HEADER PROTEIN BINDING 09-MAY-14 2MP2 TITLE SOLUTION STRUCTURE OF SUMO DIMER IN COMPLEX WITH SIM2-3 FROM RNF4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 12-92; COMPND 5 SYNONYM: SUMO-3, SMT3 HOMOLOG 1, SUMO-2, UBIQUITIN-LIKE PROTEIN COMPND 6 SMT3B, SMT3B; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 3; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 2-90; COMPND 12 SYNONYM: SUMO-3, SMT3 HOMOLOG 1, SUMO-2, UBIQUITIN-LIKE PROTEIN COMPND 13 SMT3B, SMT3B; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF4; COMPND 17 CHAIN: C; COMPND 18 FRAGMENT: UNP RESIDUES 45-69; COMPND 19 SYNONYM: RING FINGER PROTEIN 4; COMPND 20 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: SMT3B, SMT3H1, SUMO3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIS-TEV-30A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: SMT3B, SMT3H1, SUMO3; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PHIS-TEV-30A; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 24 ORGANISM_COMMON: MOUSE; SOURCE 25 ORGANISM_TAXID: 10090 KEYWDS SUMO, DIMER, SIM, RNF4, COMPLEX, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.XU,A.PLECHANOVOV,P.SIMPSON,J.MARCHANT,O.LEIDECKER,K.SEBASTIAN, AUTHOR 2 R.T.HAY,S.J.MATTHEWS REVDAT 2 09-JUL-14 2MP2 1 JRNL REVDAT 1 02-JUL-14 2MP2 0 JRNL AUTH Y.XU,A.PLECHANOVOVA,P.SIMPSON,J.MARCHANT,O.LEIDECKER, JRNL AUTH 2 S.KRAATZ,R.T.HAY,S.J.MATTHEWS JRNL TITL STRUCTURAL INSIGHT INTO SUMO CHAIN RECOGNITION AND JRNL TITL 2 MANIPULATION BY THE UBIQUITIN LIGASE RNF4. JRNL REF NAT COMMUN V. 5 4217 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24969970 JRNL DOI 10.1038/NCOMMS5217 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-14. REMARK 100 THE RCSB ID CODE IS RCSB103880. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-99% 13C; U-99% 15N] REMARK 210 SUMO 1, 0.3 MM SUMO 2, 1.0 MM REMARK 210 RNF4, 90% H2O/10% D2O; 0.3 MM REMARK 210 SUMO 1, 0.3 MM [U-99% 13C; U-99% REMARK 210 15N] SUMO 2, 1.0 MM RNF4, 90% REMARK 210 H2O/10% D2O; 0.3 MM [U-99% 13C; U REMARK 210 -99% 15N] SUMO 1, 0.3 MM SUMO 2, REMARK 210 90% H2O/10% D2O; 0.3 MM SUMO 1, REMARK 210 0.3 MM [U-99% 13C; U-99% 15N] REMARK 210 SUMO 2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, ARIA, NMRPIPE, NMRVIEW, REMARK 210 TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 H LEU B 19 O PHE B 31 1.13 REMARK 500 O LEU B 19 H PHE B 31 1.25 REMARK 500 O PHE A 49 HB ILE A 56 1.26 REMARK 500 HA HIS B 16 HA LYS B 34 1.33 REMARK 500 O LYS A 10 H ILE A 73 1.35 REMARK 500 O CYS B 47 H GLY B 51 1.35 REMARK 500 O ALA B 22 H VAL B 85 1.38 REMARK 500 O ARG A 50 H ASP A 74 1.39 REMARK 500 H ARG A 48 O PHE A 76 1.45 REMARK 500 H ARG A 50 O ASP A 74 1.46 REMARK 500 O GLY A 13 H ASP A 15 1.51 REMARK 500 O TYR B 46 H GLN B 50 1.52 REMARK 500 H PHE B 61 O GLN B 64 1.53 REMARK 500 HD21 ASN B 18 O PHE B 31 1.54 REMARK 500 O PHE B 61 H GLN B 64 1.54 REMARK 500 HA VAL A 11 O ILE A 73 1.55 REMARK 500 H VAL A 11 O VAL A 19 1.57 REMARK 500 O PRO B 72 H GLU B 76 1.58 REMARK 500 O ILE A 7 H ILE A 23 1.58 REMARK 500 O ILE B 17 H ILE B 33 1.58 REMARK 500 O GLN B 56 HE ARG B 58 1.60 REMARK 500 C GLY A 82 NZ LYS B 11 1.92 REMARK 500 N LEU B 19 O PHE B 31 2.04 REMARK 500 O ARG A 50 N ASP A 74 2.08 REMARK 500 O ASN B 67 N THR B 69 2.12 REMARK 500 O LYS A 10 N ILE A 73 2.13 REMARK 500 O PHE A 49 CB ILE A 56 2.16 REMARK 500 O LEU B 19 N PHE B 31 2.16 REMARK 500 N ARG A 50 O ASP A 74 2.16 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 ASP A 5 -155.56 -89.56 REMARK 500 1 GLN A 14 -36.49 60.95 REMARK 500 1 HIS A 26 27.47 -69.18 REMARK 500 1 GLN A 40 -106.63 -118.18 REMARK 500 1 MET A 44 -15.00 80.70 REMARK 500 1 ASP A 52 94.12 -37.88 REMARK 500 1 GLN A 54 104.79 -170.64 REMARK 500 1 MET A 67 -89.50 -85.23 REMARK 500 1 GLU A 68 -179.74 117.92 REMARK 500 1 GLU A 70 34.77 -157.26 REMARK 500 1 GLN A 78 107.10 49.13 REMARK 500 1 GLN A 79 -29.48 173.44 REMARK 500 1 GLU B 4 -146.79 -99.24 REMARK 500 1 LYS B 5 131.17 52.24 REMARK 500 1 PRO B 6 103.27 -46.88 REMARK 500 1 LYS B 7 93.41 -52.70 REMARK 500 1 GLU B 8 61.93 60.90 REMARK 500 1 LYS B 11 -76.29 -108.70 REMARK 500 1 GLU B 13 -177.98 44.06 REMARK 500 1 ASP B 15 40.60 -141.43 REMARK 500 1 HIS B 16 139.42 9.58 REMARK 500 1 SER B 27 -163.47 -161.44 REMARK 500 1 LYS B 34 -116.94 -65.44 REMARK 500 1 ARG B 35 -63.21 -158.41 REMARK 500 1 MET B 54 -45.27 84.11 REMARK 500 1 ASP B 62 94.27 -38.57 REMARK 500 1 ILE B 66 25.69 48.79 REMARK 500 1 ASN B 67 72.80 -20.40 REMARK 500 1 GLU B 68 -67.90 32.71 REMARK 500 1 THR B 69 -33.04 -39.68 REMARK 500 1 GLU B 76 40.01 94.80 REMARK 500 1 VAL C 3 93.47 41.57 REMARK 500 1 ASP C 5 -176.33 -59.16 REMARK 500 1 VAL C 8 -32.76 -178.58 REMARK 500 1 ASP C 9 107.12 46.46 REMARK 500 1 THR C 11 -166.85 -58.28 REMARK 500 1 CYS C 12 -176.87 -54.03 REMARK 500 1 VAL C 20 153.59 177.26 REMARK 500 1 HIS C 24 -118.06 -94.96 REMARK 500 1 ASN C 25 168.46 63.62 REMARK 500 2 THR A 2 -86.44 -114.99 REMARK 500 2 GLU A 3 -138.14 -150.36 REMARK 500 2 ASN A 4 44.77 -83.67 REMARK 500 2 HIS A 26 23.88 -75.71 REMARK 500 2 LEU A 42 176.40 -57.83 REMARK 500 2 MET A 44 -10.68 78.46 REMARK 500 2 ASP A 52 94.83 -37.92 REMARK 500 2 GLN A 54 104.13 -172.07 REMARK 500 2 PRO A 55 144.99 -39.40 REMARK 500 2 GLU A 70 2.55 93.83 REMARK 500 REMARK 500 THIS ENTRY HAS 478 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19961 RELATED DB: BMRB DBREF 2MP2 A 2 82 UNP P55854 SUMO3_HUMAN 12 92 DBREF 2MP2 B 2 90 UNP P55854 SUMO3_HUMAN 2 90 DBREF 2MP2 C 2 26 UNP Q9QZS2 RNF4_MOUSE 45 69 SEQADV 2MP2 GLY A 1 UNP P55854 EXPRESSION TAG SEQADV 2MP2 GLY B 1 UNP P55854 EXPRESSION TAG SEQRES 1 A 82 GLY THR GLU ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY SEQRES 2 A 82 GLN ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG HIS SEQRES 3 A 82 THR PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU ARG SEQRES 4 A 82 GLN GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE ASP SEQRES 5 A 82 GLY GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN LEU SEQRES 6 A 82 GLU MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN GLN SEQRES 7 A 82 GLN THR GLY GLY SEQRES 1 B 90 GLY SER GLU GLU LYS PRO LYS GLU GLY VAL LYS THR GLU SEQRES 2 B 90 ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY GLN ASP GLY SEQRES 3 B 90 SER VAL VAL GLN PHE LYS ILE LYS ARG HIS THR PRO LEU SEQRES 4 B 90 SER LYS LEU MET LYS ALA TYR CYS GLU ARG GLN GLY LEU SEQRES 5 B 90 SER MET ARG GLN ILE ARG PHE ARG PHE ASP GLY GLN PRO SEQRES 6 B 90 ILE ASN GLU THR ASP THR PRO ALA GLN LEU GLU MET GLU SEQRES 7 B 90 ASP GLU ASP THR ILE ASP VAL PHE GLN GLN GLN THR SEQRES 1 C 25 THR VAL GLY ASP GLU ILE VAL ASP LEU THR CYS GLU SER SEQRES 2 C 25 LEU GLU PRO VAL VAL VAL ASP LEU THR HIS ASN ASP HELIX 1 1 LEU A 29 GLN A 40 1 12 HELIX 2 2 PRO A 62 GLU A 66 5 5 HELIX 3 3 LEU B 39 GLY B 51 1 13 HELIX 4 4 THR B 71 GLU B 76 1 6 SHEET 1 A 4 VAL A 18 LYS A 22 0 SHEET 2 A 4 ASN A 8 ALA A 12 -1 N VAL A 11 O VAL A 19 SHEET 3 A 4 ASP A 71 PHE A 76 1 O ILE A 73 N LYS A 10 SHEET 4 A 4 ARG A 48 PHE A 51 -1 N ARG A 48 O PHE A 76 SHEET 1 B 3 VAL B 29 ILE B 33 0 SHEET 2 B 3 ILE B 17 GLY B 23 -1 N LEU B 19 O PHE B 31 SHEET 3 B 3 ASP B 81 VAL B 85 1 O VAL B 85 N ALA B 22 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