HEADER PROTEIN TRANSPORT 20-DEC-24 9L4O TITLE ARABIDOPSIS THALIANA PROTEASE-ASSOCIATED DOMAIN OF VACUOLAR SORTING TITLE 2 RECEPTOR 1 IN COMPLEXED WITH VICILIN-LIKE SEED STORAGE PROTEIN 22 C- TITLE 3 TERMINAL PENTAPEPTIDE SDRFV (PH 5.8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEASE ASSOCIATED DOMAIN; COMPND 5 SYNONYM: ATVSR1,BP80-LIKE PROTEIN B,ATBP80B,EPIDERMAL GROWTH FACTOR COMPND 6 RECEPTOR-LIKE PROTEIN 1,ATELP,ATELP1,SPOT 3 PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VICILIN-LIKE SEED STORAGE PROTEIN C-TERMINAL PENTAPEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: VSR1, BP80B, ELP, ELP1, AT3G52850, F8J2.20; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_TAXID: 3702 KEYWDS LIGAND BINDING DOMAIN VACUOLAR SORTING DETERMINANT RECEPTOR-CARGO KEYWDS 2 INTERACTION, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.N.LUI,K.B.WONG REVDAT 3 28-JAN-26 9L4O 1 JRNL REVDAT 2 17-SEP-25 9L4O 1 JRNL REVDAT 1 10-SEP-25 9L4O 0 JRNL AUTH S.N.LUI,H.E.TSAO,A.H.LO,L.JIANG,K.B.WONG JRNL TITL STRUCTURAL INSIGHTS INTO HOW VACUOLAR SORTING RECEPTOR JRNL TITL 2 RECOGNIZES THE C-TERMINAL SORTING DETERMINANT OF A JRNL TITL 3 VICILIN-LIKE SEED STORAGE PROTEIN. JRNL REF FEBS J. V. 293 257 2026 JRNL REFN ISSN 1742-464X JRNL PMID 40891502 JRNL DOI 10.1111/FEBS.70245 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 10867 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 500 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 3.0100 - 2.3900 0.97 2597 118 0.1848 0.2536 REMARK 3 2 2.3900 - 2.0900 0.99 2598 135 0.1711 0.2194 REMARK 3 3 2.0900 - 1.9000 0.98 2555 120 0.1734 0.2197 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 NULL REMARK 3 ANGLE : 0.807 NULL REMARK 3 CHIRALITY : 0.057 199 REMARK 3 PLANARITY : 0.006 218 REMARK 3 DIHEDRAL : 12.027 469 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): -10.5681 0.6299 -9.1589 REMARK 3 T TENSOR REMARK 3 T11: 0.1372 T22: 0.1272 REMARK 3 T33: 0.1274 T12: 0.0097 REMARK 3 T13: -0.0046 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 2.0911 L22: 1.4767 REMARK 3 L33: 1.4366 L12: 0.2533 REMARK 3 L13: 0.1270 L23: 0.5401 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: 0.1471 S13: 0.0018 REMARK 3 S21: -0.0960 S22: 0.0188 S23: 0.0424 REMARK 3 S31: -0.0632 S32: 0.0231 S33: 0.0066 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 9L4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JAN 10, 2022 REMARK 200 BUILT=20220820 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 36.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.8 30% (W/V) PEG 6000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.19200 REMARK 290 SMTRY3 2 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: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 GLN A 51 REMARK 465 TYR A 52 REMARK 465 GLY A 53 REMARK 465 VAL A 179 REMARK 465 PRO A 180 REMARK 465 HIS A 181 REMARK 465 PRO A 182 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 22 CG1 CG2 REMARK 470 GLU A 24 CD OE1 OE2 REMARK 470 LYS A 64 CD CE NZ REMARK 470 ASP A 134 CG OD1 OD2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 ASP A 137 CG OD1 OD2 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 ASN A 46 35.80 -82.18 REMARK 500 ASP A 97 -11.63 74.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 203 DBREF 9L4O A 20 182 UNP P93026 VSR1_ARATH 20 182 DBREF 9L4O B 506 511 PDB 9L4O 9L4O 506 511 SEQADV 9L4O GLY A 18 UNP P93026 EXPRESSION TAG SEQADV 9L4O SER A 19 UNP P93026 EXPRESSION TAG SEQRES 1 A 165 GLY SER ARG PHE VAL VAL GLU LYS ASN ASN LEU LYS VAL SEQRES 2 A 165 THR SER PRO ASP SER ILE LYS GLY ILE TYR GLU CYS ALA SEQRES 3 A 165 ILE GLY ASN PHE GLY VAL PRO GLN TYR GLY GLY THR LEU SEQRES 4 A 165 VAL GLY THR VAL VAL TYR PRO LYS SER ASN GLN LYS ALA SEQRES 5 A 165 CYS LYS SER TYR SER ASP PHE ASP ILE SER PHE LYS SER SEQRES 6 A 165 LYS PRO GLY ARG LEU PRO THR PHE VAL LEU ILE ASP ARG SEQRES 7 A 165 GLY ASP CYS TYR PHE THR LEU LYS ALA TRP ILE ALA GLN SEQRES 8 A 165 GLN ALA GLY ALA ALA ALA ILE LEU VAL ALA ASP SER LYS SEQRES 9 A 165 ALA GLU PRO LEU ILE THR MET ASP THR PRO GLU GLU ASP SEQRES 10 A 165 LYS SER ASP ALA ASP TYR LEU GLN ASN ILE THR ILE PRO SEQRES 11 A 165 SER ALA LEU ILE THR LYS THR LEU GLY ASP SER ILE LYS SEQRES 12 A 165 SER ALA LEU SER GLY GLY ASP MET VAL ASN MET LYS LEU SEQRES 13 A 165 ASP TRP THR GLU SER VAL PRO HIS PRO SEQRES 1 B 6 ACE SER ASP ARG PHE VAL HET ACE B 506 3 HET TRS A 201 8 HET GOL A 202 6 HET PEG A 203 6 HETNAM ACE ACETYL GROUP HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ACE C2 H4 O FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *97(H2 O) HELIX 1 AA1 SER A 72 ASP A 77 5 6 HELIX 2 AA2 TYR A 99 ALA A 110 1 12 HELIX 3 AA3 ASP A 134 ILE A 144 5 11 HELIX 4 AA4 THR A 152 GLY A 165 1 14 SHEET 1 AA1 8 LYS A 25 SER A 32 0 SHEET 2 AA1 8 GLY A 38 ILE A 44 -1 O GLY A 38 N VAL A 30 SHEET 3 AA1 8 SER A 148 ILE A 151 -1 O LEU A 150 N ALA A 43 SHEET 4 AA1 8 ALA A 114 ALA A 118 1 N VAL A 117 O ALA A 149 SHEET 5 AA1 8 THR A 89 ASP A 94 1 N ILE A 93 O LEU A 116 SHEET 6 AA1 8 THR A 55 VAL A 61 1 N VAL A 61 O LEU A 92 SHEET 7 AA1 8 ASN A 170 ASP A 174 -1 O LEU A 173 N LEU A 56 SHEET 8 AA1 8 LYS A 25 SER A 32 -1 N LYS A 29 O LYS A 172 SHEET 1 AA2 2 THR A 127 MET A 128 0 SHEET 2 AA2 2 ASP B 508 ARG B 509 1 O ARG B 509 N THR A 127 SSBOND 1 CYS A 70 CYS A 98 1555 1555 2.04 LINK C ACE B 506 N SER B 507 1555 1555 1.33 CISPEP 1 SER A 32 PRO A 33 0 -3.58 CRYST1 32.658 60.384 39.245 90.00 113.38 90.00 P 1 21 1 2 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 0.030620 0.000000 0.013235 0.00000 SCALE2 0.000000 0.016561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027759 0.00000 CONECT 362 589 CONECT 589 362 CONECT 1190 1191 1192 1193 CONECT 1191 1190 CONECT 1192 1190 CONECT 1193 1190 CONECT 1238 1239 1240 1241 1242 CONECT 1239 1238 1243 CONECT 1240 1238 1244 CONECT 1241 1238 1245 CONECT 1242 1238 CONECT 1243 1239 CONECT 1244 1240 CONECT 1245 1241 CONECT 1246 1247 1248 CONECT 1247 1246 CONECT 1248 1246 1249 1250 CONECT 1249 1248 CONECT 1250 1248 1251 CONECT 1251 1250 CONECT 1252 1253 CONECT 1253 1252 1254 CONECT 1254 1253 1255 CONECT 1255 1254 1256 CONECT 1256 1255 1257 CONECT 1257 1256 MASTER 254 0 4 4 10 0 0 6 1341 2 26 14 END