HEADER MEMBRANE PROTEIN 04-SEP-25 9Y5F TITLE CRYSTAL STRUCTURE OF RV-SNARE/SC-T-SNARE-5.S.8 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RV-SNARE/SC-T; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SC-T-SNARE-5.S.8; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE FUSION PROTEINS, SYNTHETIC FUSOGENS, SNARE, PROTEIN DESIGN, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.SOMIYA,N.KING REVDAT 1 13-MAY-26 9Y5F 0 JRNL AUTH M.SOMIYA,A.K.BERA,N.KING JRNL TITL COMPUTATIONAL DESIGN OF TWO-COMPONENT MEMBRANE FUSION JRNL TITL 2 PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 5481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 549 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 33.3000 - 5.4700 0.97 1336 145 0.2295 0.2774 REMARK 3 2 5.4700 - 4.3500 0.98 1214 137 0.2365 0.3007 REMARK 3 3 4.3500 - 3.8000 0.98 1213 136 0.2170 0.2824 REMARK 3 4 3.8000 - 3.4500 0.97 1169 131 0.2196 0.2998 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.277 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.983 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 84.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.12 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 : 0.001 2541 REMARK 3 ANGLE : 0.318 3348 REMARK 3 CHIRALITY : 0.026 353 REMARK 3 PLANARITY : 0.002 441 REMARK 3 DIHEDRAL : 3.737 330 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 9Y5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5679 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.450 REMARK 200 RESOLUTION RANGE LOW (A) : 331.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 23.80 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE PH 7.1 AND 20% REMARK 280 W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 167.15100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.54700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.57550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.54700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.54700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 250.72650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.54700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.54700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.57550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.54700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.54700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 250.72650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 167.15100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 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 SER B -4 REMARK 465 GLY B -3 REMARK 465 GLY B -2 REMARK 465 GLY B 68 REMARK 465 GLY B 69 REMARK 465 SER B 70 REMARK 465 GLY B 71 REMARK 465 LYS B 153 REMARK 465 GLU B 154 REMARK 465 LYS B 155 REMARK 465 GLY B 156 REMARK 465 GLY B 157 REMARK 465 SER B 158 REMARK 465 GLY B 159 REMARK 465 GLY B 160 REMARK 465 SER B 161 REMARK 465 GLY B 162 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 3 OE2 GLU A 41 7655 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 9Y5F A 0 70 PDB 9Y5F 9Y5F 0 70 DBREF 9Y5F B -4 244 PDB 9Y5F 9Y5F -4 244 SEQRES 1 A 71 MET SER SER SER SER ASN GLU LYS LEU ARG GLU THR LEU SEQRES 2 A 71 ARG GLU VAL GLU ASP VAL LYS ASN ILE MET GLU ASP ASN SEQRES 3 A 71 ARG ARG LEU VAL GLU ARG GLN GLY ARG GLN ILE ASP ARG SEQRES 4 A 71 LEU GLU GLU LYS ALA ASP ASP LEU GLU ARG SER ALA GLU SEQRES 5 A 71 ARG LEU SER ASP ASN SER GLU LYS LEU LYS ARG LYS TYR SEQRES 6 A 71 TRP TRP LYS ASN SER LYS SEQRES 1 B 249 SER GLY GLY SER SER SER GLU ARG GLU LYS GLU ILE ASP SEQRES 2 B 249 GLU GLY LEU ASP ARG VAL SER GLU ILE VAL LYS GLU LEU SEQRES 3 B 249 LYS LYS MET ALA GLU GLU MET ARG ARG MET ILE GLU GLU SEQRES 4 B 249 GLN GLY ARG ARG ILE GLU ARG ILE GLU GLU LYS ALA GLU SEQRES 5 B 249 GLU ALA LYS GLU LYS ILE GLU GLU ALA ASN GLU ARG ALA SEQRES 6 B 249 GLU LYS LEU LEU LYS ASP PRO GLY GLY SER GLY GLY SER SEQRES 7 B 249 GLU GLU LEU LYS LYS LEU GLU LYS GLU GLY GLU LYS LEU SEQRES 8 B 249 LYS GLU LEU VAL GLU GLU LEU ASP ARG GLU ILE LYS GLU SEQRES 9 B 249 LEU LYS GLU GLY MET GLU ARG LEU ARG GLU MET PHE GLU SEQRES 10 B 249 GLU ALA ALA LYS LEU SER GLU GLU ALA LEU GLU ILE MET SEQRES 11 B 249 ARG ARG THR ARG LYS LEU SER GLU GLU GLU LEU GLU GLU SEQRES 12 B 249 ALA LYS GLN LYS ALA LYS GLU GLN GLU LYS GLU LYS ALA SEQRES 13 B 249 LEU LYS GLU LYS GLY GLY SER GLY GLY SER GLY GLY SER SEQRES 14 B 249 GLU LYS VAL LYS ARG GLU LEU ALA GLN ILE GLU GLU ARG SEQRES 15 B 249 HIS GLN GLN ILE LEU GLU LEU GLU GLU LYS ILE LYS GLU SEQRES 16 B 249 LEU LEU GLU MET PHE LYS GLU LEU SER GLU LYS ILE GLU SEQRES 17 B 249 GLU GLN GLY GLN LYS ILE ASP ARG ILE GLU ASP LYS VAL SEQRES 18 B 249 SER LYS ALA LYS GLU HIS VAL GLU LYS GLY VAL GLU ASP SEQRES 19 B 249 THR LYS LYS ALA VAL LYS TYR GLN SER LYS ALA ARG ARG SEQRES 20 B 249 LYS LYS HELIX 1 AA1 SER A 1 TRP A 66 1 66 HELIX 2 AA2 SER B 0 ASP B 66 1 67 HELIX 3 AA3 SER B 73 LYS B 148 1 76 HELIX 4 AA4 GLU B 165 LYS B 243 1 79 CRYST1 47.094 47.094 334.302 90.00 90.00 90.00 P 41 21 2 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 0.021234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002991 0.00000 MASTER 255 0 0 4 0 0 0 6 2534 2 0 26 END