HEADER SIGNALING PROTEIN 02-FEB-21 7NE1 TITLE STRUCTURE OF THE COMPLEX BETWEEN NETRIN-1 AND ITS RECEPTOR NEOGENIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETRIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPIDIDYMIS TISSUE PROTEIN LI 131P; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HUMAN NETRIN-1 EXPRESSED IN HEK293T CELLS USING THE COMPND 7 PHLSEC VECTOR FOR SECRETED PROTEINS. CONTAINS C-TERMINAL RHO-1D4 COMPND 8 TAG.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: NEOGENIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: MOUSE NEOGENIN FN DOMAIN 4-6 (ISOFORM 2 - COMPND 14 NP_001036217.1) EXPRESSED IN HEK293T CELLS USING THE PHLSEC VECTOR COMPND 15 FOR SECRETED PROTEINS. CONTAINS C-TERMINAL HIS6-TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NTN1, NTN1L; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: NEO1; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PHLSEC KEYWDS CELL SURFACE RECEPTOR SIGNALING, AXON GUIDANCE, MIGRATION, CANCER, KEYWDS 2 GROWTH CONE, RECEPTOR CLUSTERING, NETRIN, NEOGENIN, REPULSIVE KEYWDS 3 GUIDANCE MOLECULE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.A.ROBINSON,S.C.GRIFFITHS,L.L.VAN DE HAAR,T.MALINAUSKAS,E.Y.VAN AUTHOR 2 BATTUM,P.ZELINA,R.A.SCHWAB,D.KARIA,L.MALINAUSKAITE,S.BRIGNANI,M.VAN AUTHOR 3 DEN MUNKHOF,O.DUDUKCU,A.A.DE RUITER,D.M.A.VAN DEN HEUVEL,B.BISHOP, AUTHOR 4 J.ELEGHEERT,A.R.ARICESCU,R.J.PASTERKAMP,C.SIEBOLD REVDAT 3 31-JAN-24 7NE1 1 REMARK REVDAT 2 28-APR-21 7NE1 1 JRNL REVDAT 1 31-MAR-21 7NE1 0 JRNL AUTH R.A.ROBINSON,S.C.GRIFFITHS,L.L.VAN DE HAAR,T.MALINAUSKAS, JRNL AUTH 2 E.Y.VAN BATTUM,P.ZELINA,R.A.SCHWAB,D.KARIA,L.MALINAUSKAITE, JRNL AUTH 3 S.BRIGNANI,M.H.VAN DEN MUNKHOF,O.DUDUKCU,A.A.DE RUITER, JRNL AUTH 4 D.M.A.VAN DEN HEUVEL,B.BISHOP,J.ELEGHEERT,A.R.ARICESCU, JRNL AUTH 5 R.J.PASTERKAMP,C.SIEBOLD JRNL TITL SIMULTANEOUS BINDING OF GUIDANCE CUES NET1 AND RGM BLOCKS JRNL TITL 2 EXTRACELLULAR NEO1 SIGNALING. JRNL REF CELL V. 184 2103 2021 JRNL REFN ISSN 1097-4172 JRNL PMID 33740419 JRNL DOI 10.1016/J.CELL.2021.02.045 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 19815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.53 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 397 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2521 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 378 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.3365 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.79 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.26320 REMARK 3 B22 (A**2) : -11.70640 REMARK 3 B33 (A**2) : -0.55680 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 13.66270 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.460 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.399 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5944 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8110 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2014 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1001 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5944 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 789 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6069 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.89 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.76 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.94 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|38 - A|293 } REMARK 3 ORIGIN FOR THE GROUP (A): -141.2380 -100.7790 72.2688 REMARK 3 T TENSOR REMARK 3 T11: -0.1710 T22: -0.2733 REMARK 3 T33: 0.0485 T12: -0.0139 REMARK 3 T13: 0.0247 T23: -0.0775 REMARK 3 L TENSOR REMARK 3 L11: 1.7447 L22: 1.4794 REMARK 3 L33: 3.8488 L12: 0.1496 REMARK 3 L13: 0.4959 L23: -1.2042 REMARK 3 S TENSOR REMARK 3 S11: -0.2578 S12: 0.1053 S13: -0.0865 REMARK 3 S21: -0.2137 S22: 0.1959 S23: 0.0796 REMARK 3 S31: 0.1458 S32: -0.1080 S33: 0.0619 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|294 - A|451 } REMARK 3 ORIGIN FOR THE GROUP (A): -107.5745 -103.2130 117.7954 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: -0.0672 REMARK 3 T33: -0.0218 T12: 0.1257 REMARK 3 T13: -0.2051 T23: -0.0765 REMARK 3 L TENSOR REMARK 3 L11: 3.0926 L22: 0.2154 REMARK 3 L33: 3.0510 L12: 0.1326 REMARK 3 L13: 2.1699 L23: 0.1043 REMARK 3 S TENSOR REMARK 3 S11: -0.0573 S12: -0.4424 S13: 0.1839 REMARK 3 S21: 0.4467 S22: 0.0590 S23: -0.2016 REMARK 3 S31: -0.1282 S32: 0.1670 S33: -0.0017 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|765 - B|864 } REMARK 3 ORIGIN FOR THE GROUP (A): -155.3131 -92.8426 89.8715 REMARK 3 T TENSOR REMARK 3 T11: -0.3414 T22: -0.0496 REMARK 3 T33: 0.1248 T12: 0.1475 REMARK 3 T13: 0.0317 T23: -0.1430 REMARK 3 L TENSOR REMARK 3 L11: 5.3883 L22: 3.5814 REMARK 3 L33: 3.7456 L12: -1.8914 REMARK 3 L13: -0.4007 L23: -0.2864 REMARK 3 S TENSOR REMARK 3 S11: -0.0788 S12: -0.2035 S13: 0.3288 REMARK 3 S21: -0.0001 S22: -0.0269 S23: 0.2340 REMARK 3 S31: -0.2368 S32: -0.2654 S33: 0.1057 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|885 - B|983 } REMARK 3 ORIGIN FOR THE GROUP (A): -149.6459 -114.1110 135.8438 REMARK 3 T TENSOR REMARK 3 T11: -0.0280 T22: 0.3611 REMARK 3 T33: -0.2810 T12: -0.2995 REMARK 3 T13: -0.1274 T23: -0.2620 REMARK 3 L TENSOR REMARK 3 L11: 3.3159 L22: 1.1296 REMARK 3 L33: 1.0637 L12: -0.6045 REMARK 3 L13: 0.1452 L23: -0.1516 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.1213 S13: 0.2268 REMARK 3 S21: -0.1592 S22: 0.0026 S23: -0.2144 REMARK 3 S31: -0.0648 S32: 0.0805 S33: -0.0360 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { B|984 - B|1073 } REMARK 3 ORIGIN FOR THE GROUP (A): -161.2013 -99.1983 175.5220 REMARK 3 T TENSOR REMARK 3 T11: 0.3002 T22: -0.1202 REMARK 3 T33: -0.2794 T12: -0.3449 REMARK 3 T13: -0.1605 T23: -0.1114 REMARK 3 L TENSOR REMARK 3 L11: 2.5805 L22: 1.4962 REMARK 3 L33: 6.1739 L12: -0.8371 REMARK 3 L13: -1.8612 L23: 0.3718 REMARK 3 S TENSOR REMARK 3 S11: 0.0539 S12: 0.4176 S13: -0.2103 REMARK 3 S21: -0.3009 S22: 0.0194 S23: -0.2765 REMARK 3 S31: 0.3409 S32: 0.2694 S33: -0.0734 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7NE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-13 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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19817 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 77.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.23 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 : 1.000 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: 4BQ6, 1X5I, 4PLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 20% W/V PEG REMARK 280 3350, 40 MM POTASSIUM/SODIUM TARTRATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298.15K 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 75.47500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 75.47500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.80000 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, G 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 GLU A 22 REMARK 465 THR A 23 REMARK 465 GLY A 24 REMARK 465 GLY A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 LEU A 28 REMARK 465 SER A 29 REMARK 465 MET A 30 REMARK 465 PHE A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 GLN A 34 REMARK 465 ALA A 35 REMARK 465 ALA A 36 REMARK 465 GLN A 37 REMARK 465 ILE A 452 REMARK 465 LYS A 453 REMARK 465 GLY A 454 REMARK 465 THR A 455 REMARK 465 LYS A 456 REMARK 465 THR A 457 REMARK 465 GLU A 458 REMARK 465 THR A 459 REMARK 465 SER A 460 REMARK 465 GLN A 461 REMARK 465 VAL A 462 REMARK 465 ALA A 463 REMARK 465 PRO A 464 REMARK 465 ALA A 465 REMARK 465 GLU B 763 REMARK 465 THR B 764 REMARK 465 ASP B 865 REMARK 465 PRO B 866 REMARK 465 THR B 867 REMARK 465 PRO B 868 REMARK 465 GLY B 1074 REMARK 465 LYS B 1075 REMARK 465 GLY B 1076 REMARK 465 SER B 1077 REMARK 465 ARG B 1078 REMARK 465 LEU B 1079 REMARK 465 PRO B 1080 REMARK 465 ASP B 1081 REMARK 465 LEU B 1082 REMARK 465 GLY B 1083 REMARK 465 SER B 1084 REMARK 465 ASP B 1085 REMARK 465 TYR B 1086 REMARK 465 LYS B 1087 REMARK 465 PRO B 1088 REMARK 465 PRO B 1089 REMARK 465 MET B 1090 REMARK 465 SER B 1091 REMARK 465 GLY B 1092 REMARK 465 SER B 1093 REMARK 465 ASN B 1094 REMARK 465 SER B 1095 REMARK 465 PRO B 1096 REMARK 465 HIS B 1097 REMARK 465 GLY B 1098 REMARK 465 SER B 1099 REMARK 465 PRO B 1100 REMARK 465 THR B 1101 REMARK 465 SER B 1102 REMARK 465 PRO B 1103 REMARK 465 LEU B 1104 REMARK 465 ASP B 1105 REMARK 465 SER B 1106 REMARK 465 ASN B 1107 REMARK 465 GLY B 1108 REMARK 465 THR B 1109 REMARK 465 LYS B 1110 REMARK 465 HIS B 1111 REMARK 465 HIS B 1112 REMARK 465 HIS B 1113 REMARK 465 HIS B 1114 REMARK 465 HIS B 1115 REMARK 465 HIS B 1116 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 TYR A 125 77.04 48.04 REMARK 500 LEU A 126 59.78 -113.96 REMARK 500 GLN A 196 -71.79 -64.76 REMARK 500 ASP A 209 128.03 -38.91 REMARK 500 ASN A 261 65.26 -106.83 REMARK 500 ARG A 307 -169.17 -127.59 REMARK 500 PHE A 321 -5.56 79.29 REMARK 500 HIS A 322 55.46 -102.79 REMARK 500 ASN A 370 76.51 51.25 REMARK 500 THR A 419 -60.88 -91.57 REMARK 500 PRO A 424 96.32 -68.77 REMARK 500 ASN B 999 12.78 57.42 REMARK 500 SER B1072 -141.55 60.02 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 A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 107 O REMARK 620 2 ASP A 110 OD1 74.4 REMARK 620 3 THR A 118 O 78.6 113.5 REMARK 620 4 THR A 118 OG1 106.7 67.4 64.4 REMARK 620 5 SER A 277 O 80.0 147.2 80.3 141.2 REMARK 620 N 1 2 3 4 DBREF 7NE1 A 24 453 UNP O95631 NET1_HUMAN 24 453 DBREF 7NE1 B 766 1107 UNP Q7TQG5 Q7TQG5_MOUSE 766 1107 SEQADV 7NE1 GLU A 22 UNP O95631 EXPRESSION TAG SEQADV 7NE1 THR A 23 UNP O95631 EXPRESSION TAG SEQADV 7NE1 GLY A 454 UNP O95631 EXPRESSION TAG SEQADV 7NE1 THR A 455 UNP O95631 EXPRESSION TAG SEQADV 7NE1 LYS A 456 UNP O95631 EXPRESSION TAG SEQADV 7NE1 THR A 457 UNP O95631 EXPRESSION TAG SEQADV 7NE1 GLU A 458 UNP O95631 EXPRESSION TAG SEQADV 7NE1 THR A 459 UNP O95631 EXPRESSION TAG SEQADV 7NE1 SER A 460 UNP O95631 EXPRESSION TAG SEQADV 7NE1 GLN A 461 UNP O95631 EXPRESSION TAG SEQADV 7NE1 VAL A 462 UNP O95631 EXPRESSION TAG SEQADV 7NE1 ALA A 463 UNP O95631 EXPRESSION TAG SEQADV 7NE1 PRO A 464 UNP O95631 EXPRESSION TAG SEQADV 7NE1 ALA A 465 UNP O95631 EXPRESSION TAG SEQADV 7NE1 GLU B 763 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 THR B 764 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 GLY B 765 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 GLY B 1108 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 THR B 1109 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 LYS B 1110 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1111 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1112 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1113 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1114 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1115 UNP Q7TQG5 EXPRESSION TAG SEQADV 7NE1 HIS B 1116 UNP Q7TQG5 EXPRESSION TAG SEQRES 1 A 444 GLU THR GLY GLY PRO GLY LEU SER MET PHE ALA GLY GLN SEQRES 2 A 444 ALA ALA GLN PRO ASP PRO CYS SER ASP GLU ASN GLY HIS SEQRES 3 A 444 PRO ARG ARG CYS ILE PRO ASP PHE VAL ASN ALA ALA PHE SEQRES 4 A 444 GLY LYS ASP VAL ARG VAL SER SER THR CYS GLY ARG PRO SEQRES 5 A 444 PRO ALA ARG TYR CYS VAL VAL SER GLU ARG GLY GLU GLU SEQRES 6 A 444 ARG LEU ARG SER CYS HIS LEU CYS ASN ALA SER ASP PRO SEQRES 7 A 444 LYS LYS ALA HIS PRO PRO ALA PHE LEU THR ASP LEU ASN SEQRES 8 A 444 ASN PRO HIS ASN LEU THR CYS TRP GLN SER GLU ASN TYR SEQRES 9 A 444 LEU GLN PHE PRO HIS ASN VAL THR LEU THR LEU SER LEU SEQRES 10 A 444 GLY LYS LYS PHE GLU VAL THR TYR VAL SER LEU GLN PHE SEQRES 11 A 444 CYS SER PRO ARG PRO GLU SER MET ALA ILE TYR LYS SER SEQRES 12 A 444 MET ASP TYR GLY ARG THR TRP VAL PRO PHE GLN PHE TYR SEQRES 13 A 444 SER THR GLN CYS ARG LYS MET TYR ASN ARG PRO HIS ARG SEQRES 14 A 444 ALA PRO ILE THR LYS GLN ASN GLU GLN GLU ALA VAL CYS SEQRES 15 A 444 THR ASP SER HIS THR ASP MET ARG PRO LEU SER GLY GLY SEQRES 16 A 444 LEU ILE ALA PHE SER THR LEU ASP GLY ARG PRO SER ALA SEQRES 17 A 444 HIS ASP PHE ASP ASN SER PRO VAL LEU GLN ASP TRP VAL SEQRES 18 A 444 THR ALA THR ASP ILE ARG VAL ALA PHE SER ARG LEU HIS SEQRES 19 A 444 THR PHE GLY ASP GLU ASN GLU ASP ASP SER GLU LEU ALA SEQRES 20 A 444 ARG ASP SER TYR PHE TYR ALA VAL SER ASP LEU GLN VAL SEQRES 21 A 444 GLY GLY ARG CYS LYS CYS ASN GLY HIS ALA ALA ARG CYS SEQRES 22 A 444 VAL ARG ASP ARG ASP ASP SER LEU VAL CYS ASP CYS ARG SEQRES 23 A 444 HIS ASN THR ALA GLY PRO GLU CYS ASP ARG CYS LYS PRO SEQRES 24 A 444 PHE HIS TYR ASP ARG PRO TRP GLN ARG ALA THR ALA ARG SEQRES 25 A 444 GLU ALA ASN GLU CYS VAL ALA CYS ASN CYS ASN LEU HIS SEQRES 26 A 444 ALA ARG ARG CYS ARG PHE ASN MET GLU LEU TYR LYS LEU SEQRES 27 A 444 SER GLY ARG LYS SER GLY GLY VAL CYS LEU ASN CYS ARG SEQRES 28 A 444 HIS ASN THR ALA GLY ARG HIS CYS HIS TYR CYS LYS GLU SEQRES 29 A 444 GLY TYR TYR ARG ASP MET GLY LYS PRO ILE THR HIS ARG SEQRES 30 A 444 LYS ALA CYS LYS ALA CYS ASP CYS HIS PRO VAL GLY ALA SEQRES 31 A 444 ALA GLY LYS THR CYS ASN GLN THR THR GLY GLN CYS PRO SEQRES 32 A 444 CYS LYS ASP GLY VAL THR GLY ILE THR CYS ASN ARG CYS SEQRES 33 A 444 ALA LYS GLY TYR GLN GLN SER ARG SER PRO ILE ALA PRO SEQRES 34 A 444 CYS ILE LYS GLY THR LYS THR GLU THR SER GLN VAL ALA SEQRES 35 A 444 PRO ALA SEQRES 1 B 354 GLU THR GLY GLU THR ARG VAL PRO GLU VAL PRO SER SER SEQRES 2 B 354 LEU HIS VAL ARG PRO LEU VAL THR SER ILE VAL VAL SER SEQRES 3 B 354 TRP THR PRO PRO GLU ASN GLN ASN ILE VAL VAL ARG GLY SEQRES 4 B 354 TYR ALA ILE GLY TYR GLY ILE GLY SER PRO HIS ALA GLN SEQRES 5 B 354 THR ILE LYS VAL ASP TYR LYS GLN ARG TYR TYR THR ILE SEQRES 6 B 354 GLU ASN LEU ASP PRO SER SER HIS TYR VAL ILE THR LEU SEQRES 7 B 354 LYS ALA PHE ASN ASN VAL GLY GLU GLY ILE PRO LEU TYR SEQRES 8 B 354 GLU SER ALA VAL THR ARG PRO HIS THR VAL PRO ASP PRO SEQRES 9 B 354 THR PRO MET MET PRO PRO VAL GLY VAL GLN ALA SER ILE SEQRES 10 B 354 LEU SER HIS ASP THR ILE ARG ILE THR TRP ALA ASP ASN SEQRES 11 B 354 SER LEU PRO LYS HIS GLN LYS ILE THR ASP SER ARG TYR SEQRES 12 B 354 TYR THR VAL ARG TRP LYS THR ASN ILE PRO ALA ASN THR SEQRES 13 B 354 LYS TYR LYS ASN ALA ASN ALA THR THR LEU SER TYR LEU SEQRES 14 B 354 VAL THR GLY LEU LYS PRO ASN THR LEU TYR GLU PHE SER SEQRES 15 B 354 VAL MET VAL THR LYS GLY ARG ARG SER SER THR TRP SER SEQRES 16 B 354 MET THR ALA HIS GLY ALA THR PHE GLU LEU VAL PRO THR SEQRES 17 B 354 SER PRO PRO LYS ASP VAL THR VAL VAL SER LYS GLU GLY SEQRES 18 B 354 LYS PRO ARG THR ILE ILE VAL ASN TRP GLN PRO PRO SER SEQRES 19 B 354 GLU ALA ASN GLY LYS ILE THR GLY TYR ILE ILE TYR TYR SEQRES 20 B 354 SER THR ASP VAL ASN ALA GLU ILE HIS ASP TRP VAL ILE SEQRES 21 B 354 GLU PRO VAL VAL GLY ASN ARG LEU THR HIS GLN ILE GLN SEQRES 22 B 354 GLU LEU THR LEU ASP THR PRO TYR TYR PHE LYS ILE GLN SEQRES 23 B 354 ALA ARG ASN SER LYS GLY MET GLY PRO MET SER GLU ALA SEQRES 24 B 354 VAL GLN PHE ARG THR PRO LYS ALA LEU GLY SER ALA GLY SEQRES 25 B 354 LYS GLY SER ARG LEU PRO ASP LEU GLY SER ASP TYR LYS SEQRES 26 B 354 PRO PRO MET SER GLY SER ASN SER PRO HIS GLY SER PRO SEQRES 27 B 354 THR SER PRO LEU ASP SER ASN GLY THR LYS HIS HIS HIS SEQRES 28 B 354 HIS HIS HIS HET GU4 G 1 27 HET YYJ G 2 28 HET NAG A 501 14 HET NAG A 502 14 HET NAG A 503 14 HET CA A 504 1 HET NO3 A 505 4 HET NO3 A 506 4 HET NO3 A 507 4 HET NAG B1201 14 HETNAM GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE HETNAM YYJ 1,3,4,6-TETRA-O-SULFO-BETA-D-FRUCTOFURANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM NO3 NITRATE ION HETSYN GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOSE; 2,3,4,6- HETSYN 2 GU4 TETRA-O-SULFONATO-D-GLUCOSE; 2,3,4,6-TETRA-O- HETSYN 3 GU4 SULFONATO-GLUCOSE 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 FORMUL 3 GU4 C6 H12 O18 S4 FORMUL 3 YYJ C6 H12 O18 S4 FORMUL 4 NAG 4(C8 H15 N O6) FORMUL 7 CA CA 2+ FORMUL 8 NO3 3(N O3 1-) HELIX 1 AA1 PRO A 104 THR A 109 5 6 HELIX 2 AA2 GLN A 180 ASN A 186 1 7 HELIX 3 AA3 ARG A 226 ASN A 234 5 9 HELIX 4 AA4 SER A 235 VAL A 242 1 8 HELIX 5 AA5 SER A 265 ASP A 270 1 6 HELIX 6 AA6 ASN A 353 SER A 360 1 8 HELIX 7 AA7 HIS A 397 LYS A 399 5 3 HELIX 8 AA8 GLU B 1016 TRP B 1020 5 5 SHEET 1 A 6 VAL A 64 VAL A 66 0 SHEET 2 A 6 VAL A 132 SER A 137 -1 N THR A 135 O ARG A 65 SHEET 3 A 6 ASP A 246 ARG A 253 -1 N PHE A 251 O VAL A 132 SHEET 4 A 6 SER A 158 SER A 164 -1 N SER A 164 O ASP A 246 SHEET 5 A 6 TRP A 171 TYR A 177 -1 N TYR A 177 O MET A 159 SHEET 6 A 6 VAL A 202 THR A 204 1 N VAL A 202 O PHE A 176 SHEET 1 B 2 ALA A 75 ARG A 83 0 SHEET 2 B 2 GLU A 86 CYS A 94 -1 N CYS A 94 O ALA A 75 SHEET 1 C 3 LEU A 217 SER A 221 0 SHEET 2 C 3 PHE A 142 GLN A 150 -1 N LEU A 149 O ILE A 218 SHEET 3 C 3 ASP A 278 CYS A 285 -1 N ARG A 284 O GLU A 143 SHEET 1 D 2 CYS A 294 ARG A 296 0 SHEET 2 D 2 LEU A 302 CYS A 304 -1 N VAL A 303 O VAL A 295 SHEET 1 E 2 ARG A 349 PHE A 352 0 SHEET 2 E 2 GLY A 366 LEU A 369 -1 N LEU A 369 O ARG A 349 SHEET 1 F 2 TYR A 387 ARG A 389 0 SHEET 2 F 2 CYS A 401 ALA A 403 -1 N LYS A 402 O TYR A 388 SHEET 1 G 3 SER B 775 PRO B 780 0 SHEET 2 G 3 ILE B 785 THR B 790 -1 N THR B 790 O SER B 775 SHEET 3 G 3 TYR B 824 ILE B 827 -1 N ILE B 827 O ILE B 785 SHEET 1 H 4 GLN B 814 ASP B 819 0 SHEET 2 H 4 GLY B 801 ILE B 808 -1 N TYR B 806 O GLN B 814 SHEET 3 H 4 HIS B 835 PHE B 843 -1 N PHE B 843 O GLY B 801 SHEET 4 H 4 LEU B 852 VAL B 857 -1 N ALA B 856 O TYR B 836 SHEET 1 I 3 GLN B 876 ILE B 879 0 SHEET 2 I 3 ILE B 885 THR B 888 -1 N THR B 888 O GLN B 876 SHEET 3 I 3 SER B 929 LEU B 931 -1 N TYR B 930 O ILE B 887 SHEET 1 J 4 LYS B 921 ALA B 925 0 SHEET 2 J 4 TYR B 905 THR B 912 -1 N TRP B 910 O LYS B 921 SHEET 3 J 4 LEU B 940 THR B 948 -1 N THR B 948 O TYR B 905 SHEET 4 J 4 ALA B 960 ALA B 963 -1 N GLY B 962 O TYR B 941 SHEET 1 K 3 THR B 977 SER B 980 0 SHEET 2 K 3 ILE B 988 ASN B 991 -1 N ASN B 991 O THR B 977 SHEET 3 K 3 THR B1031 ILE B1034 -1 N ILE B1034 O ILE B 988 SHEET 1 L 4 VAL B1021 VAL B1026 0 SHEET 2 L 4 GLY B1004 SER B1010 -1 N TYR B1009 O VAL B1021 SHEET 3 L 4 PRO B1042 ARG B1050 -1 N ARG B1050 O GLY B1004 SHEET 4 L 4 VAL B1062 ARG B1065 -1 N PHE B1064 O TYR B1043 SSBOND 1 CYS A 41 CYS A 51 1555 1555 2.03 SSBOND 2 CYS A 70 CYS A 94 1555 1555 2.04 SSBOND 3 CYS A 78 CYS A 91 1555 1555 2.04 SSBOND 4 CYS A 119 CYS A 152 1555 1555 2.04 SSBOND 5 CYS A 181 CYS A 203 1555 1555 2.04 SSBOND 6 CYS A 285 CYS A 294 1555 1555 2.04 SSBOND 7 CYS A 287 CYS A 304 1555 1555 2.03 SSBOND 8 CYS A 306 CYS A 315 1555 1555 2.04 SSBOND 9 CYS A 318 CYS A 338 1555 1555 2.04 SSBOND 10 CYS A 341 CYS A 350 1555 1555 2.04 SSBOND 11 CYS A 343 CYS A 368 1555 1555 2.03 SSBOND 12 CYS A 371 CYS A 380 1555 1555 2.04 SSBOND 13 CYS A 383 CYS A 401 1555 1555 2.03 SSBOND 14 CYS A 404 CYS A 416 1555 1555 2.03 SSBOND 15 CYS A 406 CYS A 423 1555 1555 2.03 SSBOND 16 CYS A 425 CYS A 434 1555 1555 2.04 SSBOND 17 CYS A 437 CYS A 451 1555 1555 2.04 LINK ND2 ASN A 95 C1 NAG A 503 1555 1555 1.43 LINK ND2 ASN A 116 C1 NAG A 501 1555 1555 1.43 LINK ND2 ASN A 131 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN B 924 C1 NAG B1201 1555 1555 1.44 LINK C1 GU4 G 1 O2 YYJ G 2 1555 1555 1.38 LINK O PHE A 107 CA CA A 504 1555 1555 2.40 LINK OD1 ASP A 110 CA CA A 504 1555 1555 2.47 LINK O THR A 118 CA CA A 504 1555 1555 2.39 LINK OG1 THR A 118 CA CA A 504 1555 1555 2.82 LINK O SER A 277 CA CA A 504 1555 1555 2.28 CISPEP 1 ARG A 72 PRO A 73 0 -0.85 CISPEP 2 PHE A 128 PRO A 129 0 4.37 CISPEP 3 ARG A 211 PRO A 212 0 3.44 CRYST1 150.950 49.600 157.250 90.00 99.38 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 0.006625 0.000000 0.001094 0.00000 SCALE2 0.000000 0.020161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006445 0.00000