HEADER PROTEIN BINDING 10-DEC-19 6V88 TITLE SOLUTION NMR STRUCTURE OF DICTYOSTELIUM DISCOIDEUM SKP1A (TRUNCATED) TITLE 2 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCF UBIQUITIN LIGASE COMPLEX PROTEIN SKP1A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLYCOPROTEIN FP21 ISOFORM A,GLYCOPROTEIN FP21 ISOFORM A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: FPAA, FP21A, FPA1, FPA1A, SKP1A, DDB_G0269230; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN LIGASE E3 SCF COMPLEX SKP1, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.W.KIM,A.ELETSKY,C.M.WEST REVDAT 4 14-JUN-23 6V88 1 REMARK REVDAT 3 16-MAR-22 6V88 1 REMARK REVDAT 2 06-MAY-20 6V88 1 JRNL REVDAT 1 15-APR-20 6V88 0 JRNL AUTH H.W.KIM,A.ELETSKY,K.J.GONZALEZ,H.VAN DER WEL,E.M.STRAUCH, JRNL AUTH 2 J.H.PRESTEGARD,C.M.WEST JRNL TITL SKP1 DIMERIZATION CONCEALS ITS F-BOX PROTEIN BINDING SITE. JRNL REF BIOCHEMISTRY V. 59 1527 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32227851 JRNL DOI 10.1021/ACS.BIOCHEM.0C00094 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN EXPLICIT WATER BATH REMARK 4 REMARK 4 6V88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245188. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-90% 13C; U-90% 15N] REMARK 210 DDSKP1, 50 MM MES, 50 MM NACL, 5 REMARK 210 MM DTT, 0.05 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D [15N, 1H]-HSQC; 2D [13C, 1H] REMARK 210 CT-HSQC ALIPHATIC; 2D [13C, 1H] REMARK 210 CT-HSQC AROMATIC; 3D 13C/15N- REMARK 210 EDITED [1H,1H] NOESY; 3D TROSY- REMARK 210 HNCACB; 3D (H)CCH-COSY AROMATIC; REMARK 210 3D (H)CCH-COSY ALIPHATIC; 3D (H) REMARK 210 CCH-TOCSY ALIPHATIC; 3D 13C/15N- REMARK 210 FILTERED 13C/15N-EDITED [1H,1H] REMARK 210 NOESY; 3D CBCA(CO)NH; 3D HBHA(CO) REMARK 210 NH; 3D HNCO; 3D (HCA)CONH; 2D REMARK 210 LONG-RANGE [15N, 1H]-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; VNMRS REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, CARA, CYANA, REMARK 210 VNMR, TALOS, PSVS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 20 ILE A 73 N ILE A 73 CA 0.144 REMARK 500 20 GLY B 69 N GLY B 69 CA 0.094 REMARK 500 20 GLY B 69 CA GLY B 69 C 0.108 REMARK 500 20 ASP B 72 CA ASP B 72 C 0.188 REMARK 500 20 ILE B 73 N ILE B 73 CA 0.150 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 GLU A 36 97.68 -60.88 REMARK 500 1 ASN A 45 -50.21 -160.61 REMARK 500 1 PRO A 65 100.00 -55.95 REMARK 500 1 LEU A 70 -74.65 -79.71 REMARK 500 1 GLU B 36 97.02 -62.63 REMARK 500 1 ASN B 45 -48.91 -158.85 REMARK 500 1 PRO B 65 96.83 -57.39 REMARK 500 1 LEU B 70 -72.73 -79.49 REMARK 500 2 GLU A 11 -1.11 74.03 REMARK 500 2 GLU A 36 89.71 -66.81 REMARK 500 2 PRO A 65 95.48 -66.27 REMARK 500 2 ASP A 72 -62.43 -146.27 REMARK 500 2 ILE A 73 87.90 47.75 REMARK 500 2 GLU B 11 -1.26 75.42 REMARK 500 2 GLU B 36 89.83 -67.12 REMARK 500 2 ASN B 45 -60.22 -98.72 REMARK 500 2 PRO B 65 95.73 -66.85 REMARK 500 2 ASP B 72 -63.38 -146.08 REMARK 500 2 ILE B 73 87.70 48.88 REMARK 500 3 GLU A 36 99.08 -163.79 REMARK 500 3 ASP A 71 -58.87 172.09 REMARK 500 3 ASP A 99 73.91 50.32 REMARK 500 3 GLU B 36 97.38 -162.98 REMARK 500 3 ASP B 71 -57.09 173.78 REMARK 500 3 ASP B 99 74.98 50.14 REMARK 500 4 GLU A 11 -1.16 75.27 REMARK 500 4 ASN A 45 -66.58 -166.75 REMARK 500 4 ASP A 72 -30.20 84.31 REMARK 500 4 ILE A 73 104.86 63.42 REMARK 500 4 GLU B 11 -0.62 75.09 REMARK 500 4 ASN B 45 -66.43 -167.89 REMARK 500 4 ASP B 72 -31.54 85.87 REMARK 500 4 ILE B 73 104.61 64.39 REMARK 500 5 PRO A 44 42.30 -82.78 REMARK 500 5 ASN A 45 -57.61 -142.73 REMARK 500 5 PRO B 44 42.34 -82.06 REMARK 500 5 ASN B 45 -56.84 -142.54 REMARK 500 6 GLU A 36 127.50 76.27 REMARK 500 6 ASN A 45 -57.24 -169.12 REMARK 500 6 ASP A 71 -31.22 -179.88 REMARK 500 6 ILE A 73 88.11 59.60 REMARK 500 6 GLU B 36 128.21 76.07 REMARK 500 6 ASN B 45 -57.38 -166.91 REMARK 500 6 ASP B 71 -31.43 -178.46 REMARK 500 6 ILE B 73 88.49 58.61 REMARK 500 7 GLU A 11 -2.39 74.07 REMARK 500 7 LEU A 70 84.70 -66.72 REMARK 500 7 GLU B 11 -2.31 72.63 REMARK 500 7 LEU B 70 85.10 -65.94 REMARK 500 8 GLU A 36 116.52 75.63 REMARK 500 REMARK 500 THIS ENTRY HAS 171 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 LEU A 70 ASP A 71 20 144.02 REMARK 500 LEU B 70 ASP B 71 20 131.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30696 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF DICTYOSTELIUM DISCOIDEUM SKP1A (TRUNCATED) REMARK 900 DIMER DBREF 6V88 A 2 65 UNP P52285 SKP1A_DICDI 2 65 DBREF 6V88 A 70 117 UNP P52285 SKP1A_DICDI 78 125 DBREF 6V88 B 2 65 UNP P52285 SKP1A_DICDI 2 65 DBREF 6V88 B 70 117 UNP P52285 SKP1A_DICDI 78 125 SEQADV 6V88 GLY A 66 UNP P52285 LINKER SEQADV 6V88 GLY A 67 UNP P52285 LINKER SEQADV 6V88 SER A 68 UNP P52285 LINKER SEQADV 6V88 GLY A 69 UNP P52285 LINKER SEQADV 6V88 GLY B 66 UNP P52285 LINKER SEQADV 6V88 GLY B 67 UNP P52285 LINKER SEQADV 6V88 SER B 68 UNP P52285 LINKER SEQADV 6V88 GLY B 69 UNP P52285 LINKER SEQRES 1 A 116 SER LEU VAL LYS LEU GLU SER SER ASP GLU LYS VAL PHE SEQRES 2 A 116 GLU ILE GLU LYS GLU ILE ALA CYS MET SER VAL THR ILE SEQRES 3 A 116 LYS ASN MET ILE GLU ASP ILE GLY GLU SER ASP SER PRO SEQRES 4 A 116 ILE PRO LEU PRO ASN VAL THR SER THR ILE LEU GLU LYS SEQRES 5 A 116 VAL LEU ASP TYR CYS ARG HIS HIS HIS GLN HIS PRO GLY SEQRES 6 A 116 GLY SER GLY LEU ASP ASP ILE PRO PRO TYR ASP ARG ASP SEQRES 7 A 116 PHE CYS LYS VAL ASP GLN PRO THR LEU PHE GLU LEU ILE SEQRES 8 A 116 LEU ALA ALA ASN TYR LEU ASP ILE LYS PRO LEU LEU ASP SEQRES 9 A 116 VAL THR CYS LYS THR VAL ALA ASN MET ILE ARG GLY SEQRES 1 B 116 SER LEU VAL LYS LEU GLU SER SER ASP GLU LYS VAL PHE SEQRES 2 B 116 GLU ILE GLU LYS GLU ILE ALA CYS MET SER VAL THR ILE SEQRES 3 B 116 LYS ASN MET ILE GLU ASP ILE GLY GLU SER ASP SER PRO SEQRES 4 B 116 ILE PRO LEU PRO ASN VAL THR SER THR ILE LEU GLU LYS SEQRES 5 B 116 VAL LEU ASP TYR CYS ARG HIS HIS HIS GLN HIS PRO GLY SEQRES 6 B 116 GLY SER GLY LEU ASP ASP ILE PRO PRO TYR ASP ARG ASP SEQRES 7 B 116 PHE CYS LYS VAL ASP GLN PRO THR LEU PHE GLU LEU ILE SEQRES 8 B 116 LEU ALA ALA ASN TYR LEU ASP ILE LYS PRO LEU LEU ASP SEQRES 9 B 116 VAL THR CYS LYS THR VAL ALA ASN MET ILE ARG GLY HELIX 1 AA1 LYS A 18 CYS A 22 1 5 HELIX 2 AA2 SER A 24 GLY A 35 1 12 HELIX 3 AA3 THR A 47 HIS A 64 1 18 HELIX 4 AA4 PRO A 74 LYS A 82 1 9 HELIX 5 AA5 ASP A 84 LEU A 98 1 15 HELIX 6 AA6 ILE A 100 GLY A 117 1 18 HELIX 7 AA7 LYS B 18 CYS B 22 1 5 HELIX 8 AA8 SER B 24 GLY B 35 1 12 HELIX 9 AA9 THR B 47 HIS B 64 1 18 HELIX 10 AB1 PRO B 74 LYS B 82 1 9 HELIX 11 AB2 ASP B 84 LEU B 98 1 15 HELIX 12 AB3 ILE B 100 GLY B 117 1 18 SHEET 1 AA1 2 LEU A 3 GLU A 7 0 SHEET 2 AA1 2 VAL A 13 GLU A 17 -1 O ILE A 16 N VAL A 4 SHEET 1 AA2 2 LEU B 3 GLU B 7 0 SHEET 2 AA2 2 VAL B 13 GLU B 17 -1 O ILE B 16 N VAL B 4 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