HEADER MEMBRANE PROTEIN 17-OCT-11 3U92 TITLE CRYSTAL STRUCTURE OF THE GLUK3 LIGAND BINDING DOMAIN COMPLEX WITH TITLE 2 KAINATE AND ZINC: P2221 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 433-546 AND 669-807; COMPND 5 SYNONYM: GLUK3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRIK3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22 MODIFIED KEYWDS MEMBRANE PROTEIN, ION CHANNEL EXPDTA X-RAY DIFFRACTION AUTHOR J.KUMAR,M.L.MAYER REVDAT 4 13-SEP-23 3U92 1 REMARK SEQADV LINK REVDAT 3 09-AUG-17 3U92 1 SOURCE REMARK REVDAT 2 19-DEC-12 3U92 1 JRNL REVDAT 1 26-SEP-12 3U92 0 JRNL AUTH J.VERAN,J.KUMAR,P.S.PINHEIRO,A.ATHANE,M.L.MAYER,D.PERRAIS, JRNL AUTH 2 C.MULLE JRNL TITL ZINC POTENTIATES GLUK3 GLUTAMATE RECEPTOR FUNCTION BY JRNL TITL 2 STABILIZING THE LIGAND BINDING DOMAIN DIMER INTERFACE. JRNL REF NEURON V. 76 565 2012 JRNL REFN ISSN 0896-6273 JRNL PMID 23141068 JRNL DOI 10.1016/J.NEURON.2012.08.027 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 51682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2643 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 42.5407 - 5.0595 0.99 2813 138 0.1902 0.1942 REMARK 3 2 5.0595 - 4.0168 1.00 2703 141 0.1405 0.1513 REMARK 3 3 4.0168 - 3.5093 1.00 2622 158 0.1858 0.2241 REMARK 3 4 3.5093 - 3.1886 1.00 2647 143 0.1959 0.2254 REMARK 3 5 3.1886 - 2.9601 1.00 2609 135 0.1952 0.2536 REMARK 3 6 2.9601 - 2.7856 1.00 2596 132 0.1949 0.2341 REMARK 3 7 2.7856 - 2.6461 0.99 2605 118 0.1941 0.2552 REMARK 3 8 2.6461 - 2.5310 0.99 2599 147 0.1881 0.2733 REMARK 3 9 2.5310 - 2.4335 0.99 2584 119 0.1918 0.2017 REMARK 3 10 2.4335 - 2.3496 0.99 2561 150 0.1903 0.2409 REMARK 3 11 2.3496 - 2.2761 0.99 2580 131 0.1910 0.2332 REMARK 3 12 2.2761 - 2.2111 0.99 2550 139 0.1809 0.2620 REMARK 3 13 2.2111 - 2.1529 0.99 2562 135 0.1932 0.2036 REMARK 3 14 2.1529 - 2.1003 0.98 2530 139 0.1976 0.2848 REMARK 3 15 2.1003 - 2.0526 0.99 2529 144 0.2050 0.2641 REMARK 3 16 2.0526 - 2.0089 0.98 2563 137 0.2247 0.2710 REMARK 3 17 2.0089 - 1.9687 0.98 2484 153 0.2325 0.2731 REMARK 3 18 1.9687 - 1.9316 0.98 2523 150 0.2441 0.3004 REMARK 3 19 1.9316 - 1.8971 0.93 2379 134 0.2657 0.3092 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 43.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.55650 REMARK 3 B22 (A**2) : -1.12640 REMARK 3 B33 (A**2) : 11.68300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.012 4170 REMARK 3 ANGLE : 1.043 5612 REMARK 3 CHIRALITY : 0.067 620 REMARK 3 PLANARITY : 0.004 702 REMARK 3 DIHEDRAL : 13.221 1558 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 3:136) REMARK 3 ORIGIN FOR THE GROUP (A): 44.7779 39.7326 15.2604 REMARK 3 T TENSOR REMARK 3 T11: 0.2767 T22: 0.1794 REMARK 3 T33: 0.2764 T12: -0.0539 REMARK 3 T13: -0.0795 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.1617 L22: 0.2478 REMARK 3 L33: 1.2544 L12: -0.3068 REMARK 3 L13: 0.4598 L23: -0.3817 REMARK 3 S TENSOR REMARK 3 S11: -0.0016 S12: -0.1271 S13: 0.0858 REMARK 3 S21: 0.0954 S22: -0.0361 S23: -0.2336 REMARK 3 S31: -0.2663 S32: 0.0668 S33: 0.0497 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 137:165) REMARK 3 ORIGIN FOR THE GROUP (A): 41.0438 25.5932 29.1067 REMARK 3 T TENSOR REMARK 3 T11: 0.3003 T22: 0.5370 REMARK 3 T33: 0.2610 T12: -0.0469 REMARK 3 T13: -0.0566 T23: 0.0633 REMARK 3 L TENSOR REMARK 3 L11: 1.2976 L22: 2.4927 REMARK 3 L33: 0.2820 L12: -0.7472 REMARK 3 L13: 0.4918 L23: -0.5369 REMARK 3 S TENSOR REMARK 3 S11: 0.0710 S12: -1.2391 S13: -0.2485 REMARK 3 S21: 0.2272 S22: -0.0315 S23: 0.3838 REMARK 3 S31: -0.1180 S32: 0.0406 S33: -0.0208 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 166:230) REMARK 3 ORIGIN FOR THE GROUP (A): 48.3435 31.2907 16.6951 REMARK 3 T TENSOR REMARK 3 T11: 0.2404 T22: 0.1992 REMARK 3 T33: 0.2813 T12: -0.0335 REMARK 3 T13: -0.1018 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.8868 L22: 0.0888 REMARK 3 L33: 0.7562 L12: -0.1481 REMARK 3 L13: 0.3032 L23: -0.1921 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: 0.0218 S13: 0.0786 REMARK 3 S21: 0.0123 S22: -0.1349 S23: -0.2336 REMARK 3 S31: -0.0399 S32: 0.1015 S33: 0.0681 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 231:256) REMARK 3 ORIGIN FOR THE GROUP (A): 48.1028 34.0687 -0.5403 REMARK 3 T TENSOR REMARK 3 T11: 0.2352 T22: 0.2695 REMARK 3 T33: 0.3047 T12: -0.0086 REMARK 3 T13: -0.0005 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.2308 L22: 1.3205 REMARK 3 L33: 0.9047 L12: -0.5532 REMARK 3 L13: 0.0996 L23: -0.2715 REMARK 3 S TENSOR REMARK 3 S11: 0.2458 S12: 0.1095 S13: 0.3134 REMARK 3 S21: -0.1139 S22: -0.2194 S23: -0.3594 REMARK 3 S31: 0.0163 S32: 0.2863 S33: 0.0163 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 3:32) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0072 19.8574 11.3963 REMARK 3 T TENSOR REMARK 3 T11: 0.2489 T22: 0.4101 REMARK 3 T33: 0.2774 T12: -0.0001 REMARK 3 T13: -0.0009 T23: 0.0288 REMARK 3 L TENSOR REMARK 3 L11: 0.1734 L22: 0.5739 REMARK 3 L33: 1.3371 L12: -0.1279 REMARK 3 L13: -0.3774 L23: 0.3277 REMARK 3 S TENSOR REMARK 3 S11: -0.0307 S12: -0.0111 S13: -0.1046 REMARK 3 S21: 0.0406 S22: -0.0018 S23: 0.2668 REMARK 3 S31: -0.0598 S32: -0.6471 S33: 0.0177 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 33:161) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0366 9.3089 22.0412 REMARK 3 T TENSOR REMARK 3 T11: 0.2637 T22: 0.2330 REMARK 3 T33: 0.3459 T12: -0.0060 REMARK 3 T13: 0.0117 T23: 0.0855 REMARK 3 L TENSOR REMARK 3 L11: 1.5717 L22: 0.2903 REMARK 3 L33: 1.7332 L12: 0.0508 REMARK 3 L13: -0.2607 L23: 0.0031 REMARK 3 S TENSOR REMARK 3 S11: -0.1143 S12: -0.1126 S13: -0.3742 REMARK 3 S21: 0.0099 S22: 0.0194 S23: -0.1018 REMARK 3 S31: 0.2393 S32: -0.0268 S33: 0.0401 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 162:237) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9900 15.3477 24.5367 REMARK 3 T TENSOR REMARK 3 T11: 0.2353 T22: 0.3612 REMARK 3 T33: 0.2726 T12: 0.0100 REMARK 3 T13: 0.0149 T23: 0.0447 REMARK 3 L TENSOR REMARK 3 L11: 1.4011 L22: 0.3500 REMARK 3 L33: 0.4469 L12: 0.1696 REMARK 3 L13: -0.0334 L23: -0.2277 REMARK 3 S TENSOR REMARK 3 S11: -0.0832 S12: -0.4306 S13: -0.1526 REMARK 3 S21: 0.0228 S22: 0.0192 S23: -0.0145 REMARK 3 S31: -0.0264 S32: 0.2072 S33: 0.0408 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 238:256) REMARK 3 ORIGIN FOR THE GROUP (A): 20.0110 29.6030 17.9322 REMARK 3 T TENSOR REMARK 3 T11: 0.3445 T22: 0.2623 REMARK 3 T33: 0.3565 T12: -0.0422 REMARK 3 T13: -0.0121 T23: -0.0574 REMARK 3 L TENSOR REMARK 3 L11: 0.4567 L22: 0.8240 REMARK 3 L33: 1.0242 L12: -0.5011 REMARK 3 L13: -0.5403 L23: 0.6923 REMARK 3 S TENSOR REMARK 3 S11: 0.1821 S12: -0.0984 S13: 0.0010 REMARK 3 S21: -0.1138 S22: -0.3570 S23: 0.2152 REMARK 3 S31: -0.3924 S32: 0.0680 S33: 0.0601 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 3U92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52357 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.58900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 1S50 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 8K, 0.1 M TRIS, 4 MM KAINATE, 2 REMARK 280 MM ZNACETATE, PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 45.02600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.02600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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 300 REMARK: THE OBSERVED BIOLOGICAL UNIT DOES NOT OCCUR FOR THE FULL REMARK 300 LENGTH PROTEIN THEREFORE, IS NOT BIOLOGICALLY RELEVANT 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -448.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 55.65400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 325 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 SER A 2 REMARK 465 GLU A 257 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 GLU B 257 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 HZ2 LYS B 241 ZN ZN B 261 1.39 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 GLU A 13 111.47 -169.74 REMARK 500 SER A 163 -76.52 -60.06 REMARK 500 LYS A 213 -153.75 -156.71 REMARK 500 SER A 253 -116.75 29.70 REMARK 500 GLU B 13 114.55 -167.66 REMARK 500 SER B 253 -110.90 65.83 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 ZN A 261 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 45 NE2 REMARK 620 2 HOH A 451 O 97.3 REMARK 620 3 HOH A 460 O 98.7 76.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 260 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 80 ND1 REMARK 620 2 HOH A 356 O 95.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 259 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 ND1 REMARK 620 2 GLU A 96 OE1 102.6 REMARK 620 3 ASP B 240 OD1 96.3 132.0 REMARK 620 4 ASP B 240 OD2 156.4 87.7 62.0 REMARK 620 5 HIS B 243 ND1 102.1 102.0 116.7 96.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 259 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 194 OE2 REMARK 620 2 GLU A 194 OE1 58.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 261 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 42 OE1 REMARK 620 2 GLU B 42 OE2 64.8 REMARK 620 3 LYS B 241 NZ 130.6 76.6 REMARK 620 4 HOH B 393 O 90.6 153.4 117.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 262 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 238 OE2 REMARK 620 2 GLU B 238 OE1 64.6 REMARK 620 3 HOH B 321 O 127.2 91.3 REMARK 620 4 HOH B 396 O 128.6 119.1 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 260 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 336 O REMARK 620 2 HOH B 361 O 82.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KAI A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KAI B 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U93 RELATED DB: PDB REMARK 900 RELATED ID: 3U94 RELATED DB: PDB REMARK 900 RELATED ID: 3S9E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE KAINATE RECEPTOR GLUK3 LIGAND BINDING REMARK 900 DOMAIN IN COMPLEX WITH (S)-GLUTAMATE REMARK 900 RELATED ID: 1S50 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE GLUR6 LIGAND BINDING CORE (S1S2A) IN COMPLEX REMARK 900 WITH GLUTAMATE AT 1.65 A RESOLUTION REMARK 900 RELATED ID: 1TXF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE IN COMPLEX WITH REMARK 900 GLUTAMATE AT 2.1 ANGSTROM RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN REMARK 999 OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REMARK 999 REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES REMARK 999 DISCONTINUOUSLY WITH THE REFERENCE DATABASE (433-546 AND 669-807) DBREF 3U92 A 3 116 UNP P42264 GRIK3_RAT 433 546 DBREF 3U92 A 119 257 UNP P42264 GRIK3_RAT 669 807 DBREF 3U92 B 3 116 UNP P42264 GRIK3_RAT 433 546 DBREF 3U92 B 119 257 UNP P42264 GRIK3_RAT 669 807 SEQADV 3U92 GLY A 1 UNP P42264 EXPRESSION TAG SEQADV 3U92 SER A 2 UNP P42264 EXPRESSION TAG SEQADV 3U92 GLY A 117 UNP P42264 LINKER SEQADV 3U92 THR A 118 UNP P42264 LINKER SEQADV 3U92 GLY B 1 UNP P42264 EXPRESSION TAG SEQADV 3U92 SER B 2 UNP P42264 EXPRESSION TAG SEQADV 3U92 GLY B 117 UNP P42264 LINKER SEQADV 3U92 THR B 118 UNP P42264 LINKER SEQRES 1 A 257 GLY SER ASN ARG SER LEU ILE VAL THR THR LEU LEU GLU SEQRES 2 A 257 GLU PRO PHE VAL MET PHE ARG LYS SER ASP ARG THR LEU SEQRES 3 A 257 TYR GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE ASP LEU SEQRES 4 A 257 LEU LYS GLU LEU ALA HIS ILE LEU GLY PHE SER TYR GLU SEQRES 5 A 257 ILE ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA GLN ASP SEQRES 6 A 257 ASP LYS GLY GLN TRP ASN GLY MET VAL LYS GLU LEU ILE SEQRES 7 A 257 ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU THR ILE SEQRES 8 A 257 THR HIS VAL ARG GLU LYS ALA ILE ASP PHE SER LYS PRO SEQRES 9 A 257 PHE MET THR LEU GLY VAL SER ILE LEU TYR ARG LYS GLY SEQRES 10 A 257 THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS GLN THR SEQRES 11 A 257 LYS ILE GLU TYR GLY ALA VAL LYS ASP GLY ALA THR MET SEQRES 12 A 257 THR PHE PHE LYS LYS SER LYS ILE SER THR PHE GLU LYS SEQRES 13 A 257 MET TRP ALA PHE MET SER SER LYS PRO SER ALA LEU VAL SEQRES 14 A 257 LYS ASN ASN GLU GLU GLY ILE GLN ARG THR LEU THR ALA SEQRES 15 A 257 ASP TYR ALA LEU LEU MET GLU SER THR THR ILE GLU TYR SEQRES 16 A 257 ILE THR GLN ARG ASN CYS ASN LEU THR GLN ILE GLY GLY SEQRES 17 A 257 LEU ILE ASP SER LYS GLY TYR GLY ILE GLY THR PRO MET SEQRES 18 A 257 GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA ILE LEU SEQRES 19 A 257 GLN LEU GLN GLU GLU ASP LYS LEU HIS ILE MET LYS GLU SEQRES 20 A 257 LYS TRP TRP ARG GLY SER GLY CYS PRO GLU SEQRES 1 B 257 GLY SER ASN ARG SER LEU ILE VAL THR THR LEU LEU GLU SEQRES 2 B 257 GLU PRO PHE VAL MET PHE ARG LYS SER ASP ARG THR LEU SEQRES 3 B 257 TYR GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE ASP LEU SEQRES 4 B 257 LEU LYS GLU LEU ALA HIS ILE LEU GLY PHE SER TYR GLU SEQRES 5 B 257 ILE ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA GLN ASP SEQRES 6 B 257 ASP LYS GLY GLN TRP ASN GLY MET VAL LYS GLU LEU ILE SEQRES 7 B 257 ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU THR ILE SEQRES 8 B 257 THR HIS VAL ARG GLU LYS ALA ILE ASP PHE SER LYS PRO SEQRES 9 B 257 PHE MET THR LEU GLY VAL SER ILE LEU TYR ARG LYS GLY SEQRES 10 B 257 THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS GLN THR SEQRES 11 B 257 LYS ILE GLU TYR GLY ALA VAL LYS ASP GLY ALA THR MET SEQRES 12 B 257 THR PHE PHE LYS LYS SER LYS ILE SER THR PHE GLU LYS SEQRES 13 B 257 MET TRP ALA PHE MET SER SER LYS PRO SER ALA LEU VAL SEQRES 14 B 257 LYS ASN ASN GLU GLU GLY ILE GLN ARG THR LEU THR ALA SEQRES 15 B 257 ASP TYR ALA LEU LEU MET GLU SER THR THR ILE GLU TYR SEQRES 16 B 257 ILE THR GLN ARG ASN CYS ASN LEU THR GLN ILE GLY GLY SEQRES 17 B 257 LEU ILE ASP SER LYS GLY TYR GLY ILE GLY THR PRO MET SEQRES 18 B 257 GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA ILE LEU SEQRES 19 B 257 GLN LEU GLN GLU GLU ASP LYS LEU HIS ILE MET LYS GLU SEQRES 20 B 257 LYS TRP TRP ARG GLY SER GLY CYS PRO GLU HET KAI A 258 28 HET ZN A 259 1 HET ZN A 260 1 HET ZN A 261 1 HET CL A 262 1 HET KAI B 258 28 HET ZN B 259 1 HET ZN B 260 1 HET ZN B 261 1 HET ZN B 262 1 HET ZN B 263 1 HET CL B 264 1 HETNAM KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN KAI KAINATE FORMUL 3 KAI 2(C10 H15 N O4) FORMUL 4 ZN 8(ZN 2+) FORMUL 7 CL 2(CL 1-) FORMUL 15 HOH *360(H2 O) HELIX 1 1 TYR A 27 ASP A 30 5 4 HELIX 2 2 GLY A 34 GLY A 48 1 15 HELIX 3 3 ASN A 71 ASP A 79 1 9 HELIX 4 4 THR A 92 LYS A 97 1 6 HELIX 5 5 SER A 122 LYS A 128 1 7 HELIX 6 6 GLY A 140 SER A 149 1 10 HELIX 7 7 ILE A 151 LYS A 164 1 14 HELIX 8 8 ASN A 171 ALA A 182 1 12 HELIX 9 9 SER A 190 GLN A 198 1 9 HELIX 10 10 PRO A 224 GLU A 239 1 16 HELIX 11 11 ASP A 240 ARG A 251 1 12 HELIX 12 12 TYR B 27 ASP B 30 5 4 HELIX 13 13 GLY B 34 GLY B 48 1 15 HELIX 14 14 ASN B 71 ASP B 79 1 9 HELIX 15 15 THR B 92 LYS B 97 1 6 HELIX 16 16 SER B 122 LYS B 128 1 7 HELIX 17 17 GLY B 140 SER B 149 1 10 HELIX 18 18 ILE B 151 LYS B 164 1 14 HELIX 19 19 PRO B 165 LEU B 168 5 4 HELIX 20 20 ASN B 171 ALA B 182 1 12 HELIX 21 21 SER B 190 GLN B 198 1 9 HELIX 22 22 TYR B 225 GLU B 239 1 15 HELIX 23 23 ASP B 240 ARG B 251 1 12 SHEET 1 A 3 TYR A 51 LEU A 55 0 SHEET 2 A 3 LEU A 6 THR A 10 1 N VAL A 8 O ARG A 54 SHEET 3 A 3 LEU A 84 ALA A 85 1 O LEU A 84 N THR A 9 SHEET 1 B 2 MET A 18 PHE A 19 0 SHEET 2 B 2 PHE A 32 GLU A 33 -1 O GLU A 33 N MET A 18 SHEET 1 C 2 ILE A 99 PHE A 101 0 SHEET 2 C 2 GLY A 218 PRO A 220 -1 O THR A 219 N ASP A 100 SHEET 1 D 2 MET A 106 LEU A 108 0 SHEET 2 D 2 LYS A 213 TYR A 215 -1 O LYS A 213 N LEU A 108 SHEET 1 E 4 GLU A 133 GLY A 135 0 SHEET 2 E 4 TYR A 184 GLU A 189 1 O LEU A 187 N GLY A 135 SHEET 3 E 4 VAL A 110 ARG A 115 -1 N LEU A 113 O LEU A 186 SHEET 4 E 4 LEU A 203 ILE A 206 -1 O THR A 204 N TYR A 114 SHEET 1 F 3 TYR B 51 LEU B 55 0 SHEET 2 F 3 LEU B 6 THR B 10 1 N VAL B 8 O ARG B 54 SHEET 3 F 3 LEU B 84 ALA B 85 1 O LEU B 84 N THR B 9 SHEET 1 G 2 MET B 18 PHE B 19 0 SHEET 2 G 2 PHE B 32 GLU B 33 -1 O GLU B 33 N MET B 18 SHEET 1 H 2 ILE B 99 PHE B 101 0 SHEET 2 H 2 GLY B 218 PRO B 220 -1 O THR B 219 N ASP B 100 SHEET 1 I 2 MET B 106 LEU B 108 0 SHEET 2 I 2 LYS B 213 TYR B 215 -1 O LYS B 213 N LEU B 108 SHEET 1 J 4 GLU B 133 GLY B 135 0 SHEET 2 J 4 TYR B 184 GLU B 189 1 O LEU B 187 N GLY B 135 SHEET 3 J 4 VAL B 110 ARG B 115 -1 N LEU B 113 O LEU B 186 SHEET 4 J 4 LEU B 203 ILE B 206 -1 O THR B 204 N TYR B 114 SSBOND 1 CYS A 201 CYS A 255 1555 1555 2.05 SSBOND 2 CYS B 201 CYS B 255 1555 1555 2.03 LINK NE2 HIS A 45 ZN ZN A 261 1555 1555 2.10 LINK ND1 HIS A 80 ZN ZN A 260 1555 1555 1.99 LINK ND1 HIS A 93 ZN ZN B 259 1555 1555 2.01 LINK OE1 GLU A 96 ZN ZN B 259 1555 1555 2.02 LINK OE2 GLU A 194 ZN ZN A 259 1555 1555 1.99 LINK OE1 GLU A 194 ZN ZN A 259 1555 1555 2.34 LINK ZN ZN A 260 O HOH A 356 1555 1555 2.12 LINK ZN ZN A 261 O HOH A 451 1555 1555 2.15 LINK ZN ZN A 261 O HOH A 460 1555 1555 2.08 LINK OE1 GLU B 42 ZN ZN B 261 1555 1555 1.99 LINK OE2 GLU B 42 ZN ZN B 261 1555 1555 2.09 LINK ND1 HIS B 80 ZN ZN B 263 1555 1555 2.00 LINK OE2 GLU B 238 ZN ZN B 262 1555 1555 2.02 LINK OE1 GLU B 238 ZN ZN B 262 1555 1555 2.07 LINK OD1 ASP B 240 ZN ZN B 259 1555 1555 1.97 LINK OD2 ASP B 240 ZN ZN B 259 1555 1555 2.18 LINK NZ LYS B 241 ZN ZN B 261 1555 1555 2.19 LINK ND1 HIS B 243 ZN ZN B 259 1555 1555 2.02 LINK ZN ZN B 260 O HOH B 336 1555 1555 2.15 LINK ZN ZN B 260 O HOH B 361 1555 1555 2.19 LINK ZN ZN B 261 O HOH B 393 1555 1555 2.08 LINK ZN ZN B 262 O HOH B 321 1555 1555 2.10 LINK ZN ZN B 262 O HOH B 396 1555 1555 2.10 CISPEP 1 GLU A 14 PRO A 15 0 0.97 CISPEP 2 ARG A 251 GLY A 252 0 -12.49 CISPEP 3 GLU B 14 PRO B 15 0 2.47 CISPEP 4 SER B 253 GLY B 254 0 26.51 SITE 1 AC1 14 GLU A 13 TYR A 61 PRO A 88 THR A 90 SITE 2 AC1 14 ARG A 95 VAL A 137 GLY A 140 ALA A 141 SITE 3 AC1 14 THR A 142 ASN A 172 GLU A 189 HOH A 270 SITE 4 AC1 14 HOH A 285 HOH A 353 SITE 1 AC2 4 GLU A 194 HIS A 243 LYS A 246 GLU A 247 SITE 1 AC3 3 HIS A 80 HOH A 356 HIS B 93 SITE 1 AC4 3 HIS A 45 HOH A 451 HOH A 460 SITE 1 AC5 2 ARG A 54 LEU A 55 SITE 1 AC6 13 GLU B 13 TYR B 61 PRO B 88 THR B 90 SITE 2 AC6 13 ARG B 95 GLY B 140 ALA B 141 THR B 142 SITE 3 AC6 13 ASN B 172 GLU B 189 HOH B 280 HOH B 287 SITE 4 AC6 13 HOH B 314 SITE 1 AC7 4 HIS A 93 GLU A 96 ASP B 240 HIS B 243 SITE 1 AC8 3 HOH B 335 HOH B 336 HOH B 361 SITE 1 AC9 4 GLU B 42 HIS B 45 LYS B 241 HOH B 393 SITE 1 BC1 3 GLU B 238 HOH B 321 HOH B 396 SITE 1 BC2 1 HIS B 80 SITE 1 BC3 2 ARG B 31 LEU B 55 CRYST1 129.537 55.654 90.052 90.00 90.00 90.00 P 2 2 21 8 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 0.007720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011105 0.00000