HEADER ENDOCYTOSIS/EXOCYTOSIS 12-OCT-01 1K5W TITLE THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: TITLE 2 SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 270-421, C2B-DOMAIN; COMPND 5 SYNONYM: SYTI, P65; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS C2B-DOMAIN, C2-DOMAIN, SYNAPTOTAGMIN I, CALCIUM-BINDING, KEYWDS 2 PHOSPHOLIPID-BINDING, SYNAPSIS, NEUROTRANSMITTER RELEASE, SYNAPTIC KEYWDS 3 VESICLE EXOCYTOSIS, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.FERNANDEZ,D.ARAC,J.UBACH,S.H.GERBER,O.SHIN,Y.GAO,R.G.W.ANDERSON, AUTHOR 2 T.C.SUDHOF,J.RIZO REVDAT 5 22-MAY-24 1K5W 1 REMARK REVDAT 4 23-FEB-22 1K5W 1 REMARK LINK REVDAT 3 24-FEB-09 1K5W 1 VERSN REVDAT 2 01-APR-03 1K5W 1 JRNL REVDAT 1 23-JAN-02 1K5W 0 JRNL AUTH I.FERNANDEZ,D.ARAC,J.UBACH,S.H.GERBER,O.SHIN,Y.GAO, JRNL AUTH 2 R.G.ANDERSON,T.C.SUDHOF,J.RIZO JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 JRNL TITL 2 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING JRNL TITL 3 MACHINE. JRNL REF NEURON V. 32 1057 2001 JRNL REFN ISSN 0896-6273 JRNL PMID 11754837 JRNL DOI 10.1016/S0896-6273(01)00548-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.8, CNS 0.9 REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), BRUNGER ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2888 UNIQUE, REMARK 3 CONFORMATIONALLY SIGNIFICANT RESTRAINTS, 2492 ARE NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 214 DIHEDRAL ANGLE RESTRAINTS, 170 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1K5W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014599. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.0013M 15N, 13C C2B-DOMAIN; REMARK 210 1.3MM 15N, C2B-DOMAIN; 0.4MM 15N, REMARK 210 C2B-DOMAIN; 1MM 10% 13C, C2B- REMARK 210 DOMAIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNHA; 3D REMARK 210 -13_15N-SEPARATED_NOESY; 1H/13C- REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, NMRVIEW 4.12 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE MINIMUM NOE REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE WITH THE MINIMUM NOE ENERGY REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLN A 270 REMARK 465 GLU A 271 REMARK 465 LYS A 420 REMARK 465 LYS A 421 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H SER A 279 O VAL A 292 1.48 REMARK 500 O LEU A 294 H TYR A 339 1.57 REMARK 500 O VAL A 359 H VAL A 376 1.58 REMARK 500 O LEU A 280 H ILE A 401 1.58 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 1 LEU A 307 -160.38 -100.82 REMARK 500 1 LEU A 323 -51.66 -125.00 REMARK 500 1 ASN A 333 83.72 44.30 REMARK 500 1 LEU A 335 -16.33 -145.06 REMARK 500 1 TYR A 339 -63.63 -133.45 REMARK 500 1 GLU A 346 79.81 -116.57 REMARK 500 1 LYS A 366 -89.66 34.78 REMARK 500 1 TYR A 380 -73.21 -46.42 REMARK 500 1 ASN A 396 70.79 -114.29 REMARK 500 1 PRO A 397 35.37 -69.08 REMARK 500 1 ARG A 398 -44.35 -159.95 REMARK 500 2 GLU A 295 148.16 -174.16 REMARK 500 2 LEU A 307 -159.13 -115.46 REMARK 500 2 THR A 329 174.07 -58.76 REMARK 500 2 ASN A 333 83.74 46.85 REMARK 500 2 LEU A 335 -16.22 -146.17 REMARK 500 2 TYR A 339 -65.38 -131.72 REMARK 500 2 LYS A 366 -84.91 28.12 REMARK 500 2 ILE A 367 -70.68 -86.38 REMARK 500 2 TYR A 380 -75.89 -50.08 REMARK 500 2 ASN A 381 80.72 -69.82 REMARK 500 2 ARG A 398 -45.69 -158.37 REMARK 500 3 LEU A 307 -161.05 -101.43 REMARK 500 3 ASN A 333 84.32 43.68 REMARK 500 3 LEU A 335 -16.27 -146.42 REMARK 500 3 TYR A 339 -51.62 -134.84 REMARK 500 3 GLU A 346 79.12 -115.50 REMARK 500 3 LYS A 366 -88.79 32.96 REMARK 500 3 ILE A 367 -86.71 -22.96 REMARK 500 3 ASN A 381 -153.78 72.84 REMARK 500 3 SER A 382 165.25 64.22 REMARK 500 3 PRO A 397 44.93 -76.98 REMARK 500 3 ARG A 398 -46.74 -159.94 REMARK 500 4 LEU A 307 -160.43 -100.63 REMARK 500 4 ASN A 333 84.45 43.94 REMARK 500 4 LEU A 335 -14.36 -140.73 REMARK 500 4 TYR A 339 -63.43 -133.99 REMARK 500 4 GLU A 346 73.55 -117.21 REMARK 500 4 LYS A 366 -91.00 31.39 REMARK 500 4 TYR A 380 156.46 -44.09 REMARK 500 4 PRO A 397 42.88 -76.87 REMARK 500 4 ARG A 398 -47.02 -158.88 REMARK 500 5 LEU A 323 -50.07 -125.89 REMARK 500 5 THR A 329 175.42 -54.68 REMARK 500 5 ASN A 333 84.81 44.81 REMARK 500 5 LEU A 335 -15.94 -144.94 REMARK 500 5 TYR A 339 -71.61 -133.20 REMARK 500 5 LYS A 366 -86.79 16.10 REMARK 500 5 ILE A 367 -77.42 -77.57 REMARK 500 5 TYR A 380 -85.97 39.68 REMARK 500 REMARK 500 THIS ENTRY HAS 207 RAMACHANDRAN OUTLIERS. 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 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 302 O REMARK 620 2 ASP A 303 OD1 81.6 REMARK 620 3 ASP A 363 OD2 127.1 100.3 REMARK 620 4 ASP A 365 OD2 158.9 116.2 63.7 REMARK 620 5 ASP A 365 OD1 146.1 70.9 78.3 46.0 REMARK 620 6 ASP A 371 OD2 100.2 167.0 68.3 65.2 111.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 500 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 303 OD1 REMARK 620 2 ASP A 303 OD2 47.7 REMARK 620 3 ASP A 309 OD2 134.3 90.5 REMARK 620 4 ASP A 363 OD1 123.1 128.2 95.5 REMARK 620 5 ASP A 363 OD2 93.1 129.2 132.1 41.1 REMARK 620 6 TYR A 364 O 141.1 157.7 71.6 68.4 72.9 REMARK 620 7 ASP A 365 OD1 74.3 114.7 121.1 105.5 70.3 66.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 DBREF 1K5W A 270 421 UNP P21707 SYT1_RAT 270 421 SEQRES 1 A 152 GLN GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR SEQRES 2 A 152 VAL PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU SEQRES 3 A 152 ALA LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER SEQRES 4 A 152 ASP PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS SEQRES 5 A 152 ARG LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR SEQRES 6 A 152 LEU ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL SEQRES 7 A 152 PRO PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR SEQRES 8 A 152 VAL LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE SEQRES 9 A 152 GLY LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU SEQRES 10 A 152 LEU ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG SEQRES 11 A 152 PRO ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU SEQRES 12 A 152 VAL ASP ALA MET LEU ALA VAL LYS LYS HET CA A 500 1 HET CA A 501 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 GLY A 384 ASN A 396 1 13 HELIX 2 2 VAL A 409 ALA A 418 1 10 SHEET 1 A 4 TYR A 338 PHE A 345 0 SHEET 2 A 4 LEU A 289 LYS A 297 -1 N LEU A 289 O PHE A 345 SHEET 3 A 4 ASP A 275 LEU A 280 -1 N SER A 279 O VAL A 292 SHEET 4 A 4 ILE A 401 THR A 406 -1 O HIS A 405 N ILE A 276 SHEET 1 B 4 ARG A 322 LYS A 327 0 SHEET 2 B 4 PRO A 310 GLN A 318 -1 N ILE A 314 O LYS A 326 SHEET 3 B 4 VAL A 355 ASP A 363 -1 O THR A 360 N LYS A 313 SHEET 4 B 4 ASP A 371 GLY A 379 -1 O VAL A 376 N VAL A 359 LINK O MET A 302 CA CA A 501 1555 1555 2.82 LINK OD1 ASP A 303 CA CA A 500 1555 1555 2.59 LINK OD2 ASP A 303 CA CA A 500 1555 1555 2.82 LINK OD1 ASP A 303 CA CA A 501 1555 1555 2.81 LINK OD2 ASP A 309 CA CA A 500 1555 1555 2.23 LINK OD1 ASP A 363 CA CA A 500 1555 1555 2.81 LINK OD2 ASP A 363 CA CA A 500 1555 1555 3.31 LINK OD2 ASP A 363 CA CA A 501 1555 1555 2.80 LINK O TYR A 364 CA CA A 500 1555 1555 2.82 LINK OD1 ASP A 365 CA CA A 500 1555 1555 2.80 LINK OD2 ASP A 365 CA CA A 501 1555 1555 2.81 LINK OD1 ASP A 365 CA CA A 501 1555 1555 2.81 LINK OD2 ASP A 371 CA CA A 501 1555 1555 2.81 SITE 1 AC1 6 ASP A 303 ASP A 309 ASP A 363 TYR A 364 SITE 2 AC1 6 ASP A 365 CA A 501 SITE 1 AC2 6 MET A 302 ASP A 303 ASP A 363 ASP A 365 SITE 2 AC2 6 ASP A 371 CA A 500 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1