HEADER SIGNALING PROTEIN 02-AUG-13 2MBO TITLE K11-LINKED DIUBIQUITIN AVERAGE SOLUTION STRUCTURE AT PH 6.8, 0 MM NACL COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-76; COMPND 5 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PJY2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS DIUBIQUITIN, K11, SIGNALING PROTEIN EXPDTA SOLUTION NMR AUTHOR C.A.CASTANEDA,D.FUSHMAN REVDAT 2 14-JUN-23 2MBO 1 REMARK REVDAT 1 04-SEP-13 2MBO 0 JRNL AUTH C.A.CASTANEDA,T.R.KASHYAP,M.A.NAKASONE,S.KRUEGER,D.FUSHMAN JRNL TITL UNIQUE STRUCTURAL, DYNAMICAL, AND FUNCTIONAL PROPERTIES OF JRNL TITL 2 K11-LINKED POLYUBIQUITIN CHAINS. JRNL REF STRUCTURE V. 21 1168 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23823328 JRNL DOI 10.1016/J.STR.2013.04.029 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, IN-HOUSE REMARK 3 AUTHORS : GODDARD (SPARKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: UB/UB ORIENTATION DETERMINED FROM RDCS REMARK 3 VIA ALIGNMENT TENSORS, AND Z-DISTANCE REFINED USING SITE- REMARK 3 DIRECTED SPIN LABELING DISTANCE CONSTRAINTS (MTSL ON DISTAL REMARK 3 POSITION 36) REMARK 4 REMARK 4 2MBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000103448. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 75 UM [U-99% 15N] UBIQUITIN, 20 REMARK 210 MM SODIUM PHOSPHATE, 93% H2O/7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N IPAP HSQC; 2D 1H-15N REMARK 210 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 : SPARKY REMARK 210 METHOD USED : IN-HOUSE RDC (ORIENTATION) AND REMARK 210 MTSL (DISTANCE) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 RES C SSSEQI REMARK 465 LEU A 73 REMARK 465 ARG A 74 REMARK 465 GLY A 75 REMARK 465 GLY A 76 REMARK 465 LEU B 73 REMARK 465 ARG B 74 REMARK 465 GLY B 75 REMARK 465 GLY B 76 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 HG3 ARG A 72 OE1 GLU B 34 0.88 REMARK 500 CZ ARG A 72 O LYS B 33 1.05 REMARK 500 HG2 ARG A 72 HA GLU B 34 1.09 REMARK 500 NE ARG A 72 O LYS B 33 1.30 REMARK 500 H3 MET A 1 O VAL A 17 1.51 REMARK 500 H3 MET B 1 O VAL B 17 1.51 REMARK 500 HE ARG A 72 O LYS B 33 1.55 REMARK 500 CG ARG A 72 HA GLU B 34 1.55 REMARK 500 C ARG A 72 O GLU B 34 1.66 REMARK 500 NH1 ARG A 72 O LYS B 33 1.72 REMARK 500 O ARG A 72 O GLU B 34 1.78 REMARK 500 CG ARG A 72 OE1 GLU B 34 1.91 REMARK 500 NH2 ARG A 72 O LYS B 33 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 54 0.15 SIDE CHAIN REMARK 500 ARG A 72 0.25 SIDE CHAIN REMARK 500 ARG B 54 0.15 SIDE CHAIN REMARK 500 ARG B 72 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19406 RELATED DB: BMRB REMARK 900 RELATED ID: 2MBQ RELATED DB: PDB REMARK 900 K11-LINKED UB2 AVERAGE SOLUTION STRUCTURE IN THE PRESENCE OF NACL REMARK 999 REMARK 999 SEQUENCE REMARK 999 DISTAL UBIQUITIN (CHAIN A) AND PROXIMAL UBIQUITIN (CHAIN B) ARE REMARK 999 CONNECTED VIA A COVALENT LINKAGE BETWEEN C GLY 76 OF CHAIN A AND NZ REMARK 999 LYS 11 OF CHAIN B. THIS LINKAGE HAS NOT BEEN MODELED IN THIS REMARK 999 STRUCTURE. DBREF 2MBO A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2MBO B 1 76 UNP P0CG48 UBC_HUMAN 1 76 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 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 GLY 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 LEU A 56 ASN A 60 5 5 HELIX 4 4 THR B 22 GLY B 35 1 14 HELIX 5 5 PRO B 37 ASP B 39 5 3 HELIX 6 6 LEU B 56 ASN B 60 5 5 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -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 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 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 LYS B 6 -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 PHE B 4 SHEET 4 B 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 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