HEADER MEMBRANE PROTEIN 20-OCT-23 8WUA TITLE CRYO-EM STRUCTURE OF HUMAN TMEM63A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CSC1-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TMEM63A; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS MECHANICALLY ACTIVATED (MA) ION CHANNEL, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.YANG REVDAT 3 08-MAY-24 8WUA 1 JRNL REVDAT 2 31-JAN-24 8WUA 1 JRNL REVDAT 1 24-JAN-24 8WUA 0 JRNL AUTH X.WU,T.SHANG,X.LU,D.LUO,D.YANG JRNL TITL A MONOMERIC STRUCTURE OF HUMAN TMEM63A PROTEIN. JRNL REF PROTEINS V. 92 750 2024 JRNL REFN ESSN 1097-0134 JRNL PMID 38217391 JRNL DOI 10.1002/PROT.26660 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 163395 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8WUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041803. 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 : HUMAN TMEM63A REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 156.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 TRP A 76 REMARK 465 ASP A 77 REMARK 465 TYR A 78 REMARK 465 GLY A 79 REMARK 465 ARG A 80 REMARK 465 ILE A 81 REMARK 465 ALA A 82 REMARK 465 LEU A 83 REMARK 465 VAL A 84 REMARK 465 SER A 85 REMARK 465 GLU A 86 REMARK 465 ALA A 87 REMARK 465 ASP A 88 REMARK 465 SER A 89 REMARK 465 GLU A 90 REMARK 465 SER A 91 REMARK 465 ARG A 92 REMARK 465 PHE A 93 REMARK 465 GLN A 94 REMARK 465 ARG A 95 REMARK 465 LEU A 96 REMARK 465 SER A 97 REMARK 465 SER A 98 REMARK 465 THR A 99 REMARK 465 SER A 100 REMARK 465 SER A 101 REMARK 465 SER A 102 REMARK 465 GLY A 103 REMARK 465 GLN A 104 REMARK 465 GLN A 105 REMARK 465 ASP A 106 REMARK 465 PHE A 107 REMARK 465 GLU A 108 REMARK 465 ASN A 109 REMARK 465 GLU A 110 REMARK 465 LEU A 111 REMARK 465 GLY A 112 REMARK 465 CYS A 113 REMARK 465 CYS A 114 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 TRP A 531 OG1 THR A 536 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 439 CA - N - CD ANGL. DEV. = -15.8 DEGREES REMARK 500 LEU A 471 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 PRO A 576 CA - N - CD ANGL. DEV. = -10.3 DEGREES 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 LEU A 9 51.05 -91.52 REMARK 500 LEU A 23 15.37 53.61 REMARK 500 ASP A 172 29.45 47.19 REMARK 500 TYR A 264 -168.89 -117.32 REMARK 500 ASN A 265 38.70 -97.62 REMARK 500 CYS A 372 -167.37 -79.38 REMARK 500 TYR A 391 60.51 60.69 REMARK 500 LYS A 453 72.02 53.97 REMARK 500 SER A 491 65.86 60.71 REMARK 500 TRP A 493 -60.91 -92.73 REMARK 500 PHE A 512 3.18 -67.80 REMARK 500 ALA A 540 -169.34 -161.86 REMARK 500 TYR A 624 51.79 -94.19 REMARK 500 CYS A 628 71.10 57.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37852 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN TMEM63A DBREF 8WUA A 6 719 UNP O94886 CSCL1_HUMAN 6 719 SEQRES 1 A 714 PHE LEU GLU LEU TRP GLN SER LYS ALA VAL SER ILE ARG SEQRES 2 A 714 GLU GLN LEU GLY LEU GLY ASP ARG PRO ASN ASP SER TYR SEQRES 3 A 714 CYS TYR ASN SER ALA LYS ASN SER THR VAL LEU GLN GLY SEQRES 4 A 714 VAL THR PHE GLY GLY ILE PRO THR VAL LEU LEU ILE ASP SEQRES 5 A 714 VAL SER CYS PHE LEU PHE LEU ILE LEU VAL PHE SER ILE SEQRES 6 A 714 ILE ARG ARG ARG PHE TRP ASP TYR GLY ARG ILE ALA LEU SEQRES 7 A 714 VAL SER GLU ALA ASP SER GLU SER ARG PHE GLN ARG LEU SEQRES 8 A 714 SER SER THR SER SER SER GLY GLN GLN ASP PHE GLU ASN SEQRES 9 A 714 GLU LEU GLY CYS CYS PRO TRP LEU THR ALA ILE PHE ARG SEQRES 10 A 714 LEU HIS ASP ASP GLN ILE LEU GLU TRP CYS GLY GLU ASP SEQRES 11 A 714 ALA ILE HIS TYR LEU SER PHE GLN ARG HIS ILE ILE PHE SEQRES 12 A 714 LEU LEU VAL VAL VAL SER PHE LEU SER LEU CYS VAL ILE SEQRES 13 A 714 LEU PRO VAL ASN LEU SER GLY ASP LEU LEU ASP LYS ASP SEQRES 14 A 714 PRO TYR SER PHE GLY ARG THR THR ILE ALA ASN LEU GLN SEQRES 15 A 714 THR ASP ASN ASP LEU LEU TRP LEU HIS THR ILE PHE ALA SEQRES 16 A 714 VAL ILE TYR LEU PHE LEU THR VAL GLY PHE MET ARG HIS SEQRES 17 A 714 HIS THR GLN SER ILE LYS TYR LYS GLU GLU ASN LEU VAL SEQRES 18 A 714 ARG ARG THR LEU PHE ILE THR GLY LEU PRO ARG ASP ALA SEQRES 19 A 714 ARG LYS GLU THR VAL GLU SER HIS PHE ARG ASP ALA TYR SEQRES 20 A 714 PRO THR CYS GLU VAL VAL ASP VAL GLN LEU CYS TYR ASN SEQRES 21 A 714 VAL ALA LYS LEU ILE TYR LEU CYS LYS GLU LYS LYS LYS SEQRES 22 A 714 THR GLU LYS SER LEU THR TYR TYR THR ASN LEU GLN VAL SEQRES 23 A 714 LYS THR GLY GLN ARG THR LEU ILE ASN PRO LYS PRO CYS SEQRES 24 A 714 GLY GLN PHE CYS CYS CYS GLU VAL LEU GLY CYS GLU TRP SEQRES 25 A 714 GLU ASP ALA ILE SER TYR TYR THR ARG MET LYS ASP ARG SEQRES 26 A 714 LEU LEU GLU ARG ILE THR GLU GLU GLU ARG HIS VAL GLN SEQRES 27 A 714 ASP GLN PRO LEU GLY MET ALA PHE VAL THR PHE GLN GLU SEQRES 28 A 714 LYS SER MET ALA THR TYR ILE LEU LYS ASP PHE ASN ALA SEQRES 29 A 714 CYS LYS CYS GLN SER LEU GLN CYS LYS GLY GLU PRO GLN SEQRES 30 A 714 PRO SER SER HIS SER ARG GLU LEU TYR THR SER LYS TRP SEQRES 31 A 714 THR VAL THR PHE ALA ALA ASP PRO GLU ASP ILE CYS TRP SEQRES 32 A 714 LYS ASN LEU SER ILE GLN GLY LEU ARG TRP TRP LEU GLN SEQRES 33 A 714 TRP LEU GLY ILE ASN PHE THR LEU PHE LEU GLY LEU PHE SEQRES 34 A 714 PHE LEU THR THR PRO SER ILE ILE LEU SER THR MET ASP SEQRES 35 A 714 LYS PHE ASN VAL THR LYS PRO ILE HIS ALA LEU ASN ASN SEQRES 36 A 714 PRO ILE ILE SER GLN PHE PHE PRO THR LEU LEU LEU TRP SEQRES 37 A 714 SER PHE SER ALA LEU LEU PRO SER ILE VAL TYR TYR SER SEQRES 38 A 714 THR LEU LEU GLU SER HIS TRP THR LYS SER GLY GLU ASN SEQRES 39 A 714 GLN ILE MET MET THR LYS VAL TYR ILE PHE LEU ILE PHE SEQRES 40 A 714 MET VAL LEU ILE LEU PRO SER LEU GLY LEU THR SER LEU SEQRES 41 A 714 ASP PHE PHE PHE ARG TRP LEU PHE ASP LYS THR SER SER SEQRES 42 A 714 GLU ALA SER ILE ARG LEU GLU CYS VAL PHE LEU PRO ASP SEQRES 43 A 714 GLN GLY ALA PHE PHE VAL ASN TYR VAL ILE ALA SER ALA SEQRES 44 A 714 PHE ILE GLY ASN GLY MET GLU LEU LEU ARG LEU PRO GLY SEQRES 45 A 714 LEU ILE LEU TYR THR PHE ARG MET ILE MET ALA LYS THR SEQRES 46 A 714 ALA ALA ASP ARG ARG ASN VAL LYS GLN ASN GLN ALA PHE SEQRES 47 A 714 GLN TYR GLU PHE GLY ALA MET TYR ALA TRP MET LEU CYS SEQRES 48 A 714 VAL PHE THR VAL ILE VAL ALA TYR SER ILE THR CYS PRO SEQRES 49 A 714 ILE ILE ALA PRO PHE GLY LEU ILE TYR ILE LEU LEU LYS SEQRES 50 A 714 HIS MET VAL ASP ARG HIS ASN LEU TYR PHE VAL TYR LEU SEQRES 51 A 714 PRO ALA LYS LEU GLU LYS GLY ILE HIS PHE ALA ALA VAL SEQRES 52 A 714 ASN GLN ALA LEU ALA ALA PRO ILE LEU CYS LEU PHE TRP SEQRES 53 A 714 LEU TYR PHE PHE SER PHE LEU ARG LEU GLY MET LYS ALA SEQRES 54 A 714 PRO ALA THR LEU PHE THR PHE LEU VAL LEU LEU LEU THR SEQRES 55 A 714 ILE LEU VAL CYS LEU ALA HIS THR CYS PHE GLY CYS HELIX 1 AA1 LYS A 13 ARG A 18 1 6 HELIX 2 AA2 GLU A 19 LEU A 21 5 3 HELIX 3 AA3 THR A 46 GLY A 48 5 3 HELIX 4 AA4 GLY A 49 PHE A 75 1 27 HELIX 5 AA5 TRP A 116 LEU A 123 1 8 HELIX 6 AA6 ASP A 126 CYS A 132 1 7 HELIX 7 AA7 GLU A 134 LEU A 158 1 25 HELIX 8 AA8 VAL A 160 SER A 167 1 8 HELIX 9 AA9 PHE A 178 THR A 182 5 5 HELIX 10 AB1 LEU A 192 LYS A 219 1 28 HELIX 11 AB2 ARG A 240 TYR A 252 1 13 HELIX 12 AB3 VAL A 266 GLY A 294 1 29 HELIX 13 AB4 CYS A 304 CYS A 308 5 5 HELIX 14 AB5 ALA A 320 HIS A 341 1 22 HELIX 15 AB6 VAL A 342 GLN A 345 5 4 HELIX 16 AB7 LYS A 357 LYS A 365 1 9 HELIX 17 AB8 GLY A 415 THR A 445 1 31 HELIX 18 AB9 PHE A 466 SER A 491 1 26 HELIX 19 AC1 THR A 494 LEU A 515 1 22 HELIX 20 AC2 ILE A 516 ASP A 534 1 19 HELIX 21 AC3 PRO A 550 GLY A 553 5 4 HELIX 22 AC4 ALA A 554 PHE A 565 1 12 HELIX 23 AC5 PHE A 565 ARG A 574 1 10 HELIX 24 AC6 ARG A 574 MET A 587 1 14 HELIX 25 AC7 ARG A 594 GLN A 599 1 6 HELIX 26 AC8 GLU A 606 TYR A 624 1 19 HELIX 27 AC9 ILE A 630 LEU A 650 1 21 HELIX 28 AD1 LYS A 661 ALA A 673 1 13 HELIX 29 AD2 ALA A 673 LEU A 690 1 18 HELIX 30 AD3 ALA A 694 VAL A 710 1 17 HELIX 31 AD4 LEU A 712 PHE A 717 1 6 SHEET 1 AA1 4 VAL A 260 LEU A 262 0 SHEET 2 AA1 4 ALA A 350 THR A 353 -1 O PHE A 351 N GLN A 261 SHEET 3 AA1 4 THR A 229 THR A 233 -1 N LEU A 230 O VAL A 352 SHEET 4 AA1 4 THR A 396 PHE A 399 -1 O THR A 398 N PHE A 231 SHEET 1 AA2 2 LEU A 298 ILE A 299 0 SHEET 2 AA2 2 GLU A 318 ASP A 319 -1 O GLU A 318 N ILE A 299 SSBOND 1 CYS A 32 CYS A 546 1555 1555 2.03 SSBOND 2 CYS A 308 CYS A 315 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