HEADER SIGNALING PROTEIN 29-JUL-22 8DVM TITLE CRYSTAL STRUCTURE OF LRP6 E3E4 IN COMPLEX WITH DISULFIDE CONSTRAINED TITLE 2 PEPTIDE E3.6 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: E3.6 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 8DVM 1 REMARK REVDAT 3 25-OCT-23 8DVM 1 REMARK REVDAT 2 03-MAY-23 8DVM 1 JRNL REVDAT 1 29-MAR-23 8DVM 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 50517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.150 REMARK 3 FREE R VALUE TEST SET COUNT : 5911 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 46.5400 - 6.2000 1.00 3059 195 0.1636 0.1559 REMARK 3 2 6.2000 - 4.9200 1.00 3076 186 0.1551 0.1845 REMARK 3 3 4.9200 - 4.3000 1.00 3047 213 0.1220 0.1680 REMARK 3 4 4.3000 - 3.9100 1.00 3044 215 0.1431 0.1579 REMARK 3 5 3.9100 - 3.6300 1.00 3090 186 0.1539 0.1653 REMARK 3 6 3.6300 - 3.4100 1.00 3048 209 0.1601 0.1961 REMARK 3 7 3.4100 - 3.2400 1.00 3051 209 0.1839 0.2266 REMARK 3 8 3.2400 - 3.1000 1.00 3070 203 0.1931 0.2255 REMARK 3 9 3.1000 - 2.9800 1.00 3049 204 0.1883 0.2426 REMARK 3 10 2.9800 - 2.8800 1.00 3064 187 0.1997 0.2312 REMARK 3 11 2.8800 - 2.7900 1.00 3043 213 0.2034 0.2860 REMARK 3 12 2.7900 - 2.7100 1.00 3061 198 0.2060 0.2832 REMARK 3 13 2.7100 - 2.6400 1.00 3071 201 0.2120 0.2543 REMARK 3 14 2.6400 - 2.5700 1.00 3073 198 0.2115 0.2504 REMARK 3 15 2.5700 - 2.5200 1.00 3063 202 0.2149 0.3117 REMARK 3 16 2.5200 - 2.4600 1.00 3057 207 0.2138 0.2924 REMARK 3 17 2.4600 - 2.4100 1.00 3023 195 0.2171 0.2581 REMARK 3 18 2.4100 - 2.3700 1.00 3089 202 0.2332 0.2803 REMARK 3 19 2.3700 - 2.3300 1.00 3107 186 0.2260 0.2905 REMARK 3 20 2.3300 - 2.2900 1.00 3050 199 0.2436 0.2719 REMARK 3 21 2.2900 - 2.2500 1.00 3038 226 0.2602 0.2976 REMARK 3 22 2.2500 - 2.2100 1.00 3085 171 0.2554 0.3015 REMARK 3 23 2.2100 - 2.1800 1.00 3063 189 0.2741 0.3356 REMARK 3 24 2.1800 - 2.1500 1.00 3013 223 0.2770 0.3353 REMARK 3 25 2.1500 - 2.1200 1.00 3103 192 0.2850 0.3093 REMARK 3 26 2.1200 - 2.0900 1.00 3017 223 0.2935 0.3591 REMARK 3 27 2.0900 - 2.0700 1.00 3076 193 0.2993 0.3375 REMARK 3 28 2.0700 - 2.0400 1.00 3055 188 0.3058 0.3151 REMARK 3 29 2.0400 - 2.0200 1.00 2986 215 0.3219 0.3565 REMARK 3 30 2.0200 - 2.0000 0.48 1497 83 0.3428 0.3795 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.36 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): -29.4192 -8.3954 3.7179 REMARK 3 T TENSOR REMARK 3 T11: 0.2938 T22: 0.2581 REMARK 3 T33: 0.3395 T12: 0.0389 REMARK 3 T13: -0.0365 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 1.9063 L22: 1.4475 REMARK 3 L33: 3.1860 L12: -0.5698 REMARK 3 L13: 0.2983 L23: 0.2534 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.1018 S13: 0.0963 REMARK 3 S21: -0.1384 S22: 0.0142 S23: -0.0394 REMARK 3 S31: -0.1173 S32: -0.1181 S33: -0.0645 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 921 THROUGH 1247 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6169 -30.9081 35.8375 REMARK 3 T TENSOR REMARK 3 T11: 0.2497 T22: 0.2745 REMARK 3 T33: 0.2279 T12: 0.0084 REMARK 3 T13: -0.0170 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 1.9409 L22: 1.3692 REMARK 3 L33: 2.1461 L12: -0.2153 REMARK 3 L13: 0.3109 L23: -0.0389 REMARK 3 S TENSOR REMARK 3 S11: -0.0949 S12: -0.0236 S13: 0.0048 REMARK 3 S21: 0.1098 S22: 0.0905 S23: -0.1145 REMARK 3 S31: -0.0854 S32: 0.0171 S33: 0.0029 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.9399 -24.7633 -5.6961 REMARK 3 T TENSOR REMARK 3 T11: 1.1418 T22: 0.8282 REMARK 3 T33: 0.8546 T12: 0.0814 REMARK 3 T13: -0.0400 T23: -0.1529 REMARK 3 L TENSOR REMARK 3 L11: 5.7866 L22: 5.7109 REMARK 3 L33: 7.4814 L12: 5.4510 REMARK 3 L13: -4.7472 L23: -5.6485 REMARK 3 S TENSOR REMARK 3 S11: -0.7378 S12: 2.0830 S13: -0.7387 REMARK 3 S21: -2.5912 S22: 0.5775 S23: -0.7085 REMARK 3 S31: 1.5110 S32: 0.1137 S33: 0.2230 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 8DVM 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_1000267445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-21 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 PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 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 (%): 50.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.3, 12% PEG 20K, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 33.23100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.38750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.48900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.38750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.23100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.48900 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: 8580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F, 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 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 SER B 10 REMARK 465 CYS B 11 REMARK 465 LYS B 12 REMARK 465 GLN B 13 REMARK 465 ASP B 14 REMARK 465 SER B 15 REMARK 465 ASP B 16 REMARK 465 CYS B 17 REMARK 465 LEU B 18 REMARK 465 ALA B 19 REMARK 465 GLY B 20 REMARK 465 CYS B 21 REMARK 465 VAL B 22 REMARK 465 CYS B 23 REMARK 465 ASN B 24 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 -123.25 57.27 REMARK 500 ASN A 650 -8.04 74.49 REMARK 500 ASN A 651 -4.10 -142.24 REMARK 500 SER A 665 -86.37 -122.28 REMARK 500 ASP A 705 -60.44 -121.29 REMARK 500 TRP A 744 -14.23 -144.93 REMARK 500 ARG A 751 -70.87 -117.39 REMARK 500 HIS A 834 59.45 -150.65 REMARK 500 GLN A 842 -126.97 49.45 REMARK 500 GLN A 864 -165.73 -102.89 REMARK 500 HIS A 919 -1.68 76.60 REMARK 500 ASN A 966 85.68 -151.37 REMARK 500 GLN A1015 74.92 -152.13 REMARK 500 ARG A1060 -77.26 -122.20 REMARK 500 ARG A1079 14.65 58.20 REMARK 500 SER A1080 60.31 -156.15 REMARK 500 GLN A1146 76.59 -151.18 REMARK 500 GLU A1154 -117.46 52.99 REMARK 500 HIS A1216 -76.00 -117.70 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 A1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 724 O REMARK 620 2 ASN A 727 OD1 82.4 REMARK 620 3 SER A 749 OG 95.2 96.5 REMARK 620 4 HOH A1431 O 175.8 94.1 87.4 REMARK 620 5 HOH A1510 O 85.9 92.2 171.3 92.1 REMARK 620 6 HOH B 101 O 81.2 163.4 83.0 102.4 88.6 REMARK 620 N 1 2 3 4 5 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 LEU A1150 O REMARK 620 2 ILE A1191 O 95.5 REMARK 620 3 HOH A1411 O 79.5 172.8 REMARK 620 4 HOH A1498 O 170.7 87.9 97.9 REMARK 620 5 HOH A1521 O 92.7 103.6 71.7 95.0 REMARK 620 6 HOH A1525 O 70.8 105.2 78.1 99.9 147.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1405 O REMARK 620 2 HOH A1411 O 97.2 REMARK 620 3 HOH A1481 O 86.8 129.0 REMARK 620 4 HOH A1498 O 155.4 102.1 69.2 REMARK 620 5 HOH A1544 O 100.7 143.1 84.3 72.4 REMARK 620 N 1 2 3 4 DBREF 8DVM A 631 1253 UNP O75581 LRP6_HUMAN 631 1253 DBREF 8DVM B 1 30 PDB 8DVM 8DVM 1 30 SEQADV 8DVM SER A 630 UNP O75581 EXPRESSION TAG SEQADV 8DVM ILE A 1062 UNP O75581 VAL 1062 VARIANT SEQADV 8DVM GLY A 1254 UNP O75581 EXPRESSION TAG SEQADV 8DVM ASN A 1255 UNP O75581 EXPRESSION TAG SEQADV 8DVM SER A 1256 UNP O75581 EXPRESSION TAG SEQADV 8DVM HIS A 1257 UNP O75581 EXPRESSION TAG SEQADV 8DVM HIS A 1258 UNP O75581 EXPRESSION TAG SEQADV 8DVM HIS A 1259 UNP O75581 EXPRESSION TAG SEQADV 8DVM HIS A 1260 UNP O75581 EXPRESSION TAG SEQADV 8DVM HIS A 1261 UNP O75581 EXPRESSION TAG SEQADV 8DVM 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 30 GLY CYS ARG TRP PHE MET LYS TRP PHE SER CYS LYS GLN SEQRES 2 B 30 ASP SER ASP CYS LEU ALA GLY CYS VAL CYS ASN PRO PRO SEQRES 3 B 30 HIS TRP CYS GLY MODRES 8DVM OCS A 1032 CYS MODIFIED RESIDUE HET OCS A1032 9 HET NAG F 1 14 HET NAG F 2 14 HET NAG F 3 14 HET FUC F 4 10 HET FUC F 5 10 HET FUC F 6 10 HET FUC F 7 10 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG A1301 14 HET CA A1302 1 HET CA A1303 1 HET CA A1304 1 HET EDO A1305 4 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 HET EDO A1313 4 HET EDO A1314 4 HET EDO A1315 4 HET EDO A1316 4 HET EDO A1317 4 HET EDO A1318 4 HET MES A1319 12 HETNAM OCS CYSTEINESULFONIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 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 EDO ETHYLENE GLYCOL FORMUL 1 OCS C3 H7 N O5 S FORMUL 3 NAG 10(C8 H15 N O6) FORMUL 3 FUC 4(C6 H12 O5) FORMUL 6 BMA C6 H12 O6 FORMUL 8 CA 3(CA 2+) FORMUL 11 EDO 14(C2 H6 O2) FORMUL 25 MES C6 H13 N O4 S FORMUL 26 HOH *224(H2 O) HELIX 1 AA1 HIS A 883 GLN A 887 5 5 HELIX 2 AA2 ASN A 891 CYS A 900 5 10 HELIX 3 AA3 ASN A 1198 ARG A 1203 1 6 HELIX 4 AA4 GLN A 1204 CYS A 1214 5 11 HELIX 5 AA5 CYS B 2 PHE B 9 1 8 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 ASP A 878 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 GLU A 697 N ARG A 688 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 ASP A 756 0 SHEET 2 AA4 4 PHE A 761 GLU A 766 -1 O THR A 765 N ARG A 751 SHEET 3 AA4 4 LYS A 772 ALA A 777 -1 O ASP A 774 N TRP A 764 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 SER A 818 N LEU A 805 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 TYR A 846 N THR A 839 SHEET 3 AA6 4 SER A 854 ASN A 859 -1 O GLU A 856 N TRP A 847 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 VAL A 907 0 SHEET 2 AA7 2 GLY A 911 GLY A 915 -1 O VAL A 913 N LEU A 905 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 LEU A 936 O MET A 947 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 GLN A 993 -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 VAL A1048 N VAL A1040 SHEET 1 AB3 4 PRO A1059 ASN A1065 0 SHEET 2 AB3 4 TYR A1070 GLN A1077 -1 O TYR A1070 N ASN A1065 SHEET 3 AB3 4 SER A1080 ALA A1087 -1 O GLU A1084 N PHE A1073 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 LEU A1139 N ILE A1126 SHEET 1 AB5 4 PRO A1147 PHE A1153 0 SHEET 2 AB5 4 TRP A1156 ASP A1161 -1 O TYR A1158 N THR A1151 SHEET 3 AB5 4 MET A1166 ASP A1171 -1 O GLU A1168 N TRP A1159 SHEET 4 AB5 4 ARG A1178 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 SSBOND 1 CYS A 893 CYS A 904 1555 1555 2.02 SSBOND 2 CYS A 900 CYS A 914 1555 1555 2.03 SSBOND 3 CYS A 916 CYS A 929 1555 1555 2.05 SSBOND 4 CYS A 1207 CYS A 1218 1555 1555 2.05 SSBOND 5 CYS A 1214 CYS A 1228 1555 1555 2.04 SSBOND 6 CYS A 1230 CYS A 1243 1555 1555 2.05 SSBOND 7 CYS B 2 CYS B 29 1555 1555 2.02 LINK ND2 ASN A 692 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN A 859 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 865 C1 NAG A1301 1555 1555 1.45 LINK ND2 ASN A 926 C1 NAG D 1 1555 1555 1.44 LINK C THR A1031 N OCS A1032 1555 1555 1.32 LINK C OCS A1032 N GLU A1033 1555 1555 1.33 LINK ND2 ASN A1039 C1 NAG E 1 1555 1555 1.44 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O3 NAG F 1 C1 FUC F 6 1555 1555 1.43 LINK O6 NAG F 1 C1 FUC F 7 1555 1555 1.43 LINK O4 NAG F 2 C1 NAG F 3 1555 1555 1.44 LINK O3 NAG F 3 C1 FUC F 4 1555 1555 1.45 LINK O6 NAG F 3 C1 FUC F 5 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.42 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O THR A 724 CA CA A1303 1555 1555 2.56 LINK OD1 ASN A 727 CA CA A1303 1555 1555 2.73 LINK OG SER A 749 CA CA A1303 1555 1555 2.68 LINK O LEU A1150 CA CA A1304 1555 1555 2.71 LINK O ILE A1191 CA CA A1304 1555 1555 2.45 LINK CA CA A1302 O HOH A1405 1555 1555 2.27 LINK CA CA A1302 O HOH A1411 1555 1555 2.35 LINK CA CA A1302 O HOH A1481 1555 1555 2.41 LINK CA CA A1302 O HOH A1498 1555 1555 2.55 LINK CA CA A1302 O HOH A1544 1555 1555 2.75 LINK CA CA A1303 O HOH A1431 1555 1555 2.36 LINK CA CA A1303 O HOH A1510 1555 1555 2.49 LINK CA CA A1303 O HOH B 101 1555 1555 2.57 LINK CA CA A1304 O HOH A1411 1555 1555 2.63 LINK CA CA A1304 O HOH A1498 1555 1555 2.42 LINK CA CA A1304 O HOH A1521 1555 1555 2.58 LINK CA CA A1304 O HOH A1525 1555 1555 2.76 CRYST1 66.462 102.978 108.775 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 0.015046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009193 0.00000