HEADER MEMBRANE PROTEIN 01-JUL-21 7P16 TITLE STRUCTURE OF CASPASE-3 CLEAVED RXKR9 IN COMPLEX WITH A SYBODY AT 4.3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: XK-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SYBODY; COMPND 7 CHAIN: B; COMPND 8 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: XKR9, XRG9; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T GNTI-; SOURCE 10 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-3022; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 1211845 KEYWDS SMALL MEMBRANE PROTEIN, IN COMPLEX WITH SYBODY, APOPTOTIC LIPID KEYWDS 2 SCRAMBLING, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.S.STRAUB,M.SAWICKA,R.DUTZLER REVDAT 2 20-NOV-24 7P16 1 REMARK REVDAT 1 28-JUL-21 7P16 0 JRNL AUTH M.S.STRAUB,C.ALVADIA,M.SAWICKA,R.DUTZLER JRNL TITL CRYO-EM STRUCTURES OF THE CASPASE ACTIVATED PROTEIN XKR9 JRNL TITL 2 INVOLVED IN APOPTOTIC LIPID SCRAMBLING. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34263724 JRNL DOI 10.7554/ELIFE.69800 REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, COOT, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.300 REMARK 3 NUMBER OF PARTICLES : 444358 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7P16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292116788. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CASPASE-3 CLEAVED RXKR9 WITH REMARK 245 SYBODY; RXKR9; SYBODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 14929 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 LYS A 68 REMARK 465 LYS A 69 REMARK 465 ALA A 70 REMARK 465 GLY A 71 REMARK 465 GLY A 72 REMARK 465 GLU A 73 REMARK 465 ASN A 74 REMARK 465 GLU A 75 REMARK 465 HIS A 76 REMARK 465 TYR A 77 REMARK 465 PHE A 78 REMARK 465 LEU A 79 REMARK 465 LEU A 80 REMARK 465 HIS A 106 REMARK 465 SER A 107 REMARK 465 HIS A 108 REMARK 465 ARG A 109 REMARK 465 THR A 110 REMARK 465 SER A 111 REMARK 465 ASN A 112 REMARK 465 PHE A 113 REMARK 465 MET A 114 REMARK 465 GLU A 115 REMARK 465 GLU A 116 REMARK 465 GLN A 117 REMARK 465 THR A 118 REMARK 465 PRO A 345 REMARK 465 ASN A 346 REMARK 465 ILE A 347 REMARK 465 ASN A 348 REMARK 465 ALA A 349 REMARK 465 GLY A 350 REMARK 465 THR A 351 REMARK 465 GLN A 352 REMARK 465 HIS A 353 REMARK 465 ASP A 354 REMARK 465 GLU A 355 REMARK 465 PRO A 356 REMARK 465 ASP A 357 REMARK 465 GLY A 358 REMARK 465 LYS A 359 REMARK 465 ALA A 360 REMARK 465 PRO A 361 REMARK 465 GLN A 362 REMARK 465 ARG A 363 REMARK 465 ASP A 364 REMARK 465 CYS A 365 REMARK 465 ARG A 366 REMARK 465 ILE A 367 REMARK 465 ARG A 368 REMARK 465 TYR A 369 REMARK 465 PHE A 370 REMARK 465 LEU A 371 REMARK 465 MET A 372 REMARK 465 ASP A 373 REMARK 465 ALA A 374 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 THR A 139 N GLY A 143 2.18 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 ALA A 160 -175.81 59.65 REMARK 500 LYS A 279 -7.91 74.12 REMARK 500 LYS A 284 -8.23 72.93 REMARK 500 ALA B 112 73.44 -161.53 REMARK 500 PRO B 113 49.75 -76.58 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 PLC A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7P14 RELATED DB: PDB REMARK 900 FULL-LENGTH REMARK 900 RELATED ID: EMD-13157 RELATED DB: EMDB REMARK 900 STRUCTURE OF CASPASE-3 CLEAVED RXKR9 IN COMPLEX WITH A SYBODY AT REMARK 900 4.3A DBREF 7P16 A 1 373 UNP Q5GH54 Q5GH54_RAT 1 373 DBREF 7P16 B 6 131 PDB 7P16 7P16 6 131 SEQADV 7P16 ALA A 374 UNP Q5GH54 EXPRESSION TAG SEQRES 1 A 374 MET LYS TYR THR ILE CYS ASN PHE MET MET SER VAL LEU SEQRES 2 A 374 GLY ILE ILE ILE TYR VAL THR ASP LEU VAL ALA ASP ILE SEQRES 3 A 374 VAL LEU THR VAL ARG TYR PHE TYR ASP GLY GLN TYR VAL SEQRES 4 A 374 PHE GLY VAL LEU THR LEU SER PHE VAL LEU CYS GLY THR SEQRES 5 A 374 LEU ILE VAL HIS CYS PHE SER TYR SER TRP LEU LYS ASP SEQRES 6 A 374 ASP LEU LYS LYS ALA GLY GLY GLU ASN GLU HIS TYR PHE SEQRES 7 A 374 LEU LEU LEU HIS CYS LEU GLN GLY GLY VAL PHE THR ARG SEQRES 8 A 374 TYR TRP PHE VAL LEU ARG THR GLY TYR HIS VAL VAL PHE SEQRES 9 A 374 LYS HIS SER HIS ARG THR SER ASN PHE MET GLU GLU GLN SEQRES 10 A 374 THR ASP PRO HIS LYS GLU ALA ILE ASP MET ALA THR ASP SEQRES 11 A 374 LEU SER MET LEU ARG LEU PHE GLU THR TYR LEU GLU GLY SEQRES 12 A 374 CYS PRO GLN LEU ILE LEU GLN LEU TYR ALA PHE LEU GLU SEQRES 13 A 374 ARG GLY GLN ALA ASN PHE SER GLN TYR MET VAL ILE MET SEQRES 14 A 374 VAL SER CYS CYS ALA ILE SER TRP SER THR VAL ASP TYR SEQRES 15 A 374 GLN ILE ALA LEU ARG LYS SER LEU PRO ASP LYS ASN LEU SEQRES 16 A 374 LEU ARG GLY PHE TRP PRO LYS LEU THR TYR LEU PHE TYR SEQRES 17 A 374 LYS LEU PHE THR LEU LEU SER TRP MET LEU SER VAL VAL SEQRES 18 A 374 LEU LEU LEU PHE VAL ASP VAL ARG THR VAL LEU LEU LEU SEQRES 19 A 374 LEU LEU PHE LEU TRP THR VAL GLY PHE ILE TRP ALA PHE SEQRES 20 A 374 ILE ASN HIS THR GLN PHE CYS ASN SER LEU SER MET GLU SEQRES 21 A 374 PHE LEU TYR ARG LEU VAL VAL GLY PHE ILE LEU VAL PHE SEQRES 22 A 374 THR PHE PHE ASN ILE LYS GLY GLN ASN THR LYS CYS PRO SEQRES 23 A 374 MET SER CYS TYR TYR THR VAL ARG VAL LEU GLY THR LEU SEQRES 24 A 374 GLY ILE LEU THR VAL PHE TRP ILE TYR PRO LEU SER ILE SEQRES 25 A 374 PHE ASN SER ASP TYR PHE ILE PRO ILE SER ALA THR ILE SEQRES 26 A 374 VAL LEU SER LEU LEU PHE GLY ILE ILE PHE LEU GLY VAL SEQRES 27 A 374 TYR TYR GLY THR TYR HIS PRO ASN ILE ASN ALA GLY THR SEQRES 28 A 374 GLN HIS ASP GLU PRO ASP GLY LYS ALA PRO GLN ARG ASP SEQRES 29 A 374 CYS ARG ILE ARG TYR PHE LEU MET ASP ALA SEQRES 1 B 126 SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL SEQRES 2 B 126 GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 B 126 GLY ASN ILE ALA ASP ILE TYR TYR LEU GLY TRP PHE ARG SEQRES 4 B 126 GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL ALA ALA LEU SEQRES 5 B 126 ILE THR TYR ASN GLY ARG THR TYR TYR ALA ASP SER VAL SEQRES 6 B 126 LYS GLY ARG PHE THR VAL SER LEU ASP ASN ALA LYS ASN SEQRES 7 B 126 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 126 THR ALA LEU TYR TYR CYS ALA ALA ALA TYR ASN GLY LEU SEQRES 9 B 126 ILE ALA ALA PRO LEU LYS VAL THR ARG TYR TRP TYR TRP SEQRES 10 B 126 GLY GLN GLY THR GLN VAL THR VAL SER HET PLC A 401 40 HETNAM PLC DIUNDECYL PHOSPHATIDYL CHOLINE FORMUL 3 PLC C32 H65 N O8 P 1+ HELIX 1 AA1 THR A 4 LEU A 13 1 10 HELIX 2 AA2 GLY A 14 GLY A 36 1 23 HELIX 3 AA3 GLN A 37 LEU A 67 1 31 HELIX 4 AA4 HIS A 82 GLY A 86 1 5 HELIX 5 AA5 GLY A 87 LYS A 105 1 19 HELIX 6 AA6 PRO A 120 LEU A 141 1 22 HELIX 7 AA7 GLY A 143 GLU A 156 1 14 HELIX 8 AA8 ASN A 161 LEU A 190 1 30 HELIX 9 AA9 LYS A 193 ARG A 197 5 5 HELIX 10 AB1 GLY A 198 ASP A 227 1 30 HELIX 11 AB2 ASP A 227 HIS A 250 1 24 HELIX 12 AB3 SER A 256 THR A 274 1 19 HELIX 13 AB4 ASN A 277 GLN A 281 5 5 HELIX 14 AB5 LYS A 284 TYR A 308 1 25 HELIX 15 AB6 ASN A 314 TYR A 343 1 30 HELIX 16 AB7 ALA B 67 LYS B 71 5 5 HELIX 17 AB8 LYS B 93 THR B 97 5 5 SHEET 1 AA1 4 GLN B 9 SER B 13 0 SHEET 2 AA1 4 ARG B 25 SER B 31 -1 O ALA B 29 N VAL B 11 SHEET 3 AA1 4 THR B 84 GLN B 88 -1 O LEU B 87 N LEU B 26 SHEET 4 AA1 4 THR B 75 ASP B 79 -1 N SER B 77 O TYR B 86 SHEET 1 AA2 5 SER B 17 VAL B 18 0 SHEET 2 AA2 5 THR B 126 VAL B 130 1 O THR B 129 N VAL B 18 SHEET 3 AA2 5 ALA B 98 TYR B 101 -1 N TYR B 100 O THR B 126 SHEET 4 AA2 5 ILE B 37 GLN B 45 -1 N GLN B 45 O LEU B 99 SHEET 5 AA2 5 GLU B 52 ILE B 58 -1 O ALA B 55 N TRP B 42 SHEET 1 AA3 5 SER B 17 VAL B 18 0 SHEET 2 AA3 5 THR B 126 VAL B 130 1 O THR B 129 N VAL B 18 SHEET 3 AA3 5 ALA B 98 TYR B 101 -1 N TYR B 100 O THR B 126 SHEET 4 AA3 5 ILE B 37 GLN B 45 -1 N GLN B 45 O LEU B 99 SHEET 5 AA3 5 ALA B 104 TYR B 106 -1 O ALA B 105 N TYR B 38 SSBOND 1 CYS B 28 CYS B 102 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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