HEADER MEMBRANE PROTEIN 22-SEP-09 2KOG TITLE LIPID-BOUND SYNAPTOBREVIN SOLUTION NMR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VESICLE-ASSOCIATED MEMBRANE PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VAMP-2, SYNAPTOBREVIN-2; COMPND 5 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: VAMP2, SYB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS SYNAPTOBREVIN, VAMP2, DPC MICELLE, SNARE, COILED COIL, MEMBRANE KEYWDS 2 FUSION, TRANSMEMBRANE, SYNAPTIC VESICLE, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.F.ELLENA,B.LIANG,M.WIKTOR,A.STEIN,D.S.CAFISO,R.JAHN,L.K.TAMM REVDAT 3 16-MAR-22 2KOG 1 REMARK REVDAT 2 15-DEC-09 2KOG 1 JRNL REVDAT 1 01-DEC-09 2KOG 0 JRNL AUTH J.F.ELLENA,B.LIANG,M.WIKTOR,A.STEIN,D.S.CAFISO,R.JAHN, JRNL AUTH 2 L.K.TAMM JRNL TITL DYNAMIC STRUCTURE OF LIPID-BOUND SYNAPTOBREVIN SUGGESTS A JRNL TITL 2 NUCLEATION-PROPAGATION MECHANISM FOR TRANS-SNARE COMPLEX JRNL TITL 3 FORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 20306 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19918058 JRNL DOI 10.1073/PNAS.0908317106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000101373. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 SYNAPTOBREVIN-1, 200 MM DPC-2, REMARK 210 20 MM MES-3, 150 MM NACL-4, 5 MM REMARK 210 DTT-5, 1 MM EDTA-6, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 CBCA(CO)NH; 3D HNHA; 3D 1H-15N REMARK 210 NOESY; 3D H(CCO)NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 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 ALA A 3 112.14 -168.71 REMARK 500 1 ALA A 12 73.21 50.71 REMARK 500 1 ALA A 14 118.92 59.59 REMARK 500 1 PRO A 23 155.22 -39.29 REMARK 500 1 ASN A 29 -88.60 -159.03 REMARK 500 1 ARG A 30 -65.68 -170.09 REMARK 500 1 SER A 61 6.20 54.20 REMARK 500 1 LEU A 70 -96.64 -47.28 REMARK 500 1 GLN A 71 -77.65 -173.44 REMARK 500 1 SER A 75 154.87 57.53 REMARK 500 1 TRP A 90 78.97 -153.25 REMARK 500 2 ALA A 5 13.24 -170.22 REMARK 500 2 ALA A 6 81.65 50.85 REMARK 500 2 ALA A 12 74.82 58.83 REMARK 500 2 PRO A 19 -174.17 -60.19 REMARK 500 2 ALA A 21 164.80 -45.57 REMARK 500 2 PRO A 22 155.49 -42.36 REMARK 500 2 ASN A 25 -67.72 -173.32 REMARK 500 2 LEU A 26 141.02 58.16 REMARK 500 2 LYS A 59 85.16 56.50 REMARK 500 2 SER A 61 -39.67 172.87 REMARK 500 2 GLU A 62 -84.49 -141.20 REMARK 500 2 ASP A 65 -21.06 72.15 REMARK 500 2 ALA A 74 94.95 56.36 REMARK 500 2 SER A 75 172.90 51.00 REMARK 500 2 GLN A 76 -74.40 -103.25 REMARK 500 2 PHE A 77 -6.44 -154.43 REMARK 500 2 TRP A 90 43.35 -89.13 REMARK 500 3 THR A 4 90.58 42.35 REMARK 500 3 ALA A 6 -140.89 -59.92 REMARK 500 3 ALA A 12 74.67 -164.82 REMARK 500 3 GLU A 16 89.50 48.25 REMARK 500 3 PRO A 20 107.51 -41.19 REMARK 500 3 ASN A 25 79.33 55.61 REMARK 500 3 SER A 28 -6.68 69.96 REMARK 500 3 ARG A 30 133.51 60.82 REMARK 500 3 LEU A 32 26.26 -70.32 REMARK 500 3 GLU A 55 95.21 41.85 REMARK 500 3 GLU A 62 -79.58 -172.38 REMARK 500 3 ASP A 65 -122.89 57.26 REMARK 500 3 ALA A 67 -5.15 63.80 REMARK 500 3 ALA A 69 87.37 -66.22 REMARK 500 3 ALA A 72 16.82 -155.91 REMARK 500 3 PHE A 77 -0.06 56.63 REMARK 500 3 LYS A 91 -123.40 56.11 REMARK 500 4 SER A 2 -109.26 46.66 REMARK 500 4 ALA A 5 -6.20 -169.81 REMARK 500 4 ALA A 6 87.85 56.03 REMARK 500 4 PRO A 9 155.17 -37.18 REMARK 500 4 ALA A 12 72.84 -164.97 REMARK 500 REMARK 500 THIS ENTRY HAS 342 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16508 RELATED DB: BMRB DBREF 2KOG A 1 116 UNP P63045 VAMP2_RAT 1 116 SEQRES 1 A 119 GLY SER HIS MET SER ALA THR ALA ALA THR VAL PRO PRO SEQRES 2 A 119 ALA ALA PRO ALA GLY GLU GLY GLY PRO PRO ALA PRO PRO SEQRES 3 A 119 PRO ASN LEU THR SER ASN ARG ARG LEU GLN GLN THR GLN SEQRES 4 A 119 ALA GLN VAL ASP GLU VAL VAL ASP ILE MET ARG VAL ASN SEQRES 5 A 119 VAL ASP LYS VAL LEU GLU ARG ASP GLN LYS LEU SER GLU SEQRES 6 A 119 LEU ASP ASP ARG ALA ASP ALA LEU GLN ALA GLY ALA SER SEQRES 7 A 119 GLN PHE GLU THR SER ALA ALA LYS LEU LYS ARG LYS TYR SEQRES 8 A 119 TRP TRP LYS ASN LEU LYS MET MET ILE ILE LEU GLY VAL SEQRES 9 A 119 ILE CYS ALA ILE ILE LEU ILE ILE ILE ILE VAL TYR PHE SEQRES 10 A 119 SER THR HELIX 1 1 ARG A 30 THR A 35 1 6 HELIX 2 2 GLN A 36 GLU A 55 1 20 HELIX 3 3 ALA A 74 TRP A 89 1 16 HELIX 4 4 TRP A 90 THR A 116 1 27 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