PDB Short entry for 2LVO HEADER SIGNALING PROTEIN/LIGASE 09-JUL-12 2LVO TITLE STRUCTURE OF THE GP78CUE DOMAIN BOUND TO MONUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE AMFR; COMPND 7 CHAIN: C; COMPND 8 FRAGMENT: CUE DOMAIN RESIDUES 453-504; COMPND 9 SYNONYM: AUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2, AMF RECEPTOR, COMPND 10 ISOFORM 2, RING FINGER PROTEIN 45, GP78; COMPND 11 EC: 6.3.2.-; 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: AMFR, RNF45; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS CUE DOMAIN, SIGNALING PROTEIN-LIGASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.LIU,Y.CHEN,T.HUANG,S.G.TARASOV,A.KING,J.LI,A.M.WEISSMAN,R.A.BYRD, AUTHOR 2 R.DAS REVDAT 3 14-JUN-23 2LVO 1 REMARK REVDAT 2 26-DEC-12 2LVO 1 JRNL REVDAT 1 21-NOV-12 2LVO 0 JRNL AUTH S.LIU,Y.CHEN,J.LI,T.HUANG,S.TARASOV,A.KING,A.M.WEISSMAN, JRNL AUTH 2 R.A.BYRD,R.DAS JRNL TITL PROMISCUOUS INTERACTIONS OF GP78 E3 LIGASE CUE DOMAIN WITH JRNL TITL 2 POLYUBIQUITIN CHAINS. JRNL REF STRUCTURE V. 20 2138 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 23123110 JRNL DOI 10.1016/J.STR.2012.09.020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, X-PLOR NIH REMARK 3 AUTHORS : GODDARD (SPARKY), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL STEP IN WATER REMARK 4 REMARK 4 2LVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000102889. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM TRIS, 50 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D CBCA(CO)NH; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D HNCACB; 2D REMARK 210 1H-13C HSQC AROMATIC; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRPIPE, CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 HZ1 LYS A 63 OE2 GLU A 64 1.59 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 PRO C 469 36.03 -78.91 REMARK 500 1 GLN C 470 -3.51 -140.31 REMARK 500 1 LEU C 482 -74.87 -90.27 REMARK 500 1 GLN C 499 99.79 -67.69 REMARK 500 1 PRO C 501 105.94 -52.44 REMARK 500 2 ARG A 74 -56.90 -138.50 REMARK 500 2 PRO C 469 29.07 -79.46 REMARK 500 2 LEU C 482 -61.83 -98.66 REMARK 500 4 GLN A 62 -168.61 -103.35 REMARK 500 5 ASN C 454 19.53 58.42 REMARK 500 5 SER C 485 114.03 -162.60 REMARK 500 5 PRO C 501 109.11 -59.01 REMARK 500 6 GLN A 62 -166.35 -106.88 REMARK 500 6 PRO C 469 33.05 -85.30 REMARK 500 6 PRO C 501 75.33 -68.98 REMARK 500 6 PRO C 503 107.62 -59.64 REMARK 500 7 GLN A 62 -169.90 -102.60 REMARK 500 7 PRO C 469 37.28 -79.64 REMARK 500 7 GLN C 470 14.98 -148.50 REMARK 500 7 PRO C 503 96.53 -60.96 REMARK 500 8 GLN A 62 -165.76 -101.33 REMARK 500 8 PRO C 501 90.80 -65.20 REMARK 500 8 PRO C 503 96.28 -65.58 REMARK 500 9 GLN A 62 -164.28 -107.02 REMARK 500 9 PRO C 501 99.85 -54.98 REMARK 500 10 ALA A 46 -8.22 70.25 REMARK 500 10 GLN A 62 -166.35 -122.34 REMARK 500 11 GLN A 62 -167.07 -105.17 REMARK 500 11 PRO C 503 97.45 -60.44 REMARK 500 12 LEU C 482 -62.01 -96.34 REMARK 500 13 LYS A 33 -64.81 -92.50 REMARK 500 13 GLN A 62 -157.36 -117.86 REMARK 500 13 PRO C 469 30.87 -90.40 REMARK 500 13 PRO C 501 81.76 -65.88 REMARK 500 14 LYS A 33 -63.46 -91.15 REMARK 500 14 GLN A 62 -163.62 -102.23 REMARK 500 14 PRO C 469 32.08 -79.21 REMARK 500 14 GLN C 470 30.73 -145.59 REMARK 500 15 ALA A 46 -51.79 71.91 REMARK 500 15 PRO C 501 79.38 -65.39 REMARK 500 16 PRO C 501 85.33 -66.12 REMARK 500 17 PRO C 501 102.74 -56.70 REMARK 500 17 PRO C 503 93.85 -66.34 REMARK 500 18 GLN A 62 -160.78 -109.24 REMARK 500 18 ARG A 74 37.59 -90.95 REMARK 500 18 PRO C 501 109.12 -59.42 REMARK 500 19 LYS A 33 -60.32 -100.82 REMARK 500 19 PRO C 501 102.52 -53.93 REMARK 500 19 PRO C 503 73.66 -69.26 REMARK 500 20 PRO C 469 36.83 -81.05 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18582 RELATED DB: BMRB REMARK 900 RELATED ID: 2LVN RELATED DB: PDB REMARK 900 RELATED ID: 2LVP RELATED DB: PDB REMARK 900 RELATED ID: 2LVQ RELATED DB: PDB DBREF 2LVO A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2LVO C 453 504 UNP Q9UKV5 AMFR2_HUMAN 453 504 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 C 52 SER ASN SER GLN LEU ASN ALA MET ALA HIS GLN ILE GLN SEQRES 2 C 52 GLU MET PHE PRO GLN VAL PRO TYR HIS LEU VAL LEU GLN SEQRES 3 C 52 ASP LEU GLN LEU THR ARG SER VAL GLU ILE THR THR ASP SEQRES 4 C 52 ASN ILE LEU GLU GLY ARG ILE GLN VAL PRO PHE PRO THR HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 ASN C 454 GLU C 466 1 13 HELIX 4 4 PRO C 472 GLN C 481 1 10 HELIX 5 5 SER C 485 GLY C 496 1 12 SHEET 1 A 5 ILE A 13 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 LYS A 6 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 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