HEADER    MEMBRANE PROTEIN                        01-JUL-21   7P14              
TITLE     STRUCTURE OF FULL-LENGTH RXKR9 IN COMPLEX WITH A SYBODY AT 3.66A      
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: HEK293S 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   13-NOV-24 7P14    1       REMARK                                   
REVDAT   1   28-JUL-21 7P14    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.    3.66 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   SOFTWARE PACKAGES      : CRYOSPARC, EPU, COOT, PHENIX, CRYOSPARC   
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          : AB INITIO MODEL                     
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)  : 3.660                          
REMARK   3   NUMBER OF PARTICLES               : 866439                         
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 7P14 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_1292116783.                                   
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                 : RXKR9 WITH SYBODY; RXKR9;         
REMARK 245                                    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      : 12396                          
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: 3890 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 21660 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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     -158.92     57.10                                   
REMARK 500    LYS A 193       53.19    -91.85                                   
REMARK 500    LYS A 279       -6.68     72.25                                   
REMARK 500    LYS A 284       -6.76     73.60                                   
REMARK 500    ASP A 373     -145.42     62.55                                   
REMARK 500    PRO B 113       44.50    -83.74                                   
REMARK 500    TRP B 120      -61.03    -92.88                                   
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 610     P5S A  403                                                       
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: EMD-13155   RELATED DB: EMDB                             
REMARK 900 STRUCTURE OF FULL-LENGTH RXKR9 IN COMPLEX WITH A SYBODY AT 3.66A     
DBREF  7P14 A    1   373  UNP    Q5GH54   Q5GH54_RAT       1    373             
DBREF  7P14 B    6   131  PDB    7P14     7P14             6    131             
SEQADV 7P14 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                                                       
HET    PLC  A 402      42                                                       
HET    P5S  A 403      44                                                       
HETNAM     PLC DIUNDECYL PHOSPHATIDYL CHOLINE                                   
HETNAM     P5S O-[(R)-{[(2R)-2,3-BIS(OCTADECANOYLOXY)                           
HETNAM   2 P5S  PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE                        
HETSYN     P5S PHOSPHATIDYL SERINE                                              
FORMUL   3  PLC    2(C32 H65 N O8 P 1+)                                         
FORMUL   5  P5S    C42 H82 N O10 P                                              
HELIX    1 AA1 THR A    4  GLY A   36  1                                  33    
HELIX    2 AA2 GLN A   37  LEU A   67  1                                  31    
HELIX    3 AA3 HIS A   82  GLY A   86  1                                   5    
HELIX    4 AA4 GLY A   87  LYS A  105  1                                  19    
HELIX    5 AA5 PRO A  120  GLY A  158  1                                  39    
HELIX    6 AA6 ASN A  161  LEU A  190  1                                  30    
HELIX    7 AA7 PRO A  191  ARG A  197  5                                   7    
HELIX    8 AA8 TRP A  200  ASP A  227  1                                  28    
HELIX    9 AA9 ASP A  227  HIS A  250  1                                  24    
HELIX   10 AB1 SER A  256  THR A  274  1                                  19    
HELIX   11 AB2 ASN A  277  GLN A  281  5                                   5    
HELIX   12 AB3 LYS A  284  TYR A  308  1                                  25    
HELIX   13 AB4 ASN A  314  TYR A  343  1                                  30    
HELIX   14 AB5 LYS B   93  THR B   97  5                                   5    
HELIX   15 AB6 LYS B  115  TYR B  119  5                                   5    
SHEET    1 AA1 4 GLN B   9  SER B  13  0                                        
SHEET    2 AA1 4 SER B  23  SER B  31 -1  O  SER B  31   N  GLN B   9           
SHEET    3 AA1 4 THR B  84  ASN B  90 -1  O  MET B  89   N  LEU B  24           
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 106 -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           
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