HEADER EXOCYTOSIS 20-NOV-19 6LCY TITLE CRYSTAL STRUCTURE OF SYNAPTOTAGMIN-7 C2B IN COMPLEX WITH IP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2B DOMAIN; COMPND 5 SYNONYM: SYNAPTOTAGMIN VII,SYTVII; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SYT7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SYNAPTOTAGMIN-7, IP6, INSULIN SECRETION, EXOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,X.ZHANG,F.RAO,C.WANG REVDAT 3 22-NOV-23 6LCY 1 REMARK REVDAT 2 17-NOV-21 6LCY 1 JRNL REVDAT 1 03-MAR-21 6LCY 0 JRNL AUTH X.ZHANG,N.LI,J.ZHANG,Y.ZHANG,X.YANG,Y.LUO,B.ZHANG,Z.XU, JRNL AUTH 2 Z.ZHU,X.YANG,Y.YAN,B.LIN,S.WANG,D.CHEN,C.YE,Y.DING,M.LOU, JRNL AUTH 3 Q.WU,Z.HOU,K.ZHANG,Z.LIANG,A.WEI,B.WANG,C.WANG,N.JIANG, JRNL AUTH 4 W.ZHANG,G.XIAO,C.MA,Y.REN,X.QI,W.HAN,C.WANG,F.RAO JRNL TITL 5-IP 7 IS A GPCR MESSENGER MEDIATING NEURAL CONTROL OF JRNL TITL 2 SYNAPTOTAGMIN-DEPENDENT INSULIN EXOCYTOSIS AND GLUCOSE JRNL TITL 3 HOMEOSTASIS. JRNL REF NAT METAB V. 3 1400 2021 JRNL REFN ISSN 2522-5812 JRNL PMID 34663975 JRNL DOI 10.1038/S42255-021-00468-7 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.13 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 14713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 740 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 10.0000 - 3.9336 0.99 2863 149 0.1666 0.2040 REMARK 3 2 3.9336 - 3.1224 1.00 2809 159 0.1950 0.2308 REMARK 3 3 3.1224 - 2.7278 1.00 2829 135 0.2352 0.2352 REMARK 3 4 2.7278 - 2.4784 0.99 2806 141 0.2482 0.2993 REMARK 3 5 2.4784 - 2.3010 0.96 2666 156 0.2455 0.3197 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.07 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-19 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP 3.25 REMARK 200 STARTING MODEL: 3N5A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NACL, 50MM TRIS-CL, 1MM EDTA, REMARK 280 1MM DDT, 5MM IP6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.80133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.60267 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 26.70200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.50333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.90067 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 259 REMARK 465 PRO A 260 REMARK 465 GLY A 261 REMARK 465 SER A 262 REMARK 465 GLY A 263 REMARK 465 SER A 264 REMARK 465 GLY A 265 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 ILE A 288 -71.42 -90.46 REMARK 500 THR A 301 -167.40 -125.01 REMARK 500 ASP A 303 75.96 -119.32 REMARK 500 LYS A 313 -129.58 57.53 REMARK 500 SER A 362 -154.93 -115.04 REMARK 500 SER A 376 -158.78 -128.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP A 502 DBREF 6LCY A 263 403 UNP Q9R0N7 SYT7_MOUSE 263 403 SEQADV 6LCY GLY A 259 UNP Q9R0N7 EXPRESSION TAG SEQADV 6LCY PRO A 260 UNP Q9R0N7 EXPRESSION TAG SEQADV 6LCY GLY A 261 UNP Q9R0N7 EXPRESSION TAG SEQADV 6LCY SER A 262 UNP Q9R0N7 EXPRESSION TAG SEQRES 1 A 145 GLY PRO GLY SER GLY SER GLY SER ARG GLY GLU LEU LEU SEQRES 2 A 145 LEU SER LEU CYS TYR ASN PRO SER ALA ASN SER ILE ILE SEQRES 3 A 145 VAL ASN ILE ILE LYS ALA ARG ASN LEU LYS ALA MET ASP SEQRES 4 A 145 ILE GLY GLY THR SER ASP PRO TYR VAL LYS VAL TRP LEU SEQRES 5 A 145 MET TYR LYS ASP LYS ARG VAL GLU LYS LYS LYS THR VAL SEQRES 6 A 145 THR LYS LYS ARG ASN LEU ASN PRO ILE PHE ASN GLU SER SEQRES 7 A 145 PHE ALA PHE ASP ILE PRO THR GLU LYS LEU ARG GLU THR SEQRES 8 A 145 THR ILE ILE ILE THR VAL MET ASP LYS ASP LYS LEU SER SEQRES 9 A 145 ARG ASN ASP VAL ILE GLY LYS ILE TYR LEU SER TRP LYS SEQRES 10 A 145 SER GLY PRO GLY GLU VAL LYS HIS TRP LYS ASP MET ILE SEQRES 11 A 145 ALA ARG PRO ARG GLN PRO VAL ALA GLN TRP HIS GLN LEU SEQRES 12 A 145 LYS ALA HET IHP A 501 42 HET IHP A 502 42 HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 IHP 2(C6 H18 O24 P6) FORMUL 4 HOH *34(H2 O) HELIX 1 AA1 PRO A 342 ARG A 347 5 6 HELIX 2 AA2 GLY A 377 ARG A 390 1 14 SHEET 1 AA1 4 ILE A 332 ASP A 340 0 SHEET 2 AA1 4 SER A 282 ARG A 291 -1 N VAL A 285 O PHE A 337 SHEET 3 AA1 4 GLU A 269 ASN A 277 -1 N LEU A 271 O LYS A 289 SHEET 4 AA1 4 VAL A 395 GLN A 400 -1 O VAL A 395 N LEU A 274 SHEET 1 AA2 4 LYS A 315 LYS A 321 0 SHEET 2 AA2 4 PRO A 304 TYR A 312 -1 N LEU A 310 O VAL A 317 SHEET 3 AA2 4 THR A 349 ASP A 357 -1 O MET A 356 N TYR A 305 SHEET 4 AA2 4 ASP A 365 LEU A 372 -1 O LEU A 372 N ILE A 351 SITE 1 AC1 12 TYR A 305 LYS A 307 TRP A 309 TYR A 312 SITE 2 AC1 12 LYS A 313 LYS A 315 ARG A 316 LYS A 319 SITE 3 AC1 12 LYS A 321 LYS A 345 ASN A 364 HOH A 625 SITE 1 AC2 6 LYS A 289 ARG A 291 LYS A 326 ARG A 327 SITE 2 AC2 6 LYS A 360 TRP A 398 CRYST1 104.406 104.406 53.404 90.00 90.00 120.00 P 61 6 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 0.009578 0.005530 0.000000 0.00000 SCALE2 0.000000 0.011060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018725 0.00000