HEADER SIGNALING PROTEIN 04-DEC-19 6V5D TITLE EROS3 RDC AND NOE DERIVED UBIQUITIN ENSEMBLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS UBIQUITIN, RDC, RESIDUAL DIPOLAR COUPLING, CYTOPLASM, NUCLEUS, UBL KEYWDS 2 CONJUGATION, SIGNALLING PROTEIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 176 AUTHOR O.F.LANGE,N.A.LAKOMEK,C.A.SMITH,C.GRIESINGER,B.L.DE GROOT REVDAT 3 01-MAY-24 6V5D 1 REMARK REVDAT 2 26-FEB-20 6V5D 1 JRNL REVDAT 1 01-JAN-20 6V5D 0 JRNL AUTH C.A.SMITH,A.MAZUR,A.K.ROUT,S.BECKER,D.LEE,B.L.DE GROOT, JRNL AUTH 2 C.GRIESINGER JRNL TITL ENHANCING NMR DERIVED ENSEMBLES WITH KINETICS ON MULTIPLE JRNL TITL 2 TIMESCALES. JRNL REF J.BIOMOL.NMR V. 74 27 2020 JRNL REFN ISSN 0925-2738 JRNL PMID 31838619 JRNL DOI 10.1007/S10858-019-00288-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.F.LANGE,N.A.LAKOMEK,C.FARES,G.F.SCHROEDER,K.F.WALTER, REMARK 1 AUTH 2 S.BECKER,J.MEILER,H.GRUBMUELLER,C.GRIESINGER,B.L.DE GROOT REMARK 1 TITL RECOGNITION DYNAMICS UP TO MICROSECONDS REVEALED FROM AN REMARK 1 TITL 2 RDC-DERIVED UBIQUITIN ENSEMBLE IN SOLUTION. REMARK 1 REF SCIENCE V. 320 1471 2008 REMARK 1 REFN ESSN 1095-9203 REMARK 1 PMID 18556554 REMARK 1 DOI 10.1126/SCIENCE.1157092 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS REMARK 3 AUTHORS : LINDAHL, VAN DER SPOEL, HESS, ABRAHAM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6V5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245530. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 176 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 16 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 19 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 21 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 22 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 22 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 23 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 23 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 23 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 24 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 26 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 26 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 28 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 29 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 29 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 30 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 30 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 31 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 31 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 31 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 32 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 32 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 32 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 33 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 300 ANGLE DEVIATIONS. 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 2 ARG A 74 13.26 58.17 REMARK 500 5 GLU A 64 11.30 58.70 REMARK 500 5 LEU A 73 -143.23 -129.76 REMARK 500 6 GLU A 64 18.13 58.55 REMARK 500 7 LYS A 63 125.24 -36.42 REMARK 500 10 LEU A 73 -51.56 -132.27 REMARK 500 12 LYS A 33 -64.53 -97.51 REMARK 500 14 LEU A 73 -133.41 -116.37 REMARK 500 15 LYS A 63 129.76 -39.17 REMARK 500 15 ARG A 74 -139.29 -122.63 REMARK 500 16 ASP A 52 108.84 -56.56 REMARK 500 16 GLU A 64 10.86 58.28 REMARK 500 20 GLU A 64 16.37 56.64 REMARK 500 21 THR A 9 0.37 -69.17 REMARK 500 23 GLU A 64 8.80 59.91 REMARK 500 24 GLU A 64 12.94 57.93 REMARK 500 33 ARG A 74 37.06 -77.98 REMARK 500 36 LEU A 73 74.67 -117.20 REMARK 500 40 THR A 9 30.90 -76.39 REMARK 500 46 LYS A 63 124.87 -37.89 REMARK 500 46 LEU A 73 24.20 -148.93 REMARK 500 47 LEU A 73 -30.55 58.94 REMARK 500 47 ARG A 74 44.92 -83.27 REMARK 500 53 LEU A 73 -32.63 -132.55 REMARK 500 54 GLU A 64 17.01 57.46 REMARK 500 54 ARG A 72 75.31 -116.05 REMARK 500 55 GLU A 64 17.87 59.01 REMARK 500 55 ARG A 72 62.30 -113.43 REMARK 500 57 ARG A 74 16.17 54.58 REMARK 500 58 LYS A 63 154.66 -47.17 REMARK 500 64 ARG A 74 -32.26 63.61 REMARK 500 65 GLU A 64 -4.88 66.50 REMARK 500 65 ARG A 74 16.52 51.35 REMARK 500 69 ARG A 74 72.09 46.20 REMARK 500 70 LEU A 73 -53.96 -132.91 REMARK 500 74 ARG A 72 50.35 -149.87 REMARK 500 75 LYS A 63 -67.45 50.55 REMARK 500 77 GLU A 64 11.64 59.69 REMARK 500 81 GLU A 64 15.76 59.56 REMARK 500 81 ARG A 74 -71.61 56.08 REMARK 500 82 LYS A 63 150.17 -46.60 REMARK 500 82 GLU A 64 -1.41 63.97 REMARK 500 82 ARG A 74 -11.33 -151.00 REMARK 500 87 GLU A 64 16.97 59.75 REMARK 500 89 LYS A 63 129.19 -39.99 REMARK 500 90 GLU A 64 -4.62 60.60 REMARK 500 90 ARG A 74 9.56 57.76 REMARK 500 91 ARG A 74 -36.73 -133.56 REMARK 500 92 ARG A 72 33.61 -81.40 REMARK 500 94 ARG A 72 57.49 -94.95 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 41 ARG A 42 2 148.63 REMARK 500 GLN A 41 ARG A 42 21 147.36 REMARK 500 VAL A 17 GLU A 18 33 149.80 REMARK 500 GLN A 41 ARG A 42 45 147.17 REMARK 500 GLN A 41 ARG A 42 72 148.79 REMARK 500 GLN A 41 ARG A 42 97 147.98 REMARK 500 GLN A 41 ARG A 42 127 149.02 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 41 ARG A 42 0.09 SIDE CHAIN REMARK 500 48 ARG A 74 0.10 SIDE CHAIN REMARK 500 65 ARG A 54 0.09 SIDE CHAIN REMARK 500 83 ARG A 74 0.09 SIDE CHAIN REMARK 500 88 ARG A 54 0.08 SIDE CHAIN REMARK 500 43 ARG A 42 0.08 SIDE CHAIN REMARK 500 65 ARG A 54 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K39 RELATED DB: PDB REMARK 900 OTHER REFINEMENT WITH SAME EXPERIMENTAL DATA REMARK 900 RELATED ID: 30693 RELATED DB: BMRB REMARK 900 EROS3 RDC AND NOE DERIVED UBIQUITIN ENSEMBLE DBREF 6V5D A 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 HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 CISPEP 1 LYS A 63 GLU A 64 17 -23.47 CISPEP 2 LYS A 63 GLU A 64 122 8.67 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