PDB Short entry for 2PE9 HEADER SIGNALING PROTEIN 02-APR-07 2PE9 TITLE NMR BASED STRUCTURE OF THE OPEN CONFORMATION OF LYS48-LINKED DI- TITLE 2 UBIQUITIN USING EXPERIMENTAL GLOBAL ROTATIONAL DIFFUSION TENSOR FROM TITLE 3 NMR RELAXATION MEASUREMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UBIQUITIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, LYS48-LINKED POLYUBIQUITIN, POLYUBIQUITIN, SIGNALING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR AUTHOR Y.RYABOV,D.FUSHMAN REVDAT 3 16-MAR-22 2PE9 1 REMARK REVDAT 2 24-FEB-09 2PE9 1 VERSN REVDAT 1 10-JUL-07 2PE9 0 JRNL AUTH Y.RYABOV,D.FUSHMAN JRNL TITL STRUCTURAL ASSEMBLY OF MULTIDOMAIN PROTEINS AND PROTEIN JRNL TITL 2 COMPLEXES GUIDED BY THE OVERALL ROTATIONAL DIFFUSION TENSOR. JRNL REF J.AM.CHEM.SOC. V. 129 7894 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17550252 JRNL DOI 10.1021/JA071185D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.RYABOV,C.GERAGHTY,A.VARSHNEY,D.FUSHMAN REMARK 1 TITL AN EFFICIENT COMPUTATIONAL METHOD FOR PREDICTING ROTATIONAL REMARK 1 TITL 2 DIFFUSION TENSORS OF GLOBULAR PROTEINS USING AN ELLIPSOID REMARK 1 TITL 3 REPRESENTATION. REMARK 1 REF J.AM.CHEM.SOC. V. 128 15432 2006 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 17132010 REMARK 1 DOI 10.1021/JA062715T REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.RYABOV,D.FUSHMAN REMARK 1 TITL A MODEL OF INTERDOMAIN MOBILITY IN A MULTIDOMAIN PROTEIN REMARK 1 REF J.AM.CHEM.SOC. V. 129 3315 2007 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 17319663 REMARK 1 DOI 10.1021/JA067667R REMARK 1 REFERENCE 3 REMARK 1 AUTH R.VARADAN,O.WALKER,C.PICART,D.FUSHMAN REMARK 1 TITL STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN SOLUTION REMARK 1 REF J.MOL.BIOL. V. 324 637 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12460567 REMARK 1 DOI 10.1016/S0022-2836(02)01198-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ELM, ELM REMARK 3 AUTHORS : Y.RYABOV, D.FUSHMAN (ELM) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS DETERMINED WITH REMARK 3 PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- REMARK 3 UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND REMARK 3 POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE REMARK 3 MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY REMARK 3 ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF REMARK 3 THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN REMARK 3 POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY REMARK 3 TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED REMARK 3 ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS. REMARK 3 FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER REMARK 3 OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION REMARK 3 REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE REMARK 3 CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION REMARK 3 PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 10%. CHAIN A REMARK 3 CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN REMARK 3 DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN REMARK 3 DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C- REMARK 3 TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS REMARK 3 PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER, REMARK 3 BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION REMARK 3 AND TRANSLATION AND NO CONSTRAINTS REPRESENTING REMARK 3 THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE REMARK 3 IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH REMARK 3 UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR REMARK 3 DATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE. REMARK 4 REMARK 4 2PE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : DI-UBIQUITIN, 90% WATER/10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N T1; 15N T2; HETERONUCLEAR REMARK 210 NOE; HSQC; TOCSY 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 : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 CE1 HIS A 68 HD12 LEU B 71 0.42 REMARK 500 O ALA A 46 CB GLN B 40 0.43 REMARK 500 CD LYS A 6 OG1 THR B 9 0.46 REMARK 500 HB2 LYS A 6 HG22 THR B 9 0.58 REMARK 500 HB3 LYS A 6 HG21 THR B 9 0.58 REMARK 500 CB LYS A 6 HG22 THR B 9 0.60 REMARK 500 C ALA A 46 HB3 GLN B 40 0.61 REMARK 500 HB3 LYS A 6 CG2 THR B 9 0.67 REMARK 500 CB LYS A 48 HE21 GLN B 40 0.68 REMARK 500 HZ PHE A 45 O GLY B 35 0.69 REMARK 500 HE2 PHE A 45 HD3 PRO B 37 0.75 REMARK 500 HD1 HIS A 68 HD13 LEU B 71 0.77 REMARK 500 CB LYS A 6 CG2 THR B 9 0.83 REMARK 500 HG2 LYS A 6 HB THR B 9 0.86 REMARK 500 HB2 LYS A 48 HE22 GLN B 40 0.87 REMARK 500 HB2 LYS A 48 NE2 GLN B 40 0.88 REMARK 500 C GLY A 47 O ARG B 72 0.89 REMARK 500 HE3 LYS A 6 HG1 THR B 9 0.90 REMARK 500 HA2 GLY A 47 H ARG B 72 0.92 REMARK 500 C ALA A 46 CB GLN B 40 0.95 REMARK 500 N GLY A 47 HB3 GLN B 40 0.98 REMARK 500 HG3 LYS A 48 HG2 GLN B 40 1.00 REMARK 500 CE LYS A 6 HG1 THR B 9 1.02 REMARK 500 HB2 LYS A 48 HE21 GLN B 40 1.02 REMARK 500 HB3 ALA A 46 HD2 PRO B 37 1.04 REMARK 500 HE1 HIS A 68 HD12 LEU B 71 1.08 REMARK 500 HZ PHE A 45 C GLY B 35 1.09 REMARK 500 O PHE A 45 OE1 GLN B 40 1.12 REMARK 500 ND1 HIS A 68 CD1 LEU B 71 1.12 REMARK 500 O ALA A 46 CA GLN B 40 1.13 REMARK 500 CG LYS A 48 HE21 GLN B 40 1.15 REMARK 500 O GLY A 47 O ARG B 72 1.16 REMARK 500 HG3 LYS A 48 CG GLN B 40 1.17 REMARK 500 HD3 LYS A 6 OG1 THR B 9 1.18 REMARK 500 CE2 PHE A 45 HD3 PRO B 37 1.19 REMARK 500 O ALA A 46 HB2 GLN B 40 1.21 REMARK 500 HE2 LYS A 6 HG1 THR B 7 1.22 REMARK 500 HB2 LYS A 6 CG2 THR B 9 1.24 REMARK 500 ND1 HIS A 68 HD11 LEU B 71 1.25 REMARK 500 ND1 HIS A 68 HD12 LEU B 71 1.28 REMARK 500 C ALA A 46 HB2 GLN B 40 1.29 REMARK 500 ND1 HIS A 68 HD13 LEU B 71 1.29 REMARK 500 CG HIS A 68 HD11 LEU B 71 1.30 REMARK 500 HD3 LYS A 6 CB THR B 9 1.31 REMARK 500 HB1 ALA A 46 HG22 ILE B 36 1.35 REMARK 500 CB LYS A 6 HG21 THR B 9 1.35 REMARK 500 CG LYS A 6 OG1 THR B 9 1.36 REMARK 500 CD LYS A 6 HG1 THR B 9 1.36 REMARK 500 HA2 GLY A 47 N ARG B 72 1.37 REMARK 500 CE LYS A 6 OG1 THR B 9 1.38 REMARK 500 REMARK 500 THIS ENTRY HAS 85 CLOSE CONTACTS 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: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1AAR RELATED DB: PDB REMARK 900 DI-UBIQUITIN REMARK 900 RELATED ID: 2BGF RELATED DB: PDB REMARK 900 DI-UBIQUITIN REMARK 900 RELATED ID: 2PEA RELATED DB: PDB REMARK 900 DI-UBIQUITIN DBREF 2PE9 A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2PE9 B 1 76 UNP P62988 UBIQ_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