HEADER LIGASE/PROTEIN BINDING 28-MAY-09 2KJH TITLE NMR BASED STRUCTURAL MODEL OF THE UBCH8-UBIQUITIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN/ISG15-CONJUGATING ENZYME E2 L6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE L6, UBIQUITIN CARRIER PROTEIN L6, COMPND 5 UBCH8, RETINOIC ACID-INDUCED GENE B PROTEIN, RIG-B; COMPND 6 EC: 6.3.2.19; 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: UBE2L6, UBCH8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: P11; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: RPS27A UBA80, UBCEP1, UBA52, UBB, UBC; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS PROTEIN-PROTEIN INTERACTION, HADDOCK MODEL, E2 ENZYME, ATP-BINDING, KEYWDS 2 LIGASE, NUCLEOTIDE-BINDING, UBL CONJUGATION PATHWAY, CYTOPLASM, KEYWDS 3 ISOPEPTIDE BOND, NUCLEUS, UBL CONJUGATION, LIGASE-PROTEIN BINDING KEYWDS 4 COMPLEX EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR S.A.SERNIWKA,G.S.SHAW REVDAT 4 13-OCT-21 2KJH 1 SEQADV REVDAT 3 26-FEB-20 2KJH 1 REMARK REVDAT 2 09-FEB-10 2KJH 1 JRNL REVDAT 1 08-DEC-09 2KJH 0 JRNL AUTH S.A.SERNIWKA,G.S.SHAW JRNL TITL THE STRUCTURE OF THE UBCH8-UBIQUITIN COMPLEX SHOWS A UNIQUE JRNL TITL 2 UBIQUITIN INTERACTION SITE. JRNL REF BIOCHEMISTRY V. 48 12169 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19928833 JRNL DOI 10.1021/BI901686J REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ 2.1, HADDOCK 2.0, CNS 1.2 REMARK 3 AUTHORS : VARIAN (VNMRJ), DOMINGUEZ, BOELENS, BONVIN REMARK 3 (HADDOCK), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEMI-RIGID BODY DOCKING USING REMARK 3 PREVIOUSLY DETERMINED STRUCTURES OF UBCH8 AND UBIQUITIN; REMARK 3 CALCULATED 1000 STRUCTURES-200 LOW ENERGY STRUCTURES SELECTED, REMARK 3 SEMI-FLEXIBLE SIMULATED ANNEALING AND REFINEMENT WITH EXPLICIT REMARK 3 WATER REMARK 4 REMARK 4 2KJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101196. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.35 MM [U-100% 13C; U-100% 15N] REMARK 210 UBCH8-1, 0.35 MM UBIQUITIN-2, 20 REMARK 210 MM SODIUM PHOSPHATE-3, 1 MM EDTA- REMARK 210 4, 250 MM SODIUM CHLORIDE-5, 50 REMARK 210 MM ARGININE-6, 50 MM GLUTAMIC REMARK 210 ACID-7, 90% H2O/10% D2O; 0.35 MM REMARK 210 UBCH8-8, 0.35 MM [U-100% 13C; U- REMARK 210 100% 15N] UBIQUITIN-9, 20 MM REMARK 210 SODIUM PHOSPHATE-10, 1 MM EDTA- REMARK 210 11, 250 MM SODIUM CHLORIDE-12, REMARK 210 50 MM ARGININE-13, 50 MM REMARK 210 GLUTAMIC ACID-14, 90% H2O/10% REMARK 210 D2O; 0.35 MM [U-100% 15N; U-99% REMARK 210 2H] UBCH8-15, 0.35 MM UBIQUITIN- REMARK 210 16, 20 MM SODIUM PHOSPHATE-17, 1 REMARK 210 MM EDTA-18, 250 MM SODIUM REMARK 210 CHLORIDE-19, 50 MM ARGININE-20, REMARK 210 50 MM GLUTAMIC ACID-21, 90% H2O/ REMARK 210 10% D2O; 0.35 MM UBCH8-22, 0.35 REMARK 210 MM [U-100% 15N; U-99% 2H] REMARK 210 UBIQUITIN-23, 20 MM SODIUM REMARK 210 PHOSPHATE-24, 1 MM EDTA-25, 250 REMARK 210 MM SODIUM CHLORIDE-26, 50 MM REMARK 210 ARGININE-27, 50 MM GLUTAMIC ACID- REMARK 210 28, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 2D 1H-15N HSQC WITH REMARK 210 CROSS SATURATION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.2.2, REMARK 210 HADDOCK 2.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY IN THE LOWEST ENERGY REMARK 210 CLUSTER 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-16 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 152 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 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 ARG A 145 -52.72 -120.37 REMARK 500 1 ARG B 74 77.29 -100.40 REMARK 500 2 ARG A 145 -45.19 -132.70 REMARK 500 3 ASN A 23 74.69 56.88 REMARK 500 3 ARG A 145 -56.90 -127.14 REMARK 500 3 GLU B 34 -75.37 -87.49 REMARK 500 4 ASN A 93 41.30 -153.63 REMARK 500 4 ALA B 46 19.17 58.04 REMARK 500 5 GLU B 34 -74.14 -87.28 REMARK 500 5 GLN B 62 -165.57 -106.17 REMARK 500 6 ASN A 93 39.68 -142.66 REMARK 500 6 GLU A 118 74.84 -119.25 REMARK 500 6 ARG A 145 -50.80 -122.23 REMARK 500 7 LYS A 16 83.69 -154.47 REMARK 500 7 ARG A 145 -39.78 -136.68 REMARK 500 7 GLU B 64 -7.41 72.85 REMARK 500 8 ARG A 145 -56.07 -122.04 REMARK 500 8 GLU B 34 -62.91 -96.32 REMARK 500 9 SER A 91 0.53 -65.95 REMARK 500 9 ARG A 145 -41.94 -130.56 REMARK 500 9 GLN B 62 -165.70 -114.42 REMARK 500 10 ASN A 93 53.21 -149.13 REMARK 500 10 GLN B 62 -169.43 -108.86 REMARK 500 11 ASN A 93 103.15 -163.59 REMARK 500 14 ASN A 93 47.21 -165.80 REMARK 500 15 SER A 91 0.22 -69.87 REMARK 500 15 GLN B 62 -169.99 -118.18 REMARK 500 15 ARG B 74 32.20 -99.74 REMARK 500 16 SER A 91 32.79 -80.08 REMARK 500 16 GLU A 92 -56.73 -140.64 REMARK 500 16 GLN B 62 -165.60 -105.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WZV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBCH8 REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBIQUITIN REMARK 900 RELATED ID: 16321 RELATED DB: BMRB REMARK 900 NMR ASSIGNMENTS FOR UBCH8 DBREF 2KJH A 1 152 UNP O14933 UB2L6_HUMAN 1 152 DBREF 2KJH B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2KJH CYS B 76 UNP P62988 GLY 76 ENGINEERED MUTATION SEQRES 1 A 152 MET ALA SER MET ARG VAL VAL LYS GLU LEU GLU ASP LEU SEQRES 2 A 152 GLN LYS LYS PRO PRO PRO TYR LEU ARG ASN LEU SER SER SEQRES 3 A 152 ASP ASP ALA ASN VAL LEU VAL TRP HIS ALA LEU LEU LEU SEQRES 4 A 152 PRO ASP GLN PRO PRO TYR HIS LEU LYS ALA PHE ASN LEU SEQRES 5 A 152 ARG ILE SER PHE PRO PRO GLU TYR PRO PHE LYS PRO PRO SEQRES 6 A 152 MET ILE LYS PHE THR THR LYS ILE TYR HIS PRO ASN VAL SEQRES 7 A 152 ASP GLU ASN GLY GLN ILE CYS LEU PRO ILE ILE SER SER SEQRES 8 A 152 GLU ASN TRP LYS PRO CYS THR LYS THR CYS GLN VAL LEU SEQRES 9 A 152 GLU ALA LEU ASN VAL LEU VAL ASN ARG PRO ASN ILE ARG SEQRES 10 A 152 GLU PRO LEU ARG MET ASP LEU ALA ASP LEU LEU THR GLN SEQRES 11 A 152 ASN PRO GLU LEU PHE ARG LYS ASN ALA GLU GLU PHE THR SEQRES 12 A 152 LEU ARG PHE GLY VAL ASP ARG PRO SER 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 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 CYS HELIX 1 1 ALA A 2 GLN A 14 1 13 HELIX 2 2 PRO A 44 HIS A 46 5 3 HELIX 3 3 LEU A 86 SER A 90 5 5 HELIX 4 4 LYS A 99 ARG A 113 1 15 HELIX 5 5 ARG A 121 THR A 129 1 9 HELIX 6 6 ASN A 131 LEU A 144 1 14 HELIX 7 7 THR B 22 GLU B 34 1 13 HELIX 8 8 PRO B 37 ASP B 39 5 3 SHEET 1 A 4 LEU A 21 ASP A 27 0 SHEET 2 A 4 ASN A 30 LEU A 38 -1 O LEU A 37 N ARG A 22 SHEET 3 A 4 LYS A 48 SER A 55 -1 O PHE A 50 N LEU A 38 SHEET 4 A 4 MET A 66 PHE A 69 -1 O LYS A 68 N ARG A 53 SHEET 1 B 4 LEU A 21 ASP A 27 0 SHEET 2 B 4 ASN A 30 LEU A 38 -1 O LEU A 37 N ARG A 22 SHEET 3 B 4 LYS A 48 SER A 55 -1 O PHE A 50 N LEU A 38 SHEET 4 B 4 VAL A 148 ASP A 149 -1 O VAL A 148 N ALA A 49 SHEET 1 C 5 THR B 12 GLU B 16 0 SHEET 2 C 5 GLN B 2 THR B 7 -1 N ILE B 3 O LEU B 15 SHEET 3 C 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 C 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 C 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SSBOND 1 CYS A 85 CYS B 76 1555 1555 2.58 CISPEP 1 PRO A 43 PRO A 44 1 -0.43 CISPEP 2 TYR A 60 PRO A 61 1 0.43 CISPEP 3 PRO A 43 PRO A 44 2 -0.08 CISPEP 4 TYR A 60 PRO A 61 2 0.41 CISPEP 5 PRO A 43 PRO A 44 3 0.01 CISPEP 6 TYR A 60 PRO A 61 3 0.06 CISPEP 7 PRO A 43 PRO A 44 4 -0.08 CISPEP 8 TYR A 60 PRO A 61 4 0.39 CISPEP 9 PRO A 43 PRO A 44 5 0.03 CISPEP 10 TYR A 60 PRO A 61 5 0.68 CISPEP 11 PRO A 43 PRO A 44 6 -0.18 CISPEP 12 TYR A 60 PRO A 61 6 0.25 CISPEP 13 PRO A 43 PRO A 44 7 -0.20 CISPEP 14 TYR A 60 PRO A 61 7 0.76 CISPEP 15 PRO A 43 PRO A 44 8 -0.02 CISPEP 16 TYR A 60 PRO A 61 8 0.61 CISPEP 17 PRO A 43 PRO A 44 9 -0.24 CISPEP 18 TYR A 60 PRO A 61 9 0.77 CISPEP 19 PRO A 43 PRO A 44 10 -0.08 CISPEP 20 TYR A 60 PRO A 61 10 0.38 CISPEP 21 PRO A 43 PRO A 44 11 0.13 CISPEP 22 TYR A 60 PRO A 61 11 0.65 CISPEP 23 PRO A 43 PRO A 44 12 0.52 CISPEP 24 TYR A 60 PRO A 61 12 0.53 CISPEP 25 PRO A 43 PRO A 44 13 0.42 CISPEP 26 TYR A 60 PRO A 61 13 0.25 CISPEP 27 PRO A 43 PRO A 44 14 0.02 CISPEP 28 TYR A 60 PRO A 61 14 0.51 CISPEP 29 PRO A 43 PRO A 44 15 0.11 CISPEP 30 TYR A 60 PRO A 61 15 0.50 CISPEP 31 PRO A 43 PRO A 44 16 -0.07 CISPEP 32 TYR A 60 PRO A 61 16 -0.03 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