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