HEADER METAL BINDING PROTEIN 03-APR-24 9BA1 TITLE SOLUTION NMR STRUCTURE OF THE HUMAN LETM1 F-EF-HAND DOMAIN IN THE TITLE 2 PRESENCE OF CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL PROTON/CALCIUM EXCHANGER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ELECTRONEUTRAL MITOCHONDRIAL K(+)/H(+)EXCHANGER,KHE,LEUCINE COMPND 5 ZIPPER-EF-HAND-CONTAINING TRANSMEMBRANE PROTEIN 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: LETM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EF-HAND, F-EF-HAND, LETM1, MITOCHONDRIAL, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Q.T.LIN,P.B.STATHOPULOS REVDAT 2 27-NOV-24 9BA1 1 JRNL REVDAT 1 16-OCT-24 9BA1 0 JRNL AUTH Q.T.LIN,D.M.COLUSSI,T.LAKE,P.B.STATHOPULOS JRNL TITL AN AI-INFORMED NMR STRUCTURE REVEALS AN EXTRAORDINARY LETM1 JRNL TITL 2 F-EF-HAND DOMAIN THAT FUNCTIONS AS A TWO-WAY REGULATOR OF JRNL TITL 3 MITOCHONDRIAL CALCIUM. JRNL REF STRUCTURE V. 32 2063 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 39317198 JRNL DOI 10.1016/J.STR.2024.08.020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9BA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000282561. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.15; 308.15 REMARK 210 PH : 7.8; 8.2 REMARK 210 IONIC STRENGTH : 140; 140 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 15N] HUMAN LEUCINE REMARK 210 ZIPPER EF-HAND CONTAINING REMARK 210 TRANSMEMBRANE PROTEIN-1 (LETM1) REMARK 210 RESIDUES 643-699, 20 MM TRIS, 50 REMARK 210 MM SODIUM CHLORIDE, 10 MM CHAPS, REMARK 210 30 MM CALCIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-99% 13C; U-99% REMARK 210 15N] HUMAN LEUCINE ZIPPER EF- REMARK 210 HAND CONTAINING TRANSMEMBRANE REMARK 210 PROTEIN-1 (LETM1) RESIDUES 643- REMARK 210 699, 20 MM TRIS, 50 MM SODIUM REMARK 210 CHLORIDE, 10 MM CHAPS, 30 MM REMARK 210 CALCIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-99% 13C; U-99% 15N] REMARK 210 HUMAN LEUCINE ZIPPER EF-HAND REMARK 210 CONTAINING TRANSMEMBRANE PROTEIN- REMARK 210 1 (LETM1) RESIDUES 643-699, 20 REMARK 210 MM TRIS, 50 MM SODIUM CHLORIDE, REMARK 210 10 MM CHAPS, 30 MM CALCIUM REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 H(CCO)NH; 3D HNCO; 2D 1H-13C REMARK 210 HSQC; 3D HCCH-TOCSY; 3D 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.9.1B12, CYANA 2.1, REMARK 210 NMRPIPE 10.9 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 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 OD2 ASP A 687 HZ1 LYS A 690 1.58 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 1 HIS A -3 -41.55 -140.27 REMARK 500 1 ASN A 646 -179.68 -62.80 REMARK 500 1 HIS A 662 54.05 -143.35 REMARK 500 2 ASN A 646 170.74 -52.53 REMARK 500 3 ASN A 646 161.69 -44.15 REMARK 500 4 SER A -4 -176.85 56.13 REMARK 500 4 ALA A -1 88.78 -175.55 REMARK 500 4 ASN A 646 -174.80 -62.18 REMARK 500 5 SER A -4 84.42 59.33 REMARK 500 5 ALA A -1 20.76 167.17 REMARK 500 5 ASN A 646 121.62 -30.90 REMARK 500 6 ASN A 646 167.95 -45.28 REMARK 500 7 ALA A -1 88.07 62.88 REMARK 500 7 ASN A 646 170.47 -50.00 REMARK 500 8 HIS A -3 146.78 70.23 REMARK 500 8 ALA A -1 74.47 60.39 REMARK 500 8 ASN A 646 157.32 -42.01 REMARK 500 9 ALA A -1 85.55 64.84 REMARK 500 9 ASN A 646 -176.69 -54.35 REMARK 500 9 LYS A 661 -169.27 -117.70 REMARK 500 10 ALA A -1 38.00 74.03 REMARK 500 10 PRO A 664 106.76 -59.97 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 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 676 OD1 REMARK 620 2 GLU A 677 OE2 79.7 REMARK 620 3 ASN A 678 OD1 112.7 67.9 REMARK 620 4 ASP A 680 OD1 107.7 135.9 69.3 REMARK 620 5 ASP A 680 OD2 74.0 153.0 117.4 51.2 REMARK 620 6 LYS A 682 O 82.7 109.1 162.6 114.9 73.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31155 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF THE HUMAN LETM1 F-EF-HAND DOMAIN IN THE REMARK 900 PRESENCE OF CALCIUM. DBREF 9BA1 A 643 699 UNP O95202 LETM1_HUMAN 643 699 SEQADV 9BA1 GLY A -5 UNP O95202 EXPRESSION TAG SEQADV 9BA1 SER A -4 UNP O95202 EXPRESSION TAG SEQADV 9BA1 HIS A -3 UNP O95202 EXPRESSION TAG SEQADV 9BA1 MET A -2 UNP O95202 EXPRESSION TAG SEQADV 9BA1 ALA A -1 UNP O95202 EXPRESSION TAG SEQADV 9BA1 SER A 0 UNP O95202 EXPRESSION TAG SEQRES 1 A 63 GLY SER HIS MET ALA SER THR GLY GLU ASN VAL ILE SER SEQRES 2 A 63 VAL ALA GLU LEU ILE ASN ALA MET LYS GLN VAL LYS HIS SEQRES 3 A 63 ILE PRO GLU SER LYS LEU THR SER LEU ALA ALA ALA LEU SEQRES 4 A 63 ASP GLU ASN LYS ASP GLY LYS VAL ASN ILE ASP ASP LEU SEQRES 5 A 63 VAL LYS VAL ILE GLU LEU VAL ASP LYS GLU ASP HET CA A 701 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 AA1 VAL A 650 LYS A 661 1 12 HELIX 2 AA2 PRO A 664 ASP A 676 1 13 HELIX 3 AA3 ILE A 685 LYS A 697 1 13 SHEET 1 AA1 2 VAL A 647 SER A 649 0 SHEET 2 AA1 2 LYS A 682 ASN A 684 -1 O VAL A 683 N ILE A 648 LINK OD1 ASP A 676 CA CA A 701 1555 1555 2.29 LINK OE2 GLU A 677 CA CA A 701 1555 1555 2.26 LINK OD1 ASN A 678 CA CA A 701 1555 1555 2.45 LINK OD1 ASP A 680 CA CA A 701 1555 1555 2.43 LINK OD2 ASP A 680 CA CA A 701 1555 1555 2.35 LINK O LYS A 682 CA CA A 701 1555 1555 2.36 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 583 958 CONECT 597 958 CONECT 610 958 CONECT 646 958 CONECT 647 958 CONECT 662 958 CONECT 958 583 597 610 646 CONECT 958 647 662 MASTER 159 0 1 3 2 0 0 6 473 1 8 5 END