HEADER MEMBRANE PROTEIN 04-SEP-25 9Y5H TITLE CRYSTAL STRUCTURE OF RV-SNARE/SC-T-SNARE-DIFF-#3.3 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-DIFF-#3.3; 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 9Y5H 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. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 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 42.7200 - 5.2400 0.98 1385 154 0.2478 0.2702 REMARK 3 2 5.2400 - 4.1600 0.99 1307 144 0.1912 0.2623 REMARK 3 3 4.1600 - 3.6300 1.00 1314 146 0.2031 0.2619 REMARK 3 4 3.6300 - 3.3000 1.00 1296 144 0.2307 0.2951 REMARK 3 5 3.3000 - 3.0700 1.00 1297 144 0.2922 0.3532 REMARK 3 6 3.0700 - 2.8800 1.00 1266 142 0.2564 0.3175 REMARK 3 7 2.8800 - 2.7400 1.00 1284 142 0.2688 0.3695 REMARK 3 8 2.7400 - 2.6200 1.00 1279 141 0.3093 0.3562 REMARK 3 9 2.6200 - 2.5200 1.00 1268 142 0.3288 0.4356 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) : 0.401 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.946 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.42 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 2603 REMARK 3 ANGLE : 0.282 3437 REMARK 3 CHIRALITY : 0.024 369 REMARK 3 PLANARITY : 0.002 448 REMARK 3 DIHEDRAL : 13.544 1128 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.4843 8.3276 37.4490 REMARK 3 T TENSOR REMARK 3 T11: 0.3439 T22: 0.3266 REMARK 3 T33: 0.4581 T12: 0.0115 REMARK 3 T13: 0.0209 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.4526 L22: 0.1701 REMARK 3 L33: 6.4433 L12: -0.1463 REMARK 3 L13: -0.9315 L23: 0.3753 REMARK 3 S TENSOR REMARK 3 S11: -0.0352 S12: 0.0092 S13: 0.0721 REMARK 3 S21: -0.0418 S22: -0.0397 S23: -0.0069 REMARK 3 S31: -0.0378 S32: -0.3131 S33: 0.0726 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 9Y5H 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_1000299570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 2.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03753 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 REMARK 200 RESOLUTION RANGE LOW (A) : 46.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.94100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 46.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CACODYLATE TRIHYDRATE PH REMARK 280 6.5, 20%V/V GLYCEROL, 0.16M CALCIUM ACETATE HYDRATE AND 14.4% (W/ REMARK 280 V) PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 24.96050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.20500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.20500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.96050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.27500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 MET A 0 REMARK 465 LYS A 70 REMARK 465 SER B -4 REMARK 465 GLY B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 SER B 0 REMARK 465 ALA B 153 REMARK 465 LYS B 154 REMARK 465 LYS B 155 REMARK 465 LYS B 156 REMARK 465 GLY B 157 REMARK 465 GLU B 158 REMARK 465 GLU B 159 REMARK 465 GLY B 160 REMARK 465 CYS B 245 REMARK 465 CYS B 246 REMARK 465 CYS B 247 REMARK 465 CYS B 248 REMARK 465 CYS B 249 REMARK 465 CYS B 250 REMARK 465 CYS B 251 REMARK 465 CYS B 252 REMARK 465 CYS B 253 REMARK 465 CYS B 254 REMARK 465 SER B 255 DBREF 9Y5H A 0 70 PDB 9Y5H 9Y5H 0 70 DBREF 9Y5H B -4 255 PDB 9Y5H 9Y5H -4 255 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 260 SER GLY GLY SER SER SER SER LEU GLU LYS LYS ILE ASP SEQRES 2 B 260 GLU ASN LEU GLU LYS ALA LEU GLU LEU LEU GLU GLU LEU SEQRES 3 B 260 LYS GLU LYS LEU GLU GLU MET ARG ARG LEU LEU GLU GLU SEQRES 4 B 260 SER GLY ARG LEU GLN ASP GLU LEU GLU GLU LEU MET ASP SEQRES 5 B 260 GLU THR GLN LYS GLN GLN GLU GLU LEU GLU LYS LEU LEU SEQRES 6 B 260 GLU LYS LEU LEU LYS MET ASP ASP SER ASP GLU GLN TYR SEQRES 7 B 260 GLU LEU LEU LYS GLU ALA LEU LYS LYS GLN LYS GLU LEU SEQRES 8 B 260 LYS GLU GLN LEU GLU GLU LEU GLU GLU LYS LEU LYS GLU SEQRES 9 B 260 LEU ARG ARG ALA HIS GLU GLU THR ARG ARG LYS MET GLU SEQRES 10 B 260 GLU ALA GLU GLU LEU LEU LYS GLU LEU GLU GLU VAL MET SEQRES 11 B 260 GLU GLU LEU LYS LYS ALA GLN GLU GLU LEU LEU LYS GLU SEQRES 12 B 260 LYS LYS LYS LYS TYR GLU GLU ALA LYS LYS GLU LEU GLU SEQRES 13 B 260 GLU ALA LYS LYS LYS GLY GLU GLU GLY LYS GLU LYS LEU SEQRES 14 B 260 GLU LYS VAL LYS ARG GLU LEU ALA GLN ILE GLU GLU ARG SEQRES 15 B 260 HIS GLN GLN ILE LEU GLU LEU GLU GLU LYS ILE LYS GLU SEQRES 16 B 260 LEU LEU GLU MET PHE LYS GLU LEU SER GLU LYS ILE GLU SEQRES 17 B 260 GLU GLN GLY GLN LYS ILE ASP ARG ILE GLU ASP LYS VAL SEQRES 18 B 260 SER LYS ALA LYS GLU HIS VAL GLU LYS GLY VAL GLU ASP SEQRES 19 B 260 THR LYS LYS ALA VAL LYS TYR GLN SER LYS ALA ARG ARG SEQRES 20 B 260 LYS LYS CYS CYS CYS CYS CYS CYS CYS CYS CYS CYS SER FORMUL 3 HOH *30(H2 O) HELIX 1 AA1 SER A 1 ASN A 68 1 68 HELIX 2 AA2 SER B 2 LYS B 65 1 64 HELIX 3 AA3 SER B 69 GLU B 151 1 83 HELIX 4 AA4 GLU B 162 LYS B 244 1 83 CRYST1 49.921 56.550 130.410 90.00 90.00 90.00 P 21 21 21 4 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 0.020032 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007668 0.00000 MASTER 249 0 0 4 0 0 0 6 2624 2 0 26 END