HEADER METAL BINDING PROTEIN 08-JUN-20 6ZBI TITLE TERNARY COMPLEX OF CALMODULIN BOUND TO 2 MOLECULES OF NHE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SODIUM/HYDROGEN EXCHANGER 1; COMPND 7 CHAIN: B, C; COMPND 8 SYNONYM: APNH,NA(+)/H(+) ANTIPORTER,AMILORIDE-SENSITIVE,NA(+)/H(+) COMPND 9 EXCHANGER 1,NHE-1,SOLUTE CARRIER FAMILY 9 MEMBER 1; COMPND 10 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: CALM1, CALM, CAM, CAM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODONPLUS (DE3)-RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET5; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: SLC9A1, APNH1, NHE1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS KEYWDS COMPLEX, NHE1, CALMODULIN, SIGNALING, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.PRESTEL,B.B.KRAGELUND,E.S.PEDERSEN,S.F.PEDERSEN,L.M.SJOEGAARD-FRICH REVDAT 3 15-MAY-24 6ZBI 1 REMARK REVDAT 2 14-APR-21 6ZBI 1 JRNL REVDAT 1 17-MAR-21 6ZBI 0 JRNL AUTH L.M.SJOGAARD-FRICH,A.PRESTEL,E.S.PEDERSEN,M.SEVERIN, JRNL AUTH 2 K.K.KRISTENSEN,J.G.OLSEN,B.B.KRAGELUND,S.F.PEDERSEN JRNL TITL DYNAMIC NA + /H + EXCHANGER 1 (NHE1) - CALMODULIN COMPLEXES JRNL TITL 2 OF VARYING STOICHIOMETRY AND STRUCTURE REGULATE CA 2+ JRNL TITL 3 -DEPENDENT NHE1 ACTIVATION. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 33655882 JRNL DOI 10.7554/ELIFE.60889 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.44 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109151. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 CALMODULIN, 1.15 MM SODIUM/ REMARK 210 HYDROGEN EXCHANGER 1 (NHE1, REMARK 210 SLC9A1), 95% H2O/5% D2O; 1 MM [U- REMARK 210 99% 13C; U-99% 15N] SODIUM/ REMARK 210 HYDROGEN EXCHANGER 1 (NHE1, REMARK 210 SLC9A1), 0.5 MM CALMODULIN, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY ALIPHATIC; 3D 1H REMARK 210 -13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N NOESY 12C/14N REMARK 210 FILTERED; 3D 1H-13C NOESY 12C/ REMARK 210 14N FILTERED; 3D HNCO; 3D HNCACB; REMARK 210 3D HN(CA)CO; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HBHA(CO)NH; 3D REMARK 210 CBCA(CO)NH; 2D 1H-13C HSQC; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98.5, CCPNMR ANALYSIS REMARK 210 2.4.2, NMRPIPE, TOPSPIN 3.5, REMARK 210 QMDD, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: CLOSE CONTACTS 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 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 2 THR A 79 -69.36 -147.73 REMARK 500 2 VAL B 655 67.53 63.02 REMARK 500 3 ARG A 74 -88.08 73.45 REMARK 500 4 LEU B 654 -176.47 71.76 REMARK 500 4 TYR C 849 59.09 -103.00 REMARK 500 4 LEU C 854 -84.72 134.99 REMARK 500 5 ASP A 78 -60.75 -132.24 REMARK 500 7 THR A 79 -159.35 72.69 REMARK 500 9 LYS A 75 -113.16 73.06 REMARK 500 9 MET A 76 -58.55 79.13 REMARK 500 9 ASP A 80 65.62 -113.35 REMARK 500 10 LYS A 75 132.63 81.93 REMARK 500 11 ARG A 74 -63.39 70.48 REMARK 500 12 ASP A 80 42.61 -156.21 REMARK 500 13 ARG A 74 -65.52 75.99 REMARK 500 13 ALA B 656 -135.42 66.62 REMARK 500 14 THR A 79 -103.52 -103.11 REMARK 500 14 TYR B 649 62.33 -105.39 REMARK 500 14 ALA B 656 -131.95 68.71 REMARK 500 14 LEU C 854 -57.43 79.98 REMARK 500 16 ASP A 78 97.51 -163.39 REMARK 500 16 THR A 79 -81.33 -135.89 REMARK 500 16 THR B 653 79.60 60.89 REMARK 500 16 LEU C 854 -64.59 77.74 REMARK 500 17 ARG A 74 -33.48 75.98 REMARK 500 17 ALA B 656 -131.59 67.44 REMARK 500 17 ALA C 856 -105.32 67.03 REMARK 500 18 ASP A 80 -64.06 -163.43 REMARK 500 18 VAL B 655 74.92 63.86 REMARK 500 18 LEU C 854 -171.85 63.26 REMARK 500 19 GLN A 3 122.47 77.80 REMARK 500 19 ALA C 856 -51.89 -127.84 REMARK 500 20 MET A 76 36.49 -149.34 REMARK 500 20 THR B 653 -61.01 74.52 REMARK 500 20 LEU B 654 64.74 65.37 REMARK 500 20 THR C 853 -92.71 68.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 22 OD1 REMARK 620 2 GLU A 31 OE1 69.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 GLU A 67 OE1 84.6 REMARK 620 3 GLU A 67 OE2 76.9 51.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD1 REMARK 620 2 GLU A 104 OE1 73.8 REMARK 620 3 GLU A 104 OE2 87.6 54.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 GLU A 140 OE1 74.1 REMARK 620 3 GLU A 140 OE2 84.5 52.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34521 RELATED DB: BMRB REMARK 900 TERNARY COMPLEX OF CALMODULIN BOUND TO 2 MOLECULES OF NHE1 DBREF 6ZBI A 1 148 UNP P0DP23 CALM1_HUMAN 2 149 DBREF 6ZBI B 622 657 UNP P19634 SL9A1_HUMAN 622 657 DBREF 6ZBI C 822 857 UNP P19634 SL9A1_HUMAN 622 657 SEQRES 1 A 148 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 148 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 148 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 148 GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 148 ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 148 PRO GLU PHE LEU THR MET MET ALA ARG LYS MET LYS ASP SEQRES 7 A 148 THR ASP SER GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL SEQRES 8 A 148 PHE ASP LYS ASP GLY ASN GLY TYR ILE SER ALA ALA GLU SEQRES 9 A 148 LEU ARG HIS VAL MET THR ASN LEU GLY GLU LYS LEU THR SEQRES 10 A 148 ASP GLU GLU VAL ASP GLU MET ILE ARG GLU ALA ASP ILE SEQRES 11 A 148 ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN SEQRES 12 A 148 MET MET THR ALA LYS SEQRES 1 B 36 ALA LEU SER LYS ASP LYS GLU GLU GLU ILE ARG LYS ILE SEQRES 2 B 36 LEU ARG ASN ASN LEU GLN LYS THR ARG GLN ARG LEU ARG SEQRES 3 B 36 SER TYR ASN ARG HIS THR LEU VAL ALA ASP SEQRES 1 C 36 ALA LEU SER LYS ASP LYS GLU GLU GLU ILE ARG LYS ILE SEQRES 2 C 36 LEU ARG ASN ASN LEU GLN LYS THR ARG GLN ARG LEU ARG SEQRES 3 C 36 SER TYR ASN ARG HIS THR LEU VAL ALA ASP HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HET CA A 204 1 HETNAM CA CALCIUM ION FORMUL 4 CA 4(CA 2+) HELIX 1 AA1 THR A 5 ASP A 20 1 16 HELIX 2 AA2 THR A 28 LEU A 39 1 12 HELIX 3 AA3 THR A 44 ASP A 56 1 13 HELIX 4 AA4 ASP A 64 MET A 72 1 9 HELIX 5 AA5 ASP A 80 ASP A 93 1 14 HELIX 6 AA6 SER A 101 ASN A 111 1 11 HELIX 7 AA7 THR A 117 ASP A 129 1 13 HELIX 8 AA8 ASN A 137 THR A 146 1 10 HELIX 9 AA9 SER B 624 TYR B 649 1 26 HELIX 10 AB1 ASN B 650 LEU B 654 5 5 HELIX 11 AB2 SER C 824 LEU C 854 1 31 LINK OD1 ASP A 22 CA CA A 201 1555 1555 2.07 LINK OE1 GLU A 31 CA CA A 201 1555 1555 2.65 LINK OD1 ASP A 58 CA CA A 202 1555 1555 1.88 LINK OE1 GLU A 67 CA CA A 202 1555 1555 2.45 LINK OE2 GLU A 67 CA CA A 202 1555 1555 2.56 LINK OD1 ASP A 95 CA CA A 203 1555 1555 2.09 LINK OE1 GLU A 104 CA CA A 203 1555 1555 2.66 LINK OE2 GLU A 104 CA CA A 203 1555 1555 1.86 LINK OD1 ASP A 131 CA CA A 204 1555 1555 1.87 LINK OE1 GLU A 140 CA CA A 204 1555 1555 2.62 LINK OE2 GLU A 140 CA CA A 204 1555 1555 2.31 SITE 1 AC1 5 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 5 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 5 GLU A 67 SITE 1 AC3 5 ASP A 93 ASP A 95 ASN A 97 TYR A 99 SITE 2 AC3 5 GLU A 104 SITE 1 AC4 5 ASP A 129 ASP A 131 ASP A 133 GLN A 135 SITE 2 AC4 5 GLU A 140 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 MODEL 1