HEADER MEMBRANE PROTEIN 03-JAN-21 7DSW TITLE STRUCTURE OF A HUMAN NHE1-CHP1 COMPLEX UNDER PH 7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM/HYDROGEN EXCHANGER 1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: APNH,NA(+)/H(+) ANTIPORTER,AMILORIDE-SENSITIVE,NA(+)/H(+) COMPND 5 EXCHANGER 1,NHE-1,SOLUTE CARRIER FAMILY 9 MEMBER 1; 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: SLC9A1, APNH1, NHE1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.DONG,Y.GAO,B.LI,X.C.ZHANG,Y.ZHAO REVDAT 2 27-MAR-24 7DSW 1 REMARK REVDAT 1 23-JUN-21 7DSW 0 JRNL AUTH Y.DONG,Y.GAO,A.ILIE,D.KIM,A.BOUCHER,B.LI,X.C.ZHANG, JRNL AUTH 2 J.ORLOWSKI,Y.ZHAO JRNL TITL STRUCTURE AND MECHANISM OF THE HUMAN NHE1-CHP1 COMPLEX. JRNL REF NAT COMMUN V. 12 3474 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34108458 JRNL DOI 10.1038/S41467-021-23496-Z REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH, TOPAZ, SERIALEM, GCTF, REMARK 3 COOT, PHENIX, RELION, CRYOSPARC, RELION, REMARK 3 RELION 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 : 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 108712 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 7DSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020069. 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 NHE1-CHP1 COMPLEX UNDER REMARK 245 PH 7.5 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.50 REMARK 245 SAMPLE DETAILS : CALCINEURIN B HOMOLOGOUS REMARK 245 PROTEIN 1 (CHP1) WAS NOT SUCCESSFULLY RESOLVED IN THIS MAP REMARK 245 BECAUSE OF CONFORMATIONAL HETEROGENEITY. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2462 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 13000 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: B, 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 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 PHE B 89 76.87 53.31 REMARK 500 ARG B 100 -50.56 -121.99 REMARK 500 GLN B 157 45.24 -89.40 REMARK 500 SER B 158 -2.76 58.96 REMARK 500 GLU B 217 -12.74 72.71 REMARK 500 GLN B 218 -30.84 -132.27 REMARK 500 HIS B 250 -2.99 68.11 REMARK 500 GLU B 368 -9.94 71.20 REMARK 500 ALA B 460 -9.81 72.42 REMARK 500 PHE B 474 72.92 49.23 REMARK 500 PHE A 89 76.95 53.25 REMARK 500 ARG A 100 -50.63 -121.99 REMARK 500 GLN A 157 45.25 -89.40 REMARK 500 SER A 158 -2.76 58.98 REMARK 500 GLU A 217 -12.77 72.72 REMARK 500 GLN A 218 -30.90 -132.25 REMARK 500 HIS A 250 -2.98 68.09 REMARK 500 GLU A 368 -9.94 71.20 REMARK 500 ALA A 460 -9.92 72.50 REMARK 500 PHE A 474 72.90 49.24 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 LBN B 601 REMARK 610 LBN B 602 REMARK 610 LBN B 603 REMARK 610 LBN B 604 REMARK 610 LBN B 605 REMARK 610 LBN B 606 REMARK 610 LBN A 801 REMARK 610 LBN A 802 REMARK 610 LBN A 803 REMARK 610 LBN A 804 REMARK 610 LBN A 805 REMARK 610 LBN A 806 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30848 RELATED DB: EMDB REMARK 900 STRUCTURE OF A COMPLEX DBREF 7DSW B 87 506 UNP P19634 SL9A1_HUMAN 87 506 DBREF 7DSW A 87 506 UNP P19634 SL9A1_HUMAN 87 506 SEQRES 1 B 420 LYS ALA PHE PRO VAL LEU GLY ILE ASP TYR THR HIS VAL SEQRES 2 B 420 ARG THR PRO PHE GLU ILE SER LEU TRP ILE LEU LEU ALA SEQRES 3 B 420 CYS LEU MET LYS ILE GLY PHE HIS VAL ILE PRO THR ILE SEQRES 4 B 420 SER SER ILE VAL PRO GLU SER CYS LEU LEU ILE VAL VAL SEQRES 5 B 420 GLY LEU LEU VAL GLY GLY LEU ILE LYS GLY VAL GLY GLU SEQRES 6 B 420 THR PRO PRO PHE LEU GLN SER ASP VAL PHE PHE LEU PHE SEQRES 7 B 420 LEU LEU PRO PRO ILE ILE LEU ASP ALA GLY TYR PHE LEU SEQRES 8 B 420 PRO LEU ARG GLN PHE THR GLU ASN LEU GLY THR ILE LEU SEQRES 9 B 420 ILE PHE ALA VAL VAL GLY THR LEU TRP ASN ALA PHE PHE SEQRES 10 B 420 LEU GLY GLY LEU MET TYR ALA VAL CYS LEU VAL GLY GLY SEQRES 11 B 420 GLU GLN ILE ASN ASN ILE GLY LEU LEU ASP ASN LEU LEU SEQRES 12 B 420 PHE GLY SER ILE ILE SER ALA VAL ASP PRO VAL ALA VAL SEQRES 13 B 420 LEU ALA VAL PHE GLU GLU ILE HIS ILE ASN GLU LEU LEU SEQRES 14 B 420 HIS ILE LEU VAL PHE GLY GLU SER LEU LEU ASN ASP ALA SEQRES 15 B 420 VAL THR VAL VAL LEU TYR HIS LEU PHE GLU GLU PHE ALA SEQRES 16 B 420 ASN TYR GLU HIS VAL GLY ILE VAL ASP ILE PHE LEU GLY SEQRES 17 B 420 PHE LEU SER PHE PHE VAL VAL ALA LEU GLY GLY VAL LEU SEQRES 18 B 420 VAL GLY VAL VAL TYR GLY VAL ILE ALA ALA PHE THR SER SEQRES 19 B 420 ARG PHE THR SER HIS ILE ARG VAL ILE GLU PRO LEU PHE SEQRES 20 B 420 VAL PHE LEU TYR SER TYR MET ALA TYR LEU SER ALA GLU SEQRES 21 B 420 LEU PHE HIS LEU SER GLY ILE MET ALA LEU ILE ALA SER SEQRES 22 B 420 GLY VAL VAL MET ARG PRO TYR VAL GLU ALA ASN ILE SER SEQRES 23 B 420 HIS LYS SER HIS THR THR ILE LYS TYR PHE LEU LYS MET SEQRES 24 B 420 TRP SER SER VAL SER GLU THR LEU ILE PHE ILE PHE LEU SEQRES 25 B 420 GLY VAL SER THR VAL ALA GLY SER HIS HIS TRP ASN TRP SEQRES 26 B 420 THR PHE VAL ILE SER THR LEU LEU PHE CYS LEU ILE ALA SEQRES 27 B 420 ARG VAL LEU GLY VAL LEU GLY LEU THR TRP PHE ILE ASN SEQRES 28 B 420 LYS PHE ARG ILE VAL LYS LEU THR PRO LYS ASP GLN PHE SEQRES 29 B 420 ILE ILE ALA TYR GLY GLY LEU ARG GLY ALA ILE ALA PHE SEQRES 30 B 420 SER LEU GLY TYR LEU LEU ASP LYS LYS HIS PHE PRO MET SEQRES 31 B 420 CYS ASP LEU PHE LEU THR ALA ILE ILE THR VAL ILE PHE SEQRES 32 B 420 PHE THR VAL PHE VAL GLN GLY MET THR ILE ARG PRO LEU SEQRES 33 B 420 VAL ASP LEU LEU SEQRES 1 A 420 LYS ALA PHE PRO VAL LEU GLY ILE ASP TYR THR HIS VAL SEQRES 2 A 420 ARG THR PRO PHE GLU ILE SER LEU TRP ILE LEU LEU ALA SEQRES 3 A 420 CYS LEU MET LYS ILE GLY PHE HIS VAL ILE PRO THR ILE SEQRES 4 A 420 SER SER ILE VAL PRO GLU SER CYS LEU LEU ILE VAL VAL SEQRES 5 A 420 GLY LEU LEU VAL GLY GLY LEU ILE LYS GLY VAL GLY GLU SEQRES 6 A 420 THR PRO PRO PHE LEU GLN SER ASP VAL PHE PHE LEU PHE SEQRES 7 A 420 LEU LEU PRO PRO ILE ILE LEU ASP ALA GLY TYR PHE LEU SEQRES 8 A 420 PRO LEU ARG GLN PHE THR GLU ASN LEU GLY THR ILE LEU SEQRES 9 A 420 ILE PHE ALA VAL VAL GLY THR LEU TRP ASN ALA PHE PHE SEQRES 10 A 420 LEU GLY GLY LEU MET TYR ALA VAL CYS LEU VAL GLY GLY SEQRES 11 A 420 GLU GLN ILE ASN ASN ILE GLY LEU LEU ASP ASN LEU LEU SEQRES 12 A 420 PHE GLY SER ILE ILE SER ALA VAL ASP PRO VAL ALA VAL SEQRES 13 A 420 LEU ALA VAL PHE GLU GLU ILE HIS ILE ASN GLU LEU LEU SEQRES 14 A 420 HIS ILE LEU VAL PHE GLY GLU SER LEU LEU ASN ASP ALA SEQRES 15 A 420 VAL THR VAL VAL LEU TYR HIS LEU PHE GLU GLU PHE ALA SEQRES 16 A 420 ASN TYR GLU HIS VAL GLY ILE VAL ASP ILE PHE LEU GLY SEQRES 17 A 420 PHE LEU SER PHE PHE VAL VAL ALA LEU GLY GLY VAL LEU SEQRES 18 A 420 VAL GLY VAL VAL TYR GLY VAL ILE ALA ALA PHE THR SER SEQRES 19 A 420 ARG PHE THR SER HIS ILE ARG VAL ILE GLU PRO LEU PHE SEQRES 20 A 420 VAL PHE LEU TYR SER TYR MET ALA TYR LEU SER ALA GLU SEQRES 21 A 420 LEU PHE HIS LEU SER GLY ILE MET ALA LEU ILE ALA SER SEQRES 22 A 420 GLY VAL VAL MET ARG PRO TYR VAL GLU ALA ASN ILE SER SEQRES 23 A 420 HIS LYS SER HIS THR THR ILE LYS TYR PHE LEU LYS MET SEQRES 24 A 420 TRP SER SER VAL SER GLU THR LEU ILE PHE ILE PHE LEU SEQRES 25 A 420 GLY VAL SER THR VAL ALA GLY SER HIS HIS TRP ASN TRP SEQRES 26 A 420 THR PHE VAL ILE SER THR LEU LEU PHE CYS LEU ILE ALA SEQRES 27 A 420 ARG VAL LEU GLY VAL LEU GLY LEU THR TRP PHE ILE ASN SEQRES 28 A 420 LYS PHE ARG ILE VAL LYS LEU THR PRO LYS ASP GLN PHE SEQRES 29 A 420 ILE ILE ALA TYR GLY GLY LEU ARG GLY ALA ILE ALA PHE SEQRES 30 A 420 SER LEU GLY TYR LEU LEU ASP LYS LYS HIS PHE PRO MET SEQRES 31 A 420 CYS ASP LEU PHE LEU THR ALA ILE ILE THR VAL ILE PHE SEQRES 32 A 420 PHE THR VAL PHE VAL GLN GLY MET THR ILE ARG PRO LEU SEQRES 33 A 420 VAL ASP LEU LEU HET LBN B 601 9 HET LBN B 602 9 HET LBN B 603 11 HET LBN B 604 11 HET LBN B 605 6 HET LBN B 606 13 HET LBN A 801 13 HET LBN A 802 9 HET LBN A 803 9 HET LBN A 804 11 HET LBN A 805 11 HET LBN A 806 6 HETNAM LBN 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETSYN LBN (2R)-2-[(9Z)-9-OCTADECENOYLOXY]-3-(PALMITOYLOXY)PROPYL HETSYN 2 LBN 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE FORMUL 3 LBN 12(C42 H82 N O8 P) HELIX 1 AA1 ARG B 100 VAL B 121 1 22 HELIX 2 AA2 PRO B 130 GLY B 150 1 21 HELIX 3 AA3 ASP B 159 LEU B 165 1 7 HELIX 4 AA4 LEU B 165 PHE B 176 1 12 HELIX 5 AA5 PHE B 182 GLU B 184 5 3 HELIX 6 AA6 ASN B 185 GLY B 215 1 31 HELIX 7 AA7 LEU B 224 SER B 235 1 12 HELIX 8 AA8 ASP B 238 PHE B 246 5 9 HELIX 9 AA9 ASN B 252 ALA B 281 1 30 HELIX 10 AB1 GLY B 287 ARG B 321 1 35 HELIX 11 AB2 ILE B 329 PHE B 348 1 20 HELIX 12 AB3 SER B 351 VAL B 367 1 17 HELIX 13 AB4 SER B 372 ALA B 404 1 33 HELIX 14 AB5 ASN B 410 ASN B 437 1 28 HELIX 15 AB6 THR B 445 TYR B 454 1 10 HELIX 16 AB7 ILE B 461 LEU B 468 1 8 HELIX 17 AB8 MET B 476 VAL B 494 1 19 HELIX 18 AB9 ILE B 499 LEU B 505 1 7 HELIX 19 AC1 ARG A 100 VAL A 121 1 22 HELIX 20 AC2 PRO A 130 GLY A 150 1 21 HELIX 21 AC3 ASP A 159 LEU A 165 1 7 HELIX 22 AC4 LEU A 165 PHE A 176 1 12 HELIX 23 AC5 PHE A 182 GLU A 184 5 3 HELIX 24 AC6 ASN A 185 GLY A 215 1 31 HELIX 25 AC7 LEU A 224 SER A 235 1 12 HELIX 26 AC8 ASP A 238 PHE A 246 5 9 HELIX 27 AC9 ASN A 252 ALA A 281 1 30 HELIX 28 AD1 GLY A 287 ARG A 321 1 35 HELIX 29 AD2 ILE A 329 PHE A 348 1 20 HELIX 30 AD3 SER A 351 VAL A 367 1 17 HELIX 31 AD4 SER A 372 ALA A 404 1 33 HELIX 32 AD5 ASN A 410 ASN A 437 1 28 HELIX 33 AD6 THR A 445 TYR A 454 1 10 HELIX 34 AD7 ILE A 461 LEU A 468 1 8 HELIX 35 AD8 MET A 476 VAL A 494 1 19 HELIX 36 AD9 ILE A 499 LEU A 505 1 7 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