HEADER LIGASE 18-NOV-24 9HFV TITLE MYD88 PEPTIDE_2 BOUND TO SPOP MATH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECKLE-TYPE POZ PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIB HOMOLOG 1,ROADKILL HOMOLOG 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88; COMPND 8 CHAIN: B; COMPND 9 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: SPOP; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS UBIQUITINATION, LIGASE, IMMUNE SIGNALLING, DEGRADATION EXPDTA X-RAY DIFFRACTION AUTHOR L.MAKHLOUF,E.ZEQIRAJ REVDAT 2 23-JUL-25 9HFV 1 JRNL REVDAT 1 18-JUN-25 9HFV 0 JRNL AUTH L.MAKHLOUF,M.MISHRA,H.MAKHLOUF,I.MANFIELD,L.BUSINO,E.ZEQIRAJ JRNL TITL SEQUENCE RULES FOR A LONG SPOP-BINDING DEGRON REQUIRED FOR JRNL TITL 2 PROTEIN UBIQUITYLATION. JRNL REF BIOCHEM.J. V. 482 583 2025 JRNL REFN ESSN 1470-8728 JRNL PMID 40178506 JRNL DOI 10.1042/BCJ20253041 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1222 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 33.3900 - 3.0200 1.00 2882 117 0.1726 0.2345 REMARK 3 2 3.0200 - 2.3900 1.00 2729 127 0.1763 0.2352 REMARK 3 3 2.3900 - 2.0900 1.00 2708 116 0.1536 0.1751 REMARK 3 4 2.0900 - 1.9000 1.00 2673 135 0.1470 0.1885 REMARK 3 5 1.9000 - 1.7600 1.00 2669 160 0.1487 0.1950 REMARK 3 6 1.7600 - 1.6600 1.00 2618 134 0.1467 0.2158 REMARK 3 7 1.6600 - 1.5800 1.00 2662 141 0.1487 0.2201 REMARK 3 8 1.5800 - 1.5100 1.00 2628 156 0.1489 0.2001 REMARK 3 9 1.5100 - 1.4500 0.99 2598 136 0.1745 0.2286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.141 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.842 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.88 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 : 0.010 1233 REMARK 3 ANGLE : 1.030 1663 REMARK 3 CHIRALITY : 0.091 184 REMARK 3 PLANARITY : 0.008 210 REMARK 3 DIHEDRAL : 5.875 164 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 9HFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1292141619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-24 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25391 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 41.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 20,000, 20% V/V PEG MME REMARK 280 550, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM CHLORIDE, 0.1 M REMARK 280 MOPS/HEPES-NA PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.91500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.62000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.62000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.91500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.54000 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: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 VAL B 9 REMARK 465 PRO B 10 REMARK 465 ARG B 11 REMARK 465 THR B 12 REMARK 465 ALA B 13 REMARK 465 GLU B 14 REMARK 465 LEU B 15 REMARK 465 ALA B 16 REMARK 465 GLY B 17 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 492 O HOH A 536 4555 2.13 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 CYS A 93 114.24 -161.03 REMARK 500 GLN A 120 -55.31 74.69 REMARK 500 LYS A 135 67.99 -116.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 9HFV A 28 166 UNP O43791 SPOP_HUMAN 28 166 DBREF 9HFV B -2 17 UNP Q99836 MYD88_HUMAN 127 146 SEQADV 9HFV ALA A 26 UNP O43791 EXPRESSION TAG SEQADV 9HFV PRO A 27 UNP O43791 EXPRESSION TAG SEQRES 1 A 141 ALA PRO LYS VAL VAL LYS PHE SER TYR MET TRP THR ILE SEQRES 2 A 141 ASN ASN PHE SER PHE CYS ARG GLU GLU MET GLY GLU VAL SEQRES 3 A 141 ILE LYS SER SER THR PHE SER SER GLY ALA ASN ASP LYS SEQRES 4 A 141 LEU LYS TRP CYS LEU ARG VAL ASN PRO LYS GLY LEU ASP SEQRES 5 A 141 GLU GLU SER LYS ASP TYR LEU SER LEU TYR LEU LEU LEU SEQRES 6 A 141 VAL SER CYS PRO LYS SER GLU VAL ARG ALA LYS PHE LYS SEQRES 7 A 141 PHE SER ILE LEU ASN ALA LYS GLY GLU GLU THR LYS ALA SEQRES 8 A 141 MET GLU SER GLN ARG ALA TYR ARG PHE VAL GLN GLY LYS SEQRES 9 A 141 ASP TRP GLY PHE LYS LYS PHE ILE ARG ARG ASP PHE LEU SEQRES 10 A 141 LEU ASP GLU ALA ASN GLY LEU LEU PRO ASP ASP LYS LEU SEQRES 11 A 141 THR LEU PHE CYS GLU VAL SER VAL VAL GLN ASP SEQRES 1 B 20 LYS PRO LEU GLN VAL ALA ALA VAL ASP SER SER VAL PRO SEQRES 2 B 20 ARG THR ALA GLU LEU ALA GLY FORMUL 3 HOH *169(H2 O) HELIX 1 AA1 ASN A 40 CYS A 44 5 5 HELIX 2 AA2 ASP A 77 LYS A 81 5 5 HELIX 3 AA3 ARG A 139 LEU A 143 1 5 HELIX 4 AA4 ASP A 144 GLY A 148 5 5 HELIX 5 AA5 LEU A 150 LYS A 154 5 5 SHEET 1 AA1 4 LYS A 28 ILE A 38 0 SHEET 2 AA1 4 LEU A 155 GLN A 165 -1 O GLN A 165 N LYS A 28 SHEET 3 AA1 4 VAL A 98 LEU A 107 -1 N ARG A 99 O VAL A 164 SHEET 4 AA1 4 GLU A 113 GLU A 118 -1 O THR A 114 N ILE A 106 SHEET 1 AA2 4 LYS A 28 ILE A 38 0 SHEET 2 AA2 4 LEU A 155 GLN A 165 -1 O GLN A 165 N LYS A 28 SHEET 3 AA2 4 VAL A 98 LEU A 107 -1 N ARG A 99 O VAL A 164 SHEET 4 AA2 4 TYR A 123 PHE A 125 -1 O PHE A 125 N VAL A 98 SHEET 1 AA3 4 ILE A 52 LYS A 53 0 SHEET 2 AA3 4 LYS A 66 ASN A 72 -1 O VAL A 71 N ILE A 52 SHEET 3 AA3 4 TYR A 83 SER A 92 -1 O LEU A 89 N CYS A 68 SHEET 4 AA3 4 ASP A 130 ARG A 138 -1 O TRP A 131 N LEU A 88 CRYST1 39.830 57.080 61.240 90.00 90.00 90.00 P 21 21 21 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 0.025107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016329 0.00000 MASTER 268 0 0 5 12 0 0 6 1369 2 0 13 END