HEADER LIGASE 14-SEP-22 8EI0 TITLE CRYSTAL STRUCTURE OF THE STUB1 TPR DOMAIN IN COMPLEX WITH H318, A TITLE 2 HELICON POLYPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE CHIP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TPR DOMAIN; COMPND 5 SYNONYM: ANTIGEN NY-CO-7,CLL-ASSOCIATED ANTIGEN KW-8,CARBOXY TERMINUS COMPND 6 OF HSP70-INTERACTING PROTEIN,RING-TYPE E3 UBIQUITIN TRANSFERASE CHIP, COMPND 7 STIP1 HOMOLOGY AND U BOX-CONTAINING PROTEIN 1; COMPND 8 EC: 2.3.2.27; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: H318; COMPND 12 CHAIN: B; COMPND 13 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: STUB1, CHIP, PP1131; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS E3 LIGASE, COMPLEX, STAPLED PEPTIDE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LI,J.-M.SWIECICKI,O.S.TOKAREVA,T.M.THOMSON,G.L.VERDINE,J.H.MCGEE REVDAT 3 16-OCT-24 8EI0 1 REMARK REVDAT 2 15-NOV-23 8EI0 1 JRNL REVDAT 1 25-OCT-23 8EI0 0 JRNL AUTH O.S.TOKAREVA,K.LI,T.L.TRAVALINE,T.M.THOMSON,J.M.SWIECICKI, JRNL AUTH 2 M.MOUSSA,J.D.RAMIREZ,S.LITCHMAN,G.L.VERDINE,J.H.MCGEE JRNL TITL RECOGNITION AND REPROGRAMMING OF E3 UBIQUITIN LIGASE JRNL TITL 2 SURFACES BY ALPHA-HELICAL PEPTIDES. JRNL REF NAT COMMUN V. 14 6992 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37914719 JRNL DOI 10.1038/S41467-023-42395-Z REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 26777 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.7500 - 3.1700 0.97 2632 161 0.1608 0.1918 REMARK 3 2 3.1700 - 2.5100 0.96 2593 140 0.1924 0.1831 REMARK 3 3 2.5100 - 2.2000 0.96 2591 139 0.1871 0.2123 REMARK 3 4 2.2000 - 2.0000 0.95 2513 146 0.1963 0.2166 REMARK 3 5 1.9900 - 1.8500 0.95 2538 148 0.2147 0.2521 REMARK 3 6 1.8500 - 1.7400 0.95 2527 123 0.2275 0.2738 REMARK 3 7 1.7400 - 1.6600 0.95 2552 127 0.2318 0.2661 REMARK 3 8 1.6600 - 1.5800 0.94 2506 117 0.2406 0.2321 REMARK 3 9 1.5800 - 1.5200 0.93 2473 140 0.2726 0.2790 REMARK 3 10 1.5200 - 1.4700 0.93 2490 121 0.3223 0.3360 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8EI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 43.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5NSV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% W/V PEG REMARK 280 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.28000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.48000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.28000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.48000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 304 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 153 REMARK 465 ARG A 154 REMARK 465 NH2 B 17 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 ASN A 130 -75.24 -96.09 REMARK 500 GLU B 15 39.50 -86.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 8EI0 A 23 154 UNP Q9UNE7 CHIP_HUMAN 23 154 DBREF 8EI0 B 5 17 PDB 8EI0 8EI0 5 17 SEQADV 8EI0 GLY A 21 UNP Q9UNE7 EXPRESSION TAG SEQADV 8EI0 ALA A 22 UNP Q9UNE7 EXPRESSION TAG SEQRES 1 A 134 GLY ALA SER PRO SER ALA GLN GLU LEU LYS GLU GLN GLY SEQRES 2 A 134 ASN ARG LEU PHE VAL GLY ARG LYS TYR PRO GLU ALA ALA SEQRES 3 A 134 ALA CYS TYR GLY ARG ALA ILE THR ARG ASN PRO LEU VAL SEQRES 4 A 134 ALA VAL TYR TYR THR ASN ARG ALA LEU CYS TYR LEU LYS SEQRES 5 A 134 MET GLN GLN HIS GLU GLN ALA LEU ALA ASP CYS ARG ARG SEQRES 6 A 134 ALA LEU GLU LEU ASP GLY GLN SER VAL LYS ALA HIS PHE SEQRES 7 A 134 PHE LEU GLY GLN CYS GLN LEU GLU MET GLU SER TYR ASP SEQRES 8 A 134 GLU ALA ILE ALA ASN LEU GLN ARG ALA TYR SER LEU ALA SEQRES 9 A 134 LYS GLU GLN ARG LEU ASN PHE GLY ASP ASP ILE PRO SER SEQRES 10 A 134 ALA LEU ARG ILE ALA LYS LYS LYS ARG TRP ASN SER ILE SEQRES 11 A 134 GLU GLU ARG ARG SEQRES 1 B 13 ACE PRO CYS TYR GLU ALA TRP VAL LEU CYS GLU TYR NH2 HET ACE B 5 3 HET SO4 A 201 5 HET SO4 A 202 5 HET WHL B 101 14 HET EDO B 102 4 HETNAM ACE ACETYL GROUP HETNAM SO4 SULFATE ION HETNAM WHL N,N'-(1,4-PHENYLENE)DIACETAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ACE C2 H4 O FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 WHL C10 H12 N2 O2 FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *130(H2 O) HELIX 1 AA1 SER A 25 GLY A 39 1 15 HELIX 2 AA2 LYS A 41 ASN A 56 1 16 HELIX 3 AA3 VAL A 59 MET A 73 1 15 HELIX 4 AA4 GLN A 75 ASP A 90 1 16 HELIX 5 AA5 SER A 93 MET A 107 1 15 HELIX 6 AA6 SER A 109 ARG A 128 1 20 HELIX 7 AA7 ASP A 133 GLU A 152 1 20 HELIX 8 AA8 CYS B 7 CYS B 14 1 8 LINK C ACE B 5 N PRO B 6 1555 1555 1.33 LINK SG CYS B 7 CH WHL B 101 1555 1555 1.83 LINK SG CYS B 14 CK WHL B 101 1555 1555 1.75 CRYST1 82.560 46.960 53.620 90.00 126.48 90.00 C 1 2 1 4 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 0.012112 0.000000 0.008956 0.00000 SCALE2 0.000000 0.021295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023194 0.00000