HEADER SIGNALING PROTEIN 29-JUL-22 8DVL TITLE CRYSTAL STRUCTURE OF LRP6 E3E4 IN COMPLEX WITH DISULFIDE CONSTRAINED TITLE 2 PEPTIDE E3.18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LRP-6; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: E3.18 DISULFIDE CONSTRAINED PEPTIDE; 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: LRP6; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS LRP6, E3E4, WNT SIGNALING, SIGNALING PROTEIN, DISULFIDE CONSTRAINED KEYWDS 2 PEPTIDE, WNT AGONISM EXPDTA X-RAY DIFFRACTION AUTHOR A.K.THAKUR,N.P.D.LIAU,J.SUDHAMSU,R.N.HANNOUSH REVDAT 4 15-NOV-23 8DVL 1 REMARK REVDAT 3 25-OCT-23 8DVL 1 REMARK REVDAT 2 03-MAY-23 8DVL 1 JRNL REVDAT 1 29-MAR-23 8DVL 0 JRNL AUTH A.K.THAKUR,S.E.MILLER,N.P.D.LIAU,S.HWANG,S.HANSEN, JRNL AUTH 2 F.DE SOUSA E MELO,J.SUDHAMSU,R.N.HANNOUSH JRNL TITL SYNTHETIC MULTIVALENT DISULFIDE-CONSTRAINED PEPTIDE AGONISTS JRNL TITL 2 POTENTIATE WNT1/ BETA-CATENIN SIGNALING VIA LRP6 CORECEPTOR JRNL TITL 3 CLUSTERING. JRNL REF ACS CHEM.BIOL. V. 18 772 2023 JRNL REFN ESSN 1554-8937 JRNL PMID 36893429 JRNL DOI 10.1021/ACSCHEMBIO.2C00753 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC3-4406_FINAL 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 25374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.820 REMARK 3 FREE R VALUE TEST SET COUNT : 3773 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 45.5800 - 7.4800 0.99 1688 142 0.1670 0.2148 REMARK 3 2 7.4800 - 5.9400 1.00 1692 142 0.1728 0.2367 REMARK 3 3 5.9400 - 5.1900 0.99 1673 141 0.1890 0.2177 REMARK 3 4 5.1900 - 4.7200 0.93 1579 128 0.1492 0.1776 REMARK 3 5 4.7200 - 4.3800 0.95 1640 142 0.1386 0.1621 REMARK 3 6 4.3800 - 4.1200 0.96 1602 135 0.1605 0.1612 REMARK 3 7 4.1200 - 3.9100 0.97 1648 141 0.1680 0.2298 REMARK 3 8 3.9100 - 3.7400 0.96 1680 146 0.1908 0.2515 REMARK 3 9 3.7400 - 3.6000 0.96 1621 138 0.2104 0.2523 REMARK 3 10 3.6000 - 3.4800 0.98 1662 138 0.1843 0.2852 REMARK 3 11 3.4800 - 3.3700 0.98 1666 140 0.1959 0.2893 REMARK 3 12 3.3700 - 3.2700 0.97 1680 141 0.2057 0.2454 REMARK 3 13 3.2700 - 3.1800 0.97 1649 140 0.2163 0.2547 REMARK 3 14 3.1800 - 3.1100 0.98 1647 144 0.2279 0.3841 REMARK 3 15 3.1100 - 3.0400 0.98 1670 141 0.2561 0.3338 REMARK 3 16 3.0400 - 2.9700 0.98 1711 145 0.2531 0.2595 REMARK 3 17 2.9700 - 2.9100 0.98 1610 140 0.2351 0.2681 REMARK 3 18 2.9100 - 2.8600 0.98 1652 145 0.2395 0.3095 REMARK 3 19 2.8600 - 2.8100 0.97 1692 140 0.2440 0.2965 REMARK 3 20 2.8100 - 2.7600 0.97 1605 142 0.2589 0.3233 REMARK 3 21 2.7600 - 2.7100 0.96 1681 143 0.2648 0.3119 REMARK 3 22 2.7100 - 2.6700 0.93 1569 135 0.2912 0.3320 REMARK 3 23 2.6700 - 2.6300 0.94 1551 130 0.2867 0.2935 REMARK 3 24 2.6300 - 2.6000 0.97 1672 140 0.3018 0.3925 REMARK 3 25 2.6000 - 2.5600 0.97 1682 143 0.3330 0.3587 REMARK 3 26 2.5600 - 2.5300 0.97 1642 134 0.3395 0.4530 REMARK 3 27 2.5300 - 2.5000 0.96 1607 137 0.3682 0.3725 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.03 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 630 THROUGH 920 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5641 -24.4660 -7.2175 REMARK 3 T TENSOR REMARK 3 T11: 0.3528 T22: 0.4368 REMARK 3 T33: 0.4261 T12: -0.0363 REMARK 3 T13: -0.0494 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.3355 L22: 1.5758 REMARK 3 L33: 3.8591 L12: 0.0960 REMARK 3 L13: -0.6938 L23: 0.7497 REMARK 3 S TENSOR REMARK 3 S11: 0.0470 S12: 0.0528 S13: -0.0506 REMARK 3 S21: -0.1286 S22: -0.0492 S23: 0.1249 REMARK 3 S31: -0.0987 S32: -0.5538 S33: 0.0071 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 921 THROUGH 1246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5310 -1.2075 31.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.3583 T22: 0.3151 REMARK 3 T33: 0.3239 T12: 0.0556 REMARK 3 T13: 0.0083 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.7353 L22: 2.1770 REMARK 3 L33: 2.3971 L12: 0.3798 REMARK 3 L13: -0.2150 L23: 0.1627 REMARK 3 S TENSOR REMARK 3 S11: -0.0029 S12: -0.0475 S13: 0.1349 REMARK 3 S21: 0.2364 S22: -0.0219 S23: 0.1463 REMARK 3 S31: -0.1067 S32: -0.3816 S33: 0.0327 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.7154 -19.9378 -2.8654 REMARK 3 T TENSOR REMARK 3 T11: 0.5770 T22: 0.7133 REMARK 3 T33: 0.7807 T12: -0.2099 REMARK 3 T13: 0.1966 T23: -0.1348 REMARK 3 L TENSOR REMARK 3 L11: 1.9108 L22: 5.0215 REMARK 3 L33: 5.9619 L12: 0.0944 REMARK 3 L13: -0.3535 L23: 3.0389 REMARK 3 S TENSOR REMARK 3 S11: 1.0954 S12: 0.2775 S13: 0.6558 REMARK 3 S21: 0.0263 S22: -0.2222 S23: -0.9014 REMARK 3 S31: -1.3407 S32: 1.0317 S33: -0.7421 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 8DVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25374 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 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: 4A0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS 6.3, 18% PEG 10K, PH REMARK 280 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.91750 REMARK 290 SMTRY3 2 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: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 SER A 1006 REMARK 465 VAL A 1007 REMARK 465 PRO A 1008 REMARK 465 SER A 1009 REMARK 465 GLN A 1010 REMARK 465 ASN A 1011 REMARK 465 LEU A 1012 REMARK 465 PRO A 1247 REMARK 465 THR A 1248 REMARK 465 CYS A 1249 REMARK 465 SER A 1250 REMARK 465 PRO A 1251 REMARK 465 GLN A 1252 REMARK 465 GLN A 1253 REMARK 465 GLY A 1254 REMARK 465 ASN A 1255 REMARK 465 SER A 1256 REMARK 465 HIS A 1257 REMARK 465 HIS A 1258 REMARK 465 HIS A 1259 REMARK 465 HIS A 1260 REMARK 465 HIS A 1261 REMARK 465 HIS A 1262 REMARK 465 GLN B 15 REMARK 465 ASP B 16 REMARK 465 SER B 17 REMARK 465 ASP B 18 REMARK 465 CYS B 19 REMARK 465 LEU B 20 REMARK 465 ALA B 21 REMARK 465 GLY B 22 REMARK 465 CYS B 23 REMARK 465 VAL B 24 REMARK 465 CYS B 25 REMARK 465 ASP B 26 REMARK 465 VAL B 27 REMARK 465 SER B 28 REMARK 465 GLN B 29 REMARK 465 ALA B 30 REMARK 465 CYS B 31 REMARK 465 GLY B 32 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 ARG A 639 -123.69 52.97 REMARK 500 ASN A 652 95.53 -165.38 REMARK 500 SER A 665 -93.67 -114.61 REMARK 500 MET A 710 142.71 -171.59 REMARK 500 TRP A 744 -14.37 -142.63 REMARK 500 HIS A 834 59.24 -151.97 REMARK 500 PHE A 836 -62.83 -121.87 REMARK 500 GLN A 842 -125.23 55.56 REMARK 500 GLN A 864 -157.74 -91.92 REMARK 500 SER A 888 -169.96 -129.25 REMARK 500 ASN A 897 17.33 55.29 REMARK 500 HIS A 899 12.50 56.45 REMARK 500 HIS A 919 -1.63 75.69 REMARK 500 ARG A 927 -30.76 -132.33 REMARK 500 LEU A1076 56.18 -90.50 REMARK 500 SER A1080 72.88 -154.08 REMARK 500 GLN A1146 85.23 -158.13 REMARK 500 GLU A1154 -111.45 55.48 REMARK 500 GLU A1240 15.26 49.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 838 O REMARK 620 2 HOH A1413 O 128.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A1062 O REMARK 620 2 EDO A1309 O1 127.7 REMARK 620 3 HOH A1412 O 151.3 80.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A1150 O REMARK 620 2 ASP A1190 OD1 114.8 REMARK 620 3 ILE A1191 O 78.5 72.5 REMARK 620 4 EDO A1309 O2 75.8 151.5 84.8 REMARK 620 5 EDO A1309 O1 86.2 137.6 149.9 66.2 REMARK 620 6 HOH A1412 O 157.5 75.5 124.0 105.0 74.1 REMARK 620 N 1 2 3 4 5 DBREF 8DVL A 631 1253 UNP O75581 LRP6_HUMAN 631 1253 DBREF 8DVL B 1 32 PDB 8DVL 8DVL 1 32 SEQADV 8DVL SER A 630 UNP O75581 EXPRESSION TAG SEQADV 8DVL ILE A 1062 UNP O75581 VAL 1062 VARIANT SEQADV 8DVL GLY A 1254 UNP O75581 EXPRESSION TAG SEQADV 8DVL ASN A 1255 UNP O75581 EXPRESSION TAG SEQADV 8DVL SER A 1256 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1257 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1258 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1259 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1260 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1261 UNP O75581 EXPRESSION TAG SEQADV 8DVL HIS A 1262 UNP O75581 EXPRESSION TAG SEQRES 1 A 633 SER GLU ALA PHE LEU LEU PHE SER ARG ARG ALA ASP ILE SEQRES 2 A 633 ARG ARG ILE SER LEU GLU THR ASN ASN ASN ASN VAL ALA SEQRES 3 A 633 ILE PRO LEU THR GLY VAL LYS GLU ALA SER ALA LEU ASP SEQRES 4 A 633 PHE ASP VAL THR ASP ASN ARG ILE TYR TRP THR ASP ILE SEQRES 5 A 633 SER LEU LYS THR ILE SER ARG ALA PHE MET ASN GLY SER SEQRES 6 A 633 ALA LEU GLU HIS VAL VAL GLU PHE GLY LEU ASP TYR PRO SEQRES 7 A 633 GLU GLY MET ALA VAL ASP TRP LEU GLY LYS ASN LEU TYR SEQRES 8 A 633 TRP ALA ASP THR GLY THR ASN ARG ILE GLU VAL SER LYS SEQRES 9 A 633 LEU ASP GLY GLN HIS ARG GLN VAL LEU VAL TRP LYS ASP SEQRES 10 A 633 LEU ASP SER PRO ARG ALA LEU ALA LEU ASP PRO ALA GLU SEQRES 11 A 633 GLY PHE MET TYR TRP THR GLU TRP GLY GLY LYS PRO LYS SEQRES 12 A 633 ILE ASP ARG ALA ALA MET ASP GLY SER GLU ARG THR THR SEQRES 13 A 633 LEU VAL PRO ASN VAL GLY ARG ALA ASN GLY LEU THR ILE SEQRES 14 A 633 ASP TYR ALA LYS ARG ARG LEU TYR TRP THR ASP LEU ASP SEQRES 15 A 633 THR ASN LEU ILE GLU SER SER ASN MET LEU GLY LEU ASN SEQRES 16 A 633 ARG GLU VAL ILE ALA ASP ASP LEU PRO HIS PRO PHE GLY SEQRES 17 A 633 LEU THR GLN TYR GLN ASP TYR ILE TYR TRP THR ASP TRP SEQRES 18 A 633 SER ARG ARG SER ILE GLU ARG ALA ASN LYS THR SER GLY SEQRES 19 A 633 GLN ASN ARG THR ILE ILE GLN GLY HIS LEU ASP TYR VAL SEQRES 20 A 633 MET ASP ILE LEU VAL PHE HIS SER SER ARG GLN SER GLY SEQRES 21 A 633 TRP ASN GLU CYS ALA SER SER ASN GLY HIS CYS SER HIS SEQRES 22 A 633 LEU CYS LEU ALA VAL PRO VAL GLY GLY PHE VAL CYS GLY SEQRES 23 A 633 CYS PRO ALA HIS TYR SER LEU ASN ALA ASP ASN ARG THR SEQRES 24 A 633 CYS SER ALA PRO THR THR PHE LEU LEU PHE SER GLN LYS SEQRES 25 A 633 SER ALA ILE ASN ARG MET VAL ILE ASP GLU GLN GLN SER SEQRES 26 A 633 PRO ASP ILE ILE LEU PRO ILE HIS SER LEU ARG ASN VAL SEQRES 27 A 633 ARG ALA ILE ASP TYR ASP PRO LEU ASP LYS GLN LEU TYR SEQRES 28 A 633 TRP ILE ASP SER ARG GLN ASN MET ILE ARG LYS ALA GLN SEQRES 29 A 633 GLU ASP GLY SER GLN GLY PHE THR VAL VAL VAL SER SER SEQRES 30 A 633 VAL PRO SER GLN ASN LEU GLU ILE GLN PRO TYR ASP LEU SEQRES 31 A 633 SER ILE ASP ILE TYR SER ARG TYR ILE TYR TRP THR OCS SEQRES 32 A 633 GLU ALA THR ASN VAL ILE ASN VAL THR ARG LEU ASP GLY SEQRES 33 A 633 ARG SER VAL GLY VAL VAL LEU LYS GLY GLU GLN ASP ARG SEQRES 34 A 633 PRO ARG ALA ILE VAL VAL ASN PRO GLU LYS GLY TYR MET SEQRES 35 A 633 TYR PHE THR ASN LEU GLN GLU ARG SER PRO LYS ILE GLU SEQRES 36 A 633 ARG ALA ALA LEU ASP GLY THR GLU ARG GLU VAL LEU PHE SEQRES 37 A 633 PHE SER GLY LEU SER LYS PRO ILE ALA LEU ALA LEU ASP SEQRES 38 A 633 SER ARG LEU GLY LYS LEU PHE TRP ALA ASP SER ASP LEU SEQRES 39 A 633 ARG ARG ILE GLU SER SER ASP LEU SER GLY ALA ASN ARG SEQRES 40 A 633 ILE VAL LEU GLU ASP SER ASN ILE LEU GLN PRO VAL GLY SEQRES 41 A 633 LEU THR VAL PHE GLU ASN TRP LEU TYR TRP ILE ASP LYS SEQRES 42 A 633 GLN GLN GLN MET ILE GLU LYS ILE ASP MET THR GLY ARG SEQRES 43 A 633 GLU GLY ARG THR LYS VAL GLN ALA ARG ILE ALA GLN LEU SEQRES 44 A 633 SER ASP ILE HIS ALA VAL LYS GLU LEU ASN LEU GLN GLU SEQRES 45 A 633 TYR ARG GLN HIS PRO CYS ALA GLN ASP ASN GLY GLY CYS SEQRES 46 A 633 SER HIS ILE CYS LEU VAL LYS GLY ASP GLY THR THR ARG SEQRES 47 A 633 CYS SER CYS PRO MET HIS LEU VAL LEU LEU GLN ASP GLU SEQRES 48 A 633 LEU SER CYS GLY GLU PRO PRO THR CYS SER PRO GLN GLN SEQRES 49 A 633 GLY ASN SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 32 GLY CYS ILE PRO VAL ILE THR THR ARG GLY VAL ARG CYS SEQRES 2 B 32 LYS GLN ASP SER ASP CYS LEU ALA GLY CYS VAL CYS ASP SEQRES 3 B 32 VAL SER GLN ALA CYS GLY MODRES 8DVL OCS A 1032 CYS MODIFIED RESIDUE HET OCS A1032 9 HET NAG C 1 14 HET FUC C 2 10 HET NAG C 3 14 HET NAG D 1 14 HET NAG D 2 14 HET FUC D 3 10 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET MAN E 5 11 HET MAN E 6 11 HET NAG A1301 14 HET NAG A1302 14 HET CA A1303 1 HET CA A1304 1 HET CA A1305 1 HET EDO A1306 4 HET EDO A1307 4 HET EDO A1308 4 HET EDO A1309 4 HET EDO A1310 4 HET EDO A1311 4 HET EDO A1312 4 HETNAM OCS CYSTEINESULFONIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 OCS C3 H7 N O5 S FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 5 BMA C6 H12 O6 FORMUL 5 MAN 3(C6 H12 O6) FORMUL 8 CA 3(CA 2+) FORMUL 11 EDO 7(C2 H6 O2) FORMUL 18 HOH *14(H2 O) HELIX 1 AA1 HIS A 883 GLN A 887 5 5 HELIX 2 AA2 ASN A 891 ASN A 897 1 7 HELIX 3 AA3 GLY A 898 CYS A 900 5 3 HELIX 4 AA4 ASN A 1198 GLN A 1204 1 7 HELIX 5 AA5 GLN A 1209 CYS A 1214 5 6 SHEET 1 AA1 4 ASN A 653 ALA A 655 0 SHEET 2 AA1 4 ASP A 641 SER A 646 -1 N ARG A 644 O VAL A 654 SHEET 3 AA1 4 PHE A 633 ARG A 638 -1 N LEU A 634 O ILE A 645 SHEET 4 AA1 4 VAL A 876 PHE A 882 -1 O PHE A 882 N PHE A 633 SHEET 1 AA2 4 ALA A 664 ASP A 670 0 SHEET 2 AA2 4 ARG A 675 ASP A 680 -1 O TYR A 677 N ASP A 668 SHEET 3 AA2 4 THR A 685 PHE A 690 -1 O ALA A 689 N ILE A 676 SHEET 4 AA2 4 GLU A 697 VAL A 700 -1 O VAL A 700 N ILE A 686 SHEET 1 AA3 4 GLY A 709 ASP A 713 0 SHEET 2 AA3 4 ASN A 718 ASP A 723 -1 O ASN A 718 N ASP A 713 SHEET 3 AA3 4 ARG A 728 LYS A 733 -1 O SER A 732 N LEU A 719 SHEET 4 AA3 4 GLN A 740 VAL A 743 -1 O GLN A 740 N VAL A 731 SHEET 1 AA4 4 PRO A 750 LEU A 755 0 SHEET 2 AA4 4 PHE A 761 GLU A 766 -1 O TYR A 763 N ALA A 754 SHEET 3 AA4 4 LYS A 772 ALA A 777 -1 O ALA A 776 N MET A 762 SHEET 4 AA4 4 THR A 784 VAL A 787 -1 O THR A 784 N ARG A 775 SHEET 1 AA5 4 ALA A 793 ASP A 799 0 SHEET 2 AA5 4 ARG A 804 ASP A 809 -1 O ARG A 804 N ASP A 799 SHEET 3 AA5 4 LEU A 814 ASN A 819 -1 O LEU A 814 N ASP A 809 SHEET 4 AA5 4 GLU A 826 ALA A 829 -1 O ILE A 828 N ILE A 815 SHEET 1 AA6 4 PRO A 835 TYR A 841 0 SHEET 2 AA6 4 TYR A 844 ASP A 849 -1 O THR A 848 N PHE A 836 SHEET 3 AA6 4 SER A 854 ASN A 859 -1 O ALA A 858 N ILE A 845 SHEET 4 AA6 4 THR A 867 GLN A 870 -1 O THR A 867 N ARG A 857 SHEET 1 AA7 2 LEU A 903 ALA A 906 0 SHEET 2 AA7 2 PHE A 912 GLY A 915 -1 O GLY A 915 N LEU A 903 SHEET 1 AA8 2 SER A 921 LEU A 922 0 SHEET 2 AA8 2 CYS A 929 SER A 930 -1 O SER A 930 N SER A 921 SHEET 1 AA9 4 ILE A 957 ILE A 958 0 SHEET 2 AA9 4 ALA A 943 MET A 947 -1 N ARG A 946 O ILE A 957 SHEET 3 AA9 4 PHE A 935 GLN A 940 -1 N GLN A 940 O ALA A 943 SHEET 4 AA9 4 LEU A1188 VAL A1194 -1 O HIS A1192 N LEU A 937 SHEET 1 AB1 4 VAL A 967 ASP A 973 0 SHEET 2 AB1 4 GLN A 978 ASP A 983 -1 O TYR A 980 N ASP A 971 SHEET 3 AB1 4 MET A 988 ALA A 992 -1 O ALA A 992 N LEU A 979 SHEET 4 AB1 4 PHE A1000 VAL A1003 -1 O PHE A1000 N LYS A 991 SHEET 1 AB2 4 PRO A1016 ASP A1022 0 SHEET 2 AB2 4 TYR A1027 OCS A1032 -1 O TYR A1027 N ASP A1022 SHEET 3 AB2 4 VAL A1037 ARG A1042 -1 O THR A1041 N ILE A1028 SHEET 4 AB2 4 SER A1047 LYS A1053 -1 O GLY A1049 N VAL A1040 SHEET 1 AB3 4 PRO A1059 ASN A1065 0 SHEET 2 AB3 4 TYR A1070 GLN A1077 -1 O TYR A1072 N VAL A1063 SHEET 3 AB3 4 SER A1080 ALA A1087 -1 O ALA A1086 N MET A1071 SHEET 4 AB3 4 GLU A1094 PHE A1097 -1 O GLU A1094 N ARG A1085 SHEET 1 AB4 4 PRO A1104 ASP A1110 0 SHEET 2 AB4 4 LYS A1115 ASP A1120 -1 O PHE A1117 N ALA A1108 SHEET 3 AB4 4 ARG A1125 ASP A1130 -1 O SER A1129 N LEU A1116 SHEET 4 AB4 4 ILE A1137 GLU A1140 -1 O GLU A1140 N ILE A1126 SHEET 1 AB5 4 PRO A1147 PHE A1153 0 SHEET 2 AB5 4 TRP A1156 ASP A1161 -1 O TRP A1156 N PHE A1153 SHEET 3 AB5 4 MET A1166 ASP A1171 -1 O MET A1166 N ASP A1161 SHEET 4 AB5 4 THR A1179 GLN A1182 -1 O VAL A1181 N ILE A1167 SHEET 1 AB6 2 ILE A1217 VAL A1220 0 SHEET 2 AB6 2 THR A1226 SER A1229 -1 O ARG A1227 N LEU A1219 SHEET 1 AB7 2 VAL A1235 LEU A1236 0 SHEET 2 AB7 2 CYS A1243 GLY A1244 -1 O GLY A1244 N VAL A1235 SHEET 1 AB8 2 ILE B 3 THR B 7 0 SHEET 2 AB8 2 GLY B 10 LYS B 14 -1 O GLY B 10 N THR B 7 SSBOND 1 CYS A 893 CYS A 904 1555 1555 2.04 SSBOND 2 CYS A 900 CYS A 914 1555 1555 2.03 SSBOND 3 CYS A 916 CYS A 929 1555 1555 2.03 SSBOND 4 CYS A 1207 CYS A 1218 1555 1555 2.01 SSBOND 5 CYS A 1214 CYS A 1228 1555 1555 2.01 SSBOND 6 CYS A 1230 CYS A 1243 1555 1555 2.03 SSBOND 7 CYS B 2 CYS B 13 1555 1555 2.03 LINK ND2 ASN A 692 C1 NAG A1301 1555 1555 1.44 LINK ND2 ASN A 859 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN A 865 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 926 C1 NAG C 1 1555 1555 1.44 LINK C THR A1031 N OCS A1032 1555 1555 1.33 LINK C OCS A1032 N GLU A1033 1555 1555 1.33 LINK ND2 ASN A1039 C1 NAG A1302 1555 1555 1.44 LINK O3 NAG C 1 C1 FUC C 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 3 1555 1555 1.43 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O6 NAG D 1 C1 FUC D 3 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O6 BMA E 3 C1 MAN E 4 1555 1555 1.44 LINK O3 BMA E 3 C1 MAN E 6 1555 1555 1.45 LINK O3 MAN E 4 C1 MAN E 5 1555 1555 1.44 LINK O LEU A 838 CA CA A1305 1555 1555 3.08 LINK O ILE A1062 CA CA A1304 1555 1555 3.19 LINK O LEU A1150 CA CA A1303 1555 1555 3.05 LINK OD1 ASP A1190 CA CA A1303 1555 1555 3.14 LINK O ILE A1191 CA CA A1303 1555 1555 2.67 LINK CA CA A1303 O2 EDO A1309 1555 1555 3.00 LINK CA CA A1303 O1 EDO A1309 1555 1555 2.53 LINK CA CA A1303 O HOH A1412 1555 1555 3.04 LINK CA CA A1304 O1 EDO A1309 1555 1555 2.58 LINK CA CA A1304 O HOH A1412 1555 1555 2.64 LINK CA CA A1305 O HOH A1413 1555 1555 2.58 CRYST1 57.911 73.835 87.193 90.00 96.58 90.00 P 1 21 1 2 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 0.017268 0.000000 0.001992 0.00000 SCALE2 0.000000 0.013544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011545 0.00000