HEADER MEMBRANE PROTEIN 18-JUN-22 8A6M TITLE PHOSPHATIDYLSERINE-DEPENDENT SYNAPTIC VESICLE MEMBRANE SCULPTING BY TITLE 2 SYNAPTOGYRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 1B OF SYNAPTOGYRIN-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SYNGR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TETRASPAN VESICLE MEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.K.YU,G.N.EASTEP,D.FLORES,M.ZWECKSTETTER REVDAT 3 26-JUL-23 8A6M 1 JRNL REVDAT 2 31-MAY-23 8A6M 1 JRNL REVDAT 1 24-MAY-23 8A6M 0 JRNL AUTH T.YU,D.FLORES-SOLIS,G.N.EASTEP,S.BECKER,M.ZWECKSTETTER JRNL TITL PHOSPHATIDYLSERINE-DEPENDENT STRUCTURE OF SYNAPTOGYRIN JRNL TITL 2 REMODELS THE SYNAPTIC VESICLE MEMBRANE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 926 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37217654 JRNL DOI 10.1038/S41594-023-01004-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8A6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123762. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313; 313 REMARK 210 PH : 8.5; 8.5 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : AMBIENT PA; AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-15N] SYNAPTOGYRIN 1B, REMARK 210 90% H2O/10% D2O; 0.8 MM [U-13C; REMARK 210 U-15N; U-2H] SYNAPTOGYRIN 1B, 90% REMARK 210 H2O/10% D2O; 0.8 MM [U-15N; U- REMARK 210 2H] SYNAPTOGYRIN 1B, 100% D2O; REMARK 210 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 SYNAPTOGYRIN 1B, 100% D2O; 0.8 REMARK 210 MM [U-15N] SYNAPTOGYRIN 1B, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D HNCB; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS, NMRDRAW, CYANA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 470 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A -18 REMARK 465 GLY A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 ALA A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 TYR A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 PHE A 177 REMARK 465 GLN A 178 REMARK 465 GLU A 179 REMARK 465 GLU A 180 REMARK 465 TYR A 181 REMARK 465 SER A 182 REMARK 465 THR A 183 REMARK 465 LEU A 184 REMARK 465 PHE A 185 REMARK 465 PRO A 186 REMARK 465 ALA A 187 REMARK 465 SER A 188 REMARK 465 ALA A 189 REMARK 465 GLN A 190 REMARK 465 PRO A 191 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 HIS A 25 NE2 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 O ALA A 150 HG SER A 154 1.59 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 3 ALA A 52 136.42 -179.15 REMARK 500 3 CYS A 59 125.07 -170.04 REMARK 500 5 THR A 144 41.42 -97.47 REMARK 500 6 TYR A 48 -69.11 -122.99 REMARK 500 9 ASN A 45 -82.38 -89.18 REMARK 500 10 GLN A 129 -39.90 -37.79 REMARK 500 10 SER A 133 34.40 -141.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34738 RELATED DB: BMRB REMARK 900 PHOSPHATIDYLSERINE-DEPENDENT SYNAPTIC VESICLE MEMBRANE SCULPTING BY REMARK 900 SYNAPTOGYRIN DBREF 8A6M A 1 191 UNP O43759 SNG1_HUMAN 1 191 SEQADV 8A6M MET A -18 UNP O43759 INITIATING METHIONINE SEQADV 8A6M GLY A -17 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -16 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -15 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -14 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -13 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -12 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -11 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A -10 UNP O43759 EXPRESSION TAG SEQADV 8A6M ALA A -9 UNP O43759 EXPRESSION TAG SEQADV 8A6M SER A -8 UNP O43759 EXPRESSION TAG SEQADV 8A6M GLU A -7 UNP O43759 EXPRESSION TAG SEQADV 8A6M ASN A -6 UNP O43759 EXPRESSION TAG SEQADV 8A6M LEU A -5 UNP O43759 EXPRESSION TAG SEQADV 8A6M TYR A -4 UNP O43759 EXPRESSION TAG SEQADV 8A6M PHE A -3 UNP O43759 EXPRESSION TAG SEQADV 8A6M GLN A -2 UNP O43759 EXPRESSION TAG SEQADV 8A6M GLY A -1 UNP O43759 EXPRESSION TAG SEQADV 8A6M HIS A 0 UNP O43759 EXPRESSION TAG SEQRES 1 A 210 MET GLY HIS HIS HIS HIS HIS HIS HIS ALA SER GLU ASN SEQRES 2 A 210 LEU TYR PHE GLN GLY HIS MET GLU GLY GLY ALA TYR GLY SEQRES 3 A 210 ALA GLY LYS ALA GLY GLY ALA PHE ASP PRO TYR THR LEU SEQRES 4 A 210 VAL ARG GLN PRO HIS THR ILE LEU ARG VAL VAL SER TRP SEQRES 5 A 210 LEU PHE SER ILE VAL VAL PHE GLY SER ILE VAL ASN GLU SEQRES 6 A 210 GLY TYR LEU ASN SER ALA SER GLU GLY GLU GLU PHE CYS SEQRES 7 A 210 ILE TYR ASN ARG ASN PRO ASN ALA CYS SER TYR GLY VAL SEQRES 8 A 210 ALA VAL GLY VAL LEU ALA PHE LEU THR CYS LEU LEU TYR SEQRES 9 A 210 LEU ALA LEU ASP VAL TYR PHE PRO GLN ILE SER SER VAL SEQRES 10 A 210 LYS ASP ARG LYS LYS ALA VAL LEU SER ASP ILE GLY VAL SEQRES 11 A 210 SER ALA PHE TRP ALA PHE LEU TRP PHE VAL GLY PHE CYS SEQRES 12 A 210 TYR LEU ALA ASN GLN TRP GLN VAL SER LYS PRO LYS ASP SEQRES 13 A 210 ASN PRO LEU ASN GLU GLY THR ASP ALA ALA ARG ALA ALA SEQRES 14 A 210 ILE ALA PHE SER PHE PHE SER ILE PHE THR TRP SER LEU SEQRES 15 A 210 THR ALA ALA LEU ALA VAL ARG ARG PHE LYS ASP LEU SER SEQRES 16 A 210 PHE GLN GLU GLU TYR SER THR LEU PHE PRO ALA SER ALA SEQRES 17 A 210 GLN PRO HELIX 1 AA1 THR A 19 ARG A 22 5 4 HELIX 2 AA2 GLN A 23 GLY A 47 1 25 HELIX 3 AA3 GLY A 47 GLU A 54 1 8 HELIX 4 AA4 ASN A 62 TYR A 91 1 30 HELIX 5 AA5 SER A 97 LYS A 134 1 38 HELIX 6 AA6 PRO A 139 GLY A 143 5 5 HELIX 7 AA7 THR A 144 SER A 176 1 33 CISPEP 1 GLU A 54 GLY A 55 3 3.91 CISPEP 2 GLU A 56 GLU A 57 3 10.00 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