCTURE OF THE HUMAN MMS2-UBIQUITIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMS2, ENTEROCYTE DIFFERENTIATION ASSOCIATED FACTOR EDAF-1, COMPND 5 ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR, EDPF-1, VITAMIN D3 COMPND 6 INDUCIBLE PROTEIN, DDVIT 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2V2, MMS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS UEV DOMAIN, UBIQUITIN BINDING MOTIF, LIGASE-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.J.LEWIS,L.F.SALTIBUS,D.D.HAU,W.XIAO,L.SPYRACOPOULOS REVDAT 3 20-OCT-21 1ZGU 1 REMARK SEQADV REVDAT 2 24-FEB-09 1ZGU 1 VERSN REVDAT 1 04-APR-06 1ZGU 0 JRNL AUTH M.J.LEWIS,L.F.SALTIBUS,D.D.HAU,W.XIAO,L.SPYRACOPOULOS JRNL TITL STRUCTURAL BASIS FOR NON-COVALENT INTERACTION BETWEEN JRNL TITL 2 UBIQUITIN AND THE UBIQUITIN CONJUGATING ENZYME VARIANT HUMAN JRNL TITL 3 MMS2. JRNL REF J.BIOMOL.NMR V. 34 89 2006 JRNL REFN ISSN 0925-2738 JRNL PMID 16518696 JRNL DOI 10.1007/S10858-005-5583-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, HADDOCK 1.3 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), DOMINGUEZ, C., BOELENS, R., REMARK 3 BONVIN, A.M.J.J. (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK ALGORITHM REMARK 4 REMARK 4 1ZGU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032705. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 303 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 150 MM NACL; 150 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : [U-15N; U-10% 13C]-HMMS2 + REMARK 210 UBIQUITIN (1:4 RATIO) 90% H20 : REMARK 210 10% D20; [U-13C; U-15N]- REMARK 210 UBIQUITIN + HMMS2 (4:1 RATIO) 90% REMARK 210 H20 : 10% D20; [U-13C; U-15N]- REMARK 210 HMMS2 + UBIQUITIN (1:4 RATIO) 90% REMARK 210 H20 : 10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : F1-FILTERED, F3-EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, SPARKY 3.110, REMARK 210 HADDOCK 1.3 REMARK 210 METHOD USED : PROTEIN-PROTEIN DOCKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 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 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 OD2 ASP B 21 HZ1 LYS B 29 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 THR A 35 31.14 -93.52 REMARK 500 1 ASP A 43 -48.61 74.94 REMARK 500 1 LYS A 113 58.26 -108.62 REMARK 500 1 GLN B 62 -165.58 -102.80 REMARK 500 2 GLU A 41 -78.49 -77.42 REMARK 500 2 ARG A 60 -35.79 73.88 REMARK 500 2 LYS A 113 57.43 -111.33 REMARK 500 2 ASN A 136 -45.79 -135.06 REMARK 500 2 ARG B 74 98.76 -164.20 REMARK 500 3 ASP A 43 10.39 53.50 REMARK 500 3 LYS A 113 44.95 -109.32 REMARK 500 3 GLN B 62 -166.75 -109.80 REMARK 500 3 GLU B 64 -2.30 69.24 REMARK 500 4 ASP A 43 -44.59 75.54 REMARK 500 4 GLU A 64 109.32 -50.60 REMARK 500 4 LYS A 113 57.05 -115.87 REMARK 500 4 ASN A 136 -37.34 -137.12 REMARK 500 5 ASP A 42 -51.02 -163.71 REMARK 500 5 ASP A 43 -46.80 76.98 REMARK 500 5 LYS A 113 50.05 -115.62 REMARK 500 5 ASN A 136 -41.60 -136.22 REMARK 500 5 GLN B 62 -166.46 -101.54 REMARK 500 5 GLU B 64 -8.65 70.93 REMARK 500 5 LEU B 73 108.35 -59.07 REMARK 500 6 ASP A 43 -49.82 73.10 REMARK 500 7 ASP A 43 -80.79 57.41 REMARK 500 7 ARG A 60 -4.73 73.28 REMARK 500 7 ASN A 65 -5.83 76.89 REMARK 500 7 SER A 99 -62.48 -98.24 REMARK 500 7 LYS A 113 40.90 -108.35 REMARK 500 7 ASN A 136 -42.70 -131.37 REMARK 500 8 ASP A 33 -72.23 -62.55 REMARK 500 8 ASP A 43 -72.49 67.29 REMARK 500 9 LYS A 13 97.89 -69.58 REMARK 500 9 GLU A 41 -66.31 -92.45 REMARK 500 9 ASP A 43 -51.95 74.57 REMARK 500 9 LYS A 113 62.52 -112.97 REMARK 500 9 ASN A 136 -42.48 -130.13 REMARK 500 10 ASP A 43 -50.18 73.77 REMARK 500 10 ASN A 65 -10.80 72.53 REMARK 500 10 SER A 99 -60.83 -101.43 REMARK 500 10 LYS A 113 59.97 -107.90 REMARK 500 10 ASN A 136 -35.11 -134.11 REMARK 500 10 GLN B 62 -169.60 -117.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 YEAST UBIQUITIN WAS USED TO OBTAIN RESTRAINT INFORMATION, REMARK 999 WHILE HUMAN UBIQUITIN WAS USED TO MODEL THE INTERACTION. REMARK 999 THE SEQUENCE DIFFERENCES BETWEEN YEAST AND HUMAN REMARK 999 UBIQUITIN ARE ABSENT FROM THE PROTEIN-PROTEIN BINDING REMARK 999 INTERFACE. DBREF 1ZGU A 12 150 UNP Q15819 U2V2_HUMAN 7 145 DBREF 1ZGU B 1 76 UNP P61864 UBIQ_YEAST 1 76 SEQADV 1ZGU PRO B 19 UNP P61864 SER 19 SEE REMARK 999 SEQADV 1ZGU GLU B 24 UNP P61864 ASP 24 SEE REMARK 999 SEQADV 1ZGU ALA B 28 UNP P61864 SER 28 SEE REMARK 999 SEQADV 1ZGU ARG B 48 UNP P61864 LYS 48 ENGINEERED MUTATION SEQRES 1 A 139 VAL LYS VAL PRO ARG ASN PHE ARG LEU LEU GLU GLU LEU SEQRES 2 A 139 GLU GLU GLY GLN LYS GLY VAL GLY ASP GLY THR VAL SER SEQRES 3 A 139 TRP GLY LEU GLU ASP ASP GLU ASP MET THR LEU THR ARG SEQRES 4 A 139 TRP THR GLY MET ILE ILE GLY PRO PRO ARG THR ASN TYR SEQRES 5 A 139 GLU ASN ARG ILE TYR SER LEU LYS VAL GLU CYS GLY PRO SEQRES 6 A 139 LYS TYR PRO GLU ALA PRO PRO SER VAL ARG PHE VAL THR SEQRES 7 A 139 LYS ILE ASN MET ASN GLY ILE ASN ASN SER SER GLY MET SEQRES 8 A 139 VAL ASP ALA ARG SER ILE PRO VAL LEU ALA LYS TRP GLN SEQRES 9 A 139 ASN SER TYR SER ILE LYS VAL VAL LEU GLN GLU LEU ARG SEQRES 10 A 139 ARG LEU MET MET SER LYS GLU ASN MET LYS LEU PRO GLN SEQRES 11 A 139 PRO PRO GLU GLY GLN THR TYR ASN ASN 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 PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG 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 LYS A 13 GLY A 30 1 18 HELIX 2 2 ILE A 108 LYS A 113 1 6 HELIX 3 3 SER A 119 MET A 132 1 14 HELIX 4 4 SER A 133 LYS A 138 1 6 HELIX 5 5 THR B 22 GLU B 34 1 13 HELIX 6 6 PRO B 37 ASP B 39 5 3 HELIX 7 7 THR B 55 ASN B 60 5 6 SHEET 1 A 4 VAL A 36 LEU A 40 0 SHEET 2 A 4 TRP A 51 ILE A 56 -1 O THR A 52 N GLY A 39 SHEET 3 A 4 ILE A 67 GLU A 73 -1 O LEU A 70 N GLY A 53 SHEET 4 A 4 SER A 84 PHE A 87 -1 O ARG A 86 N LYS A 71 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 B 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 B 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 B 5 ARG B 48 GLN B 49 -1 O ARG B 48 N PHE B 45 CISPEP 1 TYR A 78 PRO A 79 1 0.20 CISPEP 2 TYR A 78 PRO A 79 2 0.04 CISPEP 3 TYR A 78 PRO A 79 3 -0.19 CISPEP 4 TYR A 78 PRO A 79 4 0.73 CISPEP 5 TYR A 78 PRO A 79 5 0.50 CISPEP 6 TYR A 78 PRO A 79 6 0.29 CISPEP 7 TYR A 78 PRO A 79 7 0.28 CISPEP 8 TYR A 78 PRO A 79 8 -0.24 CISPEP 9 TYR A 78 PRO A 79 9 0.44 CISPEP 10 TYR A 78 PRO A 79 10 -0.08 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