HEADER LIGASE 10-FEB-23 8G4Y TITLE STRUCTURE OF ZNRF3 ECD BOUND TO PEPTIDE MK1-3.6.10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RING FINGER PROTEIN 203,RING-TYPE E3 UBIQUITIN TRANSFERASE COMPND 5 ZNRF3,ZINC/RING FINGER PROTEIN 3; COMPND 6 EC: 2.3.2.27; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MK1-3.6.10; COMPND 10 CHAIN: B; COMPND 11 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: ZNRF3, KIAA1133, RNF203; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS UBIQUITIN LIGASE, WNT SIGNAL, CELL SURFACE, CKP, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.F.HARRIS,P.WU REVDAT 1 20-DEC-23 8G4Y 0 JRNL AUTH Y.T.KSCHONSAK,X.GAO,S.E.MILLER,S.HWANG,H.MAREI,P.WU,Y.LI, JRNL AUTH 2 K.RUIZ,K.DORIGHI,L.HOLOKAI,P.PERAMPALAM,W.K.TSAI,Y.S.KEE, JRNL AUTH 3 N.J.AGARD,S.F.HARRIS,R.N.HANNOUSH,F.DE SOUSA E MELO JRNL TITL POTENT AND SELECTIVE BINDERS OF THE E3 UBIQUITIN LIGASE JRNL TITL 2 ZNRF3 STIMULATE WNT SIGNALING AND INTESTINAL ORGANOID JRNL TITL 3 GROWTH. JRNL REF CELL CHEM BIOL 2023 JRNL REFN ESSN 2451-9456 JRNL PMID 38056465 JRNL DOI 10.1016/J.CHEMBIOL.2023.11.006 REMARK 2 REMARK 2 RESOLUTION. 1.41 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 3 NUMBER OF REFLECTIONS : 35592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1715 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 32.0200 - 3.2300 0.94 3262 159 0.1866 0.2094 REMARK 3 2 3.2300 - 2.5700 0.98 3355 151 0.2106 0.2162 REMARK 3 3 2.5600 - 2.2400 0.98 3318 149 0.2125 0.2298 REMARK 3 4 2.2400 - 2.0400 0.98 3228 209 0.2098 0.2411 REMARK 3 5 2.0400 - 1.8900 0.97 3283 142 0.2304 0.2562 REMARK 3 6 1.8900 - 1.7800 0.97 3227 182 0.2285 0.2770 REMARK 3 7 1.7800 - 1.6900 0.97 3260 155 0.2331 0.2548 REMARK 3 8 1.6900 - 1.6200 0.97 3207 162 0.2468 0.2720 REMARK 3 9 1.6200 - 1.5500 0.92 3051 159 0.2729 0.3018 REMARK 3 10 1.5500 - 1.5000 0.72 2375 130 0.3152 0.3471 REMARK 3 11 1.5000 - 1.4500 0.51 1679 90 0.3737 0.4280 REMARK 3 12 1.4500 - 1.4100 0.19 632 27 0.4558 0.4176 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 NULL REMARK 3 ANGLE : 0.916 NULL REMARK 3 CHIRALITY : 0.087 228 REMARK 3 PLANARITY : 0.009 279 REMARK 3 DIHEDRAL : 13.252 590 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 8G4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 2.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.036 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 46.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.74800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 4.5, 20% PEG REMARK 280 4000 PLUS SILVER BULLET A5 (HAMPTON RESEARCH), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 67.77550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.61300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.77550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.61300 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 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 GLY A 53 REMARK 465 PRO A 209 REMARK 465 PRO A 210 REMARK 465 ARG A 211 REMARK 465 GLN A 212 REMARK 465 PRO A 213 REMARK 465 THR A 214 REMARK 465 GLU A 215 REMARK 465 TYR A 216 REMARK 465 PHE A 217 REMARK 465 ASP A 218 REMARK 465 MET A 219 REMARK 465 GLY A 220 REMARK 465 ASN A 221 REMARK 465 SER A 222 REMARK 465 ASP A 223 REMARK 465 TYR A 224 REMARK 465 LYS A 225 REMARK 465 ASP A 226 REMARK 465 ASP A 227 REMARK 465 ASP A 228 REMARK 465 ASP A 229 REMARK 465 LYS A 230 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 PRO B 39 C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 108 O HOH B 113 1.97 REMARK 500 O HOH A 367 O HOH A 390 2.06 REMARK 500 O HOH A 387 O HOH A 407 2.07 REMARK 500 O HOH B 111 O HOH B 123 2.17 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 ASN B 18 -46.42 75.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 8G4Y A 56 220 UNP Q9ULT6 ZNRF3_HUMAN 56 220 DBREF 8G4Y B 1 39 PDB 8G4Y 8G4Y 1 39 SEQADV 8G4Y GLY A 53 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y SER A 54 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y THR A 55 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASN A 221 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y SER A 222 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASP A 223 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y TYR A 224 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y LYS A 225 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASP A 226 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASP A 227 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASP A 228 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y ASP A 229 UNP Q9ULT6 EXPRESSION TAG SEQADV 8G4Y LYS A 230 UNP Q9ULT6 EXPRESSION TAG SEQRES 1 A 178 GLY SER THR LYS GLU THR ALA PHE VAL GLU VAL VAL LEU SEQRES 2 A 178 PHE GLU SER SER PRO SER GLY ASP TYR THR THR TYR THR SEQRES 3 A 178 THR GLY LEU THR GLY ARG PHE SER ARG ALA GLY ALA THR SEQRES 4 A 178 LEU SER ALA GLU GLY GLU ILE VAL GLN MET HIS PRO LEU SEQRES 5 A 178 GLY LEU CYS ASN ASN ASN ASP GLU GLU ASP LEU TYR GLU SEQRES 6 A 178 TYR GLY TRP VAL GLY VAL VAL LYS LEU GLU GLN PRO GLU SEQRES 7 A 178 LEU ASP PRO LYS PRO CYS LEU THR VAL LEU GLY LYS ALA SEQRES 8 A 178 LYS ARG ALA VAL GLN ARG GLY ALA THR ALA VAL ILE PHE SEQRES 9 A 178 ASP VAL SER GLU ASN PRO GLU ALA ILE ASP GLN LEU ASN SEQRES 10 A 178 GLN GLY SER GLU ASP PRO LEU LYS ARG PRO VAL VAL TYR SEQRES 11 A 178 VAL LYS GLY ALA ASP ALA ILE LYS LEU MET ASN ILE VAL SEQRES 12 A 178 ASN LYS GLN LYS VAL ALA ARG ALA ARG ILE GLN HIS ARG SEQRES 13 A 178 PRO PRO ARG GLN PRO THR GLU TYR PHE ASP MET GLY ASN SEQRES 14 A 178 SER ASP TYR LYS ASP ASP ASP ASP LYS SEQRES 1 B 39 GLY CYS ASN ARG LEU ASN LYS LYS CYS ASN SER ASP ALA SEQRES 2 B 39 ASP CYS CYS ALA ASN LYS GLU LYS CYS GLU ARG PRO ILE SEQRES 3 B 39 GLY TRP LYS PHE MET TYR CYS ARG PRO ASP VAL GLY PRO FORMUL 3 HOH *141(H2 O) HELIX 1 AA1 HIS A 102 ASN A 108 1 7 HELIX 2 AA2 GLU A 112 TYR A 116 5 5 HELIX 3 AA3 GLN A 128 ASP A 132 5 5 HELIX 4 AA4 THR A 138 ARG A 149 1 12 HELIX 5 AA5 PRO A 162 GLN A 170 1 9 HELIX 6 AA6 LYS A 184 ASN A 196 1 13 HELIX 7 AA7 SER B 11 CYS B 15 5 5 SHEET 1 AA1 8 THR A 58 SER A 68 0 SHEET 2 AA1 8 TYR A 74 PHE A 85 -1 O THR A 75 N GLU A 67 SHEET 3 AA1 8 VAL A 180 VAL A 183 -1 O TYR A 182 N ARG A 84 SHEET 4 AA1 8 ALA A 151 ASP A 157 1 N VAL A 154 O VAL A 181 SHEET 5 AA1 8 TRP A 120 LYS A 125 1 N TRP A 120 O THR A 152 SHEET 6 AA1 8 ALA A 94 GLN A 100 1 N GLU A 97 O VAL A 121 SHEET 7 AA1 8 ALA A 201 HIS A 207 -1 O ILE A 205 N ALA A 94 SHEET 8 AA1 8 THR A 58 SER A 68 -1 N PHE A 60 O GLN A 206 SHEET 1 AA2 2 GLU B 20 GLU B 23 0 SHEET 2 AA2 2 TYR B 32 PRO B 35 -1 O TYR B 32 N GLU B 23 SSBOND 1 CYS A 107 CYS A 136 1555 1555 2.07 SSBOND 2 CYS B 2 CYS B 16 1555 1555 2.04 SSBOND 3 CYS B 9 CYS B 22 1555 1555 2.06 SSBOND 4 CYS B 15 CYS B 33 1555 1555 2.05 CRYST1 135.551 35.226 48.856 90.00 109.11 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 0.007377 0.000000 0.002556 0.00000 SCALE2 0.000000 0.028388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021662 0.00000