HEADER MEMBRANE PROTEIN 10-JUN-21 7N7P TITLE CRYO-EM STRUCTURE OF HUMAN TMEM120A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ION CHANNEL TACAN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRANSMEMBRANE PROTEIN 120A, TMEM120A, TRANSMEMBRANE PROTEIN COMPND 5 INDUCED BY TUMOR NECROSIS FACTOR ALPHA; COMPND 6 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: TMEM120A, TACAN, TMPIT; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSMEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.XUE,Y.HAN,Y.JIANG REVDAT 2 05-JUN-24 7N7P 1 REMARK REVDAT 1 01-SEP-21 7N7P 0 JRNL AUTH J.XUE,Y.HAN,H.BANIASADI,W.ZENG,J.PEI,N.V.GRISHIN,J.WANG, JRNL AUTH 2 B.P.TU,Y.JIANG JRNL TITL TMEM120A IS A COENZYME A-BINDING MEMBRANE PROTEIN WITH JRNL TITL 2 STRUCTURAL SIMILARITIES TO ELOVL FATTY ACID ELONGASE. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34374645 JRNL DOI 10.7554/ELIFE.71220 REMARK 2 REMARK 2 RESOLUTION. 3.24 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) : 3.240 REMARK 3 NUMBER OF PARTICLES : 701283 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 7N7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257501. 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 TMEM120A WITH COA 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 : 7.40 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) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 100.00 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: DIMERIC 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 MET A -12 REMARK 465 ASP A -11 REMARK 465 TYR A -10 REMARK 465 LYS A -9 REMARK 465 ASP A -8 REMARK 465 ASP A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 LYS A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 GLN A 2 REMARK 465 PRO A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 70 REMARK 465 SER A 71 REMARK 465 LEU A 72 REMARK 465 PRO A 73 REMARK 465 ALA A 74 REMARK 465 GLU A 75 REMARK 465 ALA A 76 REMARK 465 GLU A 77 REMARK 465 GLY A 78 REMARK 465 ALA A 79 REMARK 465 THR A 256 REMARK 465 MET A 257 REMARK 465 ASP A 258 REMARK 465 LEU A 259 REMARK 465 THR A 260 REMARK 465 GLN A 336 REMARK 465 ARG A 337 REMARK 465 HIS A 338 REMARK 465 GLY A 339 REMARK 465 SER A 340 REMARK 465 LYS A 341 REMARK 465 LYS A 342 REMARK 465 ASP A 343 REMARK 465 MET B -12 REMARK 465 ASP B -11 REMARK 465 TYR B -10 REMARK 465 LYS B -9 REMARK 465 ASP B -8 REMARK 465 ASP B -7 REMARK 465 ASP B -6 REMARK 465 ASP B -5 REMARK 465 LYS B -4 REMARK 465 GLY B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 ALA B 0 REMARK 465 SER B 1 REMARK 465 GLN B 2 REMARK 465 PRO B 3 REMARK 465 PRO B 4 REMARK 465 PRO B 5 REMARK 465 PRO B 6 REMARK 465 GLY B 7 REMARK 465 PRO B 70 REMARK 465 SER B 71 REMARK 465 LEU B 72 REMARK 465 PRO B 73 REMARK 465 ALA B 74 REMARK 465 GLU B 75 REMARK 465 ALA B 76 REMARK 465 GLU B 77 REMARK 465 GLY B 78 REMARK 465 ALA B 79 REMARK 465 THR B 256 REMARK 465 MET B 257 REMARK 465 ASP B 258 REMARK 465 LEU B 259 REMARK 465 THR B 260 REMARK 465 GLN B 336 REMARK 465 ARG B 337 REMARK 465 HIS B 338 REMARK 465 GLY B 339 REMARK 465 SER B 340 REMARK 465 LYS B 341 REMARK 465 LYS B 342 REMARK 465 ASP B 343 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 LYS A 104 -144.39 59.71 REMARK 500 ASN A 115 54.11 -90.64 REMARK 500 THR A 119 -60.94 -99.56 REMARK 500 GLU A 253 -70.04 -83.60 REMARK 500 ARG A 254 -37.57 -138.04 REMARK 500 GLN A 301 57.34 -90.04 REMARK 500 LYS B 104 -144.39 59.71 REMARK 500 ASN B 115 54.11 -90.64 REMARK 500 THR B 119 -60.94 -99.56 REMARK 500 ARG B 254 -37.59 -138.03 REMARK 500 GLN B 301 57.34 -90.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24230 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN TMEM120A DBREF 7N7P A 2 343 UNP Q9BXJ8 TACAN_HUMAN 2 343 DBREF 7N7P B 2 343 UNP Q9BXJ8 TACAN_HUMAN 2 343 SEQADV 7N7P MET A -12 UNP Q9BXJ8 INITIATING METHIONINE SEQADV 7N7P ASP A -11 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P TYR A -10 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P LYS A -9 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP A -8 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP A -7 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP A -6 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP A -5 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P LYS A -4 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P GLY A -3 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P GLY A -2 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P SER A -1 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ALA A 0 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P SER A 1 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P MET B -12 UNP Q9BXJ8 INITIATING METHIONINE SEQADV 7N7P ASP B -11 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P TYR B -10 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P LYS B -9 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP B -8 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP B -7 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP B -6 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ASP B -5 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P LYS B -4 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P GLY B -3 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P GLY B -2 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P SER B -1 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P ALA B 0 UNP Q9BXJ8 EXPRESSION TAG SEQADV 7N7P SER B 1 UNP Q9BXJ8 EXPRESSION TAG SEQRES 1 A 356 MET ASP TYR LYS ASP ASP ASP ASP LYS GLY GLY SER ALA SEQRES 2 A 356 SER GLN PRO PRO PRO PRO GLY PRO LEU GLY ASP CYS LEU SEQRES 3 A 356 ARG ASP TRP GLU ASP LEU GLN GLN ASP PHE GLN ASN ILE SEQRES 4 A 356 GLN GLU THR HIS ARG LEU TYR ARG LEU LYS LEU GLU GLU SEQRES 5 A 356 LEU THR LYS LEU GLN ASN ASN CYS THR SER SER ILE THR SEQRES 6 A 356 ARG GLN LYS LYS ARG LEU GLN GLU LEU ALA LEU ALA LEU SEQRES 7 A 356 LYS LYS CYS LYS PRO SER LEU PRO ALA GLU ALA GLU GLY SEQRES 8 A 356 ALA ALA GLN GLU LEU GLU ASN GLN MET LYS GLU ARG GLN SEQRES 9 A 356 GLY LEU PHE PHE ASP MET GLU ALA TYR LEU PRO LYS LYS SEQRES 10 A 356 ASN GLY LEU TYR LEU SER LEU VAL LEU GLY ASN VAL ASN SEQRES 11 A 356 VAL THR LEU LEU SER LYS GLN ALA LYS PHE ALA TYR LYS SEQRES 12 A 356 ASP GLU TYR GLU LYS PHE LYS LEU TYR LEU THR ILE ILE SEQRES 13 A 356 LEU ILE LEU ILE SER PHE THR CYS ARG PHE LEU LEU ASN SEQRES 14 A 356 SER ARG VAL THR ASP ALA ALA PHE ASN PHE LEU LEU VAL SEQRES 15 A 356 TRP TYR TYR CYS THR LEU THR ILE ARG GLU SER ILE LEU SEQRES 16 A 356 ILE ASN ASN GLY SER ARG ILE LYS GLY TRP TRP VAL PHE SEQRES 17 A 356 HIS HIS TYR VAL SER THR PHE LEU SER GLY VAL MET LEU SEQRES 18 A 356 THR TRP PRO ASP GLY LEU MET TYR GLN LYS PHE ARG ASN SEQRES 19 A 356 GLN PHE LEU SER PHE SER MET TYR GLN SER PHE VAL GLN SEQRES 20 A 356 PHE LEU GLN TYR TYR TYR GLN SER GLY CYS LEU TYR ARG SEQRES 21 A 356 LEU ARG ALA LEU GLY GLU ARG HIS THR MET ASP LEU THR SEQRES 22 A 356 VAL GLU GLY PHE GLN SER TRP MET TRP ARG GLY LEU THR SEQRES 23 A 356 PHE LEU LEU PRO PHE LEU PHE PHE GLY HIS PHE TRP GLN SEQRES 24 A 356 LEU PHE ASN ALA LEU THR LEU PHE ASN LEU ALA GLN ASP SEQRES 25 A 356 PRO GLN CYS LYS GLU TRP GLN VAL LEU MET CYS GLY PHE SEQRES 26 A 356 PRO PHE LEU LEU LEU PHE LEU GLY ASN PHE PHE THR THR SEQRES 27 A 356 LEU ARG VAL VAL HIS HIS LYS PHE HIS SER GLN ARG HIS SEQRES 28 A 356 GLY SER LYS LYS ASP SEQRES 1 B 356 MET ASP TYR LYS ASP ASP ASP ASP LYS GLY GLY SER ALA SEQRES 2 B 356 SER GLN PRO PRO PRO PRO GLY PRO LEU GLY ASP CYS LEU SEQRES 3 B 356 ARG ASP TRP GLU ASP LEU GLN GLN ASP PHE GLN ASN ILE SEQRES 4 B 356 GLN GLU THR HIS ARG LEU TYR ARG LEU LYS LEU GLU GLU SEQRES 5 B 356 LEU THR LYS LEU GLN ASN ASN CYS THR SER SER ILE THR SEQRES 6 B 356 ARG GLN LYS LYS ARG LEU GLN GLU LEU ALA LEU ALA LEU SEQRES 7 B 356 LYS LYS CYS LYS PRO SER LEU PRO ALA GLU ALA GLU GLY SEQRES 8 B 356 ALA ALA GLN GLU LEU GLU ASN GLN MET LYS GLU ARG GLN SEQRES 9 B 356 GLY LEU PHE PHE ASP MET GLU ALA TYR LEU PRO LYS LYS SEQRES 10 B 356 ASN GLY LEU TYR LEU SER LEU VAL LEU GLY ASN VAL ASN SEQRES 11 B 356 VAL THR LEU LEU SER LYS GLN ALA LYS PHE ALA TYR LYS SEQRES 12 B 356 ASP GLU TYR GLU LYS PHE LYS LEU TYR LEU THR ILE ILE SEQRES 13 B 356 LEU ILE LEU ILE SER PHE THR CYS ARG PHE LEU LEU ASN SEQRES 14 B 356 SER ARG VAL THR ASP ALA ALA PHE ASN PHE LEU LEU VAL SEQRES 15 B 356 TRP TYR TYR CYS THR LEU THR ILE ARG GLU SER ILE LEU SEQRES 16 B 356 ILE ASN ASN GLY SER ARG ILE LYS GLY TRP TRP VAL PHE SEQRES 17 B 356 HIS HIS TYR VAL SER THR PHE LEU SER GLY VAL MET LEU SEQRES 18 B 356 THR TRP PRO ASP GLY LEU MET TYR GLN LYS PHE ARG ASN SEQRES 19 B 356 GLN PHE LEU SER PHE SER MET TYR GLN SER PHE VAL GLN SEQRES 20 B 356 PHE LEU GLN TYR TYR TYR GLN SER GLY CYS LEU TYR ARG SEQRES 21 B 356 LEU ARG ALA LEU GLY GLU ARG HIS THR MET ASP LEU THR SEQRES 22 B 356 VAL GLU GLY PHE GLN SER TRP MET TRP ARG GLY LEU THR SEQRES 23 B 356 PHE LEU LEU PRO PHE LEU PHE PHE GLY HIS PHE TRP GLN SEQRES 24 B 356 LEU PHE ASN ALA LEU THR LEU PHE ASN LEU ALA GLN ASP SEQRES 25 B 356 PRO GLN CYS LYS GLU TRP GLN VAL LEU MET CYS GLY PHE SEQRES 26 B 356 PRO PHE LEU LEU LEU PHE LEU GLY ASN PHE PHE THR THR SEQRES 27 B 356 LEU ARG VAL VAL HIS HIS LYS PHE HIS SER GLN ARG HIS SEQRES 28 B 356 GLY SER LYS LYS ASP HET COA A 401 48 HET COA B 401 48 HETNAM COA COENZYME A FORMUL 3 COA 2(C21 H36 N7 O16 P3 S) HELIX 1 AA1 PRO A 8 LYS A 69 1 62 HELIX 2 AA2 GLN A 81 LEU A 101 1 21 HELIX 3 AA3 GLY A 106 LEU A 113 1 8 HELIX 4 AA4 SER A 122 PHE A 153 1 32 HELIX 5 AA5 SER A 157 ASN A 185 1 29 HELIX 6 AA6 LYS A 190 THR A 209 1 20 HELIX 7 AA7 GLY A 213 ARG A 254 1 42 HELIX 8 AA8 GLU A 262 ALA A 297 1 36 HELIX 9 AA9 TRP A 305 SER A 335 1 31 HELIX 10 AB1 LEU B 9 LYS B 69 1 61 HELIX 11 AB2 GLN B 81 LEU B 101 1 21 HELIX 12 AB3 GLY B 106 LEU B 113 1 8 HELIX 13 AB4 SER B 122 PHE B 153 1 32 HELIX 14 AB5 SER B 157 ASN B 185 1 29 HELIX 15 AB6 LYS B 190 THR B 209 1 20 HELIX 16 AB7 GLY B 213 ARG B 254 1 42 HELIX 17 AB8 GLU B 262 ALA B 297 1 36 HELIX 18 AB9 TRP B 305 SER B 335 1 31 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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