HEADER ELECTRON TRANSPORT 15-JUN-15 2N3Y TITLE NMR STRUCTURE OF THE Y48PCMF VARIANT OF HUMAN CYTOCHROME C IN ITS TITLE 2 REDUCED STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CYCS, CYC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCCY48AMBER KEYWDS CYTOCHROME C, HEMEPROTEIN, MITOCHONDRIA, APOPTOSIS, PHOSPHORYLATION, KEYWDS 2 ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.MORENO-BELTRAN,R.DEL CONTE,A.DIAZ-QUINTANA,M.A.DE LA ROSA,P.TURANO, AUTHOR 2 I.DIAZ-MORENO REVDAT 4 26-APR-17 2N3Y 1 JRNL REVDAT 3 19-APR-17 2N3Y 1 JRNL REVDAT 2 29-MAR-17 2N3Y 1 JRNL REVDAT 1 14-DEC-16 2N3Y 0 JRNL AUTH B.MORENO-BELTRAN,A.GUERRA-CASTELLANO,A.DIAZ-QUINTANA, JRNL AUTH 2 R.DEL CONTE,S.M.GARCIA-MAURINO,S.DIAZ-MORENO, JRNL AUTH 3 K.GONZALEZ-ARZOLA,C.SANTOS-OCANA,A.VELAZQUEZ-CAMPOY, JRNL AUTH 4 M.A.DE LA ROSA,P.TURANO,I.DIAZ-MORENO JRNL TITL STRUCTURAL BASIS OF MITOCHONDRIAL DYSFUNCTION IN RESPONSE TO JRNL TITL 2 CYTOCHROME C PHOSPHORYLATION AT TYROSINE 48. JRNL REF PROC. NATL. ACAD. SCI. V. 114 E3041 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28348229 JRNL DOI 10.1073/PNAS.1618008114 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER, CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLMAN (AMBER), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS PERFORMED IN SOLVENT REMARK 4 REMARK 4 2N3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000104391. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-99% 13C; U-99% 15N] REMARK 210 CYTOCHROME C, 90% H2O/10% D2O; REMARK 210 0.7 MM [U-99% 15N] CYTOCHROME C, REMARK 210 90% H2O/10% D2O; 0.6 MM REMARK 210 CYTOCHROME C, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HN(CO)CA; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 2D 1H-1H COSY; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D HNCACB; 3D REMARK 210 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, TALOS, CARA, XEASY REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 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 1 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 5 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 16 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 20 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 4.4 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 1 CYS A 14 -41.01 -131.38 REMARK 500 1 THR A 40 -135.72 -111.56 REMARK 500 1 GLN A 42 -16.70 -157.29 REMARK 500 1 SER A 47 75.62 58.20 REMARK 500 1 ASN A 70 94.47 -161.47 REMARK 500 1 MET A 80 91.60 -66.05 REMARK 500 2 LEU A 32 -7.34 67.88 REMARK 500 2 THR A 40 -126.92 -123.72 REMARK 500 2 GLN A 42 -21.75 -152.56 REMARK 500 2 TYR A 46 -43.05 -131.25 REMARK 500 2 1PA A 48 -52.12 -133.13 REMARK 500 2 THR A 63 -36.94 -134.42 REMARK 500 2 ASN A 70 95.75 -163.83 REMARK 500 3 CYS A 14 -43.77 -131.47 REMARK 500 3 LYS A 27 -153.56 -144.09 REMARK 500 3 LEU A 32 -4.07 67.16 REMARK 500 3 THR A 40 -162.08 -125.81 REMARK 500 3 GLN A 42 -27.25 -151.04 REMARK 500 3 THR A 49 116.79 -162.01 REMARK 500 3 ASN A 70 90.06 -164.89 REMARK 500 3 MET A 80 96.61 -62.35 REMARK 500 4 LYS A 27 -164.38 -160.41 REMARK 500 4 THR A 40 -167.73 -128.17 REMARK 500 4 GLN A 42 -12.48 -152.84 REMARK 500 4 SER A 47 167.54 59.85 REMARK 500 4 ASN A 70 83.39 -157.68 REMARK 500 5 CYS A 17 -52.16 -133.38 REMARK 500 5 LYS A 27 -162.30 -167.60 REMARK 500 5 THR A 40 -127.77 -128.94 REMARK 500 5 GLN A 42 -12.46 -158.24 REMARK 500 5 SER A 47 168.58 58.09 REMARK 500 5 1PA A 48 -57.24 -133.82 REMARK 500 5 ASN A 70 92.62 -164.72 REMARK 500 6 THR A 40 -162.77 -109.55 REMARK 500 6 GLN A 42 -25.05 -153.84 REMARK 500 6 ASN A 70 86.83 -169.15 REMARK 500 6 MET A 80 91.72 -58.16 REMARK 500 7 CYS A 17 -55.68 -121.99 REMARK 500 7 VAL A 20 45.75 -141.07 REMARK 500 7 LEU A 32 -4.22 67.86 REMARK 500 7 ASN A 70 94.22 -162.54 REMARK 500 8 CYS A 17 -52.75 -131.73 REMARK 500 8 VAL A 20 57.53 -140.97 REMARK 500 8 LEU A 32 -2.93 68.24 REMARK 500 8 1PA A 48 -83.28 -126.65 REMARK 500 8 ASN A 54 33.47 -93.79 REMARK 500 8 TRP A 59 95.37 -61.03 REMARK 500 8 ASN A 70 91.74 -165.41 REMARK 500 9 LEU A 32 -1.14 67.28 REMARK 500 9 1PA A 48 -64.48 -143.50 REMARK 500 REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 18 THR A 19 6 149.39 REMARK 500 ASN A 103 GLU A 104 6 -146.45 REMARK 500 ARG A 38 LYS A 39 7 144.79 REMARK 500 ARG A 38 LYS A 39 10 148.32 REMARK 500 LYS A 79 MET A 80 10 149.03 REMARK 500 LYS A 79 MET A 80 19 149.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 6 TYR A 67 0.09 SIDE CHAIN REMARK 500 7 ARG A 91 0.11 SIDE CHAIN REMARK 500 8 ARG A 38 0.09 SIDE CHAIN REMARK 500 10 TYR A 67 0.08 SIDE CHAIN REMARK 500 12 TYR A 67 0.09 SIDE CHAIN REMARK 500 18 HIS A 26 0.10 SIDE CHAIN REMARK 500 18 TYR A 46 0.08 SIDE CHAIN REMARK 500 18 TYR A 74 0.07 SIDE CHAIN REMARK 500 19 ARG A 91 0.10 SIDE CHAIN 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 MH0 A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 MH0 A 201 NB 88.4 REMARK 620 3 MH0 A 201 NC 87.7 91.2 REMARK 620 4 MH0 A 201 NA 90.9 92.9 175.6 REMARK 620 5 MH0 A 201 ND 89.4 177.0 86.7 89.1 REMARK 620 6 MET A 80 SD 173.8 89.2 86.7 94.9 92.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MH0 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18828 RELATED DB: BMRB REMARK 900 NMR ASSIGNMENT OF ARABIDOPSIS THALIANA REDUCED CYTOCHROME C REMARK 900 RELATED ID: 26578 RELATED DB: BMRB REMARK 900 NMR ASSIGNMENT OF HOMO SAPIENS OXIDIZED CYTOCHROME C REMARK 900 RELATED ID: 25660 RELATED DB: BMRB DBREF 2N3Y A 1 104 UNP P99999 CYC_HUMAN 2 105 SEQADV 2N3Y 1PA A 48 UNP P99999 TYR 49 ENGINEERED MUTATION SEQRES 1 A 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 A 104 CYS SER GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 A 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 A 104 THR GLY GLN ALA PRO GLY TYR SER 1PA THR ALA ALA ASN SEQRES 5 A 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP THR LEU MET SEQRES 6 A 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 A 104 LYS MET ILE PHE VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 A 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU MODRES 2N3Y 1PA A 48 PHE 4-(CARBOXYMETHYL)-L-PHENYLALANINE HET 1PA A 48 25 HET MH0 A 201 75 HETNAM 1PA 4-(CARBOXYMETHYL)-L-PHENYLALANINE HETNAM MH0 MESOHEME HETSYN 1PA P-(CARBOXYMETHYL)PHENYLALANINE FORMUL 1 1PA C11 H13 N O4 FORMUL 2 MH0 C34 H36 FE N4 O4 HELIX 1 1 ASP A 2 CYS A 14 1 13 HELIX 2 2 ALA A 50 LYS A 55 1 6 HELIX 3 3 THR A 63 ASN A 70 1 8 HELIX 4 4 ASN A 70 ILE A 75 1 6 HELIX 5 5 LYS A 87 THR A 102 1 16 LINK C SER A 47 N 1PA A 48 1555 1555 1.34 LINK C 1PA A 48 N THR A 49 1555 1555 1.34 LINK NE2 HIS A 18 FE MH0 A 201 1555 1555 2.02 LINK SD MET A 80 FE MH0 A 201 1555 1555 2.48 LINK SG CYS A 14 CAB MH0 A 201 1555 1555 1.81 LINK SG CYS A 17 CAC MH0 A 201 1555 1555 1.82 SITE 1 AC1 15 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 15 THR A 28 PRO A 30 THR A 40 SER A 47 SITE 3 AC1 15 1PA A 48 THR A 49 TYR A 67 LYS A 79 SITE 4 AC1 15 MET A 80 ILE A 85 LEU A 94 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