HEADER METAL BINDING PROTEIN 05-MAY-16 5JR0 TITLE DOMAIN 4 SEGMENT 6 OF VOLTAGE-GATED SODIUM CHANNEL NAV1.4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM CHANNEL PROTEIN TYPE 4 SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1567-1594; COMPND 5 SYNONYM: MU-1,SKM1,SODIUM CHANNEL PROTEIN SKELETAL MUSCLE SUBUNIT COMPND 6 ALPHA,SODIUM CHANNEL PROTEIN TYPE IV SUBUNIT ALPHA,VOLTAGE-GATED COMPND 7 SODIUM CHANNEL SUBUNIT ALPHA NAV1.4; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 4 ORGANISM_COMMON: RAT; SOURCE 5 ORGANISM_TAXID: 10116 KEYWDS TRANSMEMBRANE, ALPHA-HELIX, PROTEIN FRAGMENT, METAL BINDING PROTEIN EXPDTA SOLID-STATE NMR NUMMDL 10 AUTHOR A.NIITSU,A.EGAWA,K.IKEDA,K.TACHIBANA,T.FUJIWARA REVDAT 1 17-MAY-17 5JR0 0 JRNL AUTH A.NIITSU,A.EGAWA,K.IKEDA,K.TACHIBANA,T.FUJIWARA JRNL TITL VERATRIDINE BINDING TO A TRANSMEMBRANE SEGMENT OF MAMMALIAN JRNL TITL 2 SODIUM CHANNEL NAV1.4 DETERMINED BY SOLID-STATE NMR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM REMARK 3 AUTHORS : M. KARPLUS ET AL, HARVARD UNIVERSITY REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000219482. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 213 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 16 % U-13C I23, L17, V20 REMARK 210 PEPTIDE, 69 % D-54 DMPC, WATER; REMARK 210 16 % U-13C G, I, F, L, V, A REMARK 210 PEPTIDE, 69 % D-54 DMPC, WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-13C DIPOLAR-ASSISTED REMARK 210 ROTATIONAL RESONANCE; 13C REMARK 210 OBSERVATION OF 2H-SELECTIVE 1H- REMARK 210 DEPOLARIZATION REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : INFINITY PLUS 700 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, DELTA, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 23 CG TYR A 23 CD1 0.090 REMARK 500 5 TYR A 23 CE1 TYR A 23 CZ 0.091 REMARK 500 5 PHE A 31 CG PHE A 31 CD2 0.115 REMARK 500 6 LYS A 3 CA LYS A 3 CB 0.139 REMARK 500 8 TYR A 23 CG TYR A 23 CD1 0.078 REMARK 500 9 TYR A 11 CZ TYR A 11 OH 0.135 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 PHE A 8 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 PHE A 8 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 PHE A 16 CB - CG - CD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 PHE A 16 CB - CG - CD1 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 MET A 22 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 1 TYR A 23 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 PHE A 31 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 PHE A 16 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 PHE A 16 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 TYR A 23 CG - CD1 - CE1 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 TYR A 23 CD1 - CE1 - CZ ANGL. DEV. = 6.0 DEGREES REMARK 500 2 PHE A 31 CB - CG - CD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 3 PHE A 7 CB - CG - CD2 ANGL. DEV. = -7.9 DEGREES REMARK 500 3 LEU A 28 CB - CG - CD2 ANGL. DEV. = -10.7 DEGREES REMARK 500 4 PHE A 8 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 4 TYR A 11 CB - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 4 TYR A 11 CB - CG - CD1 ANGL. DEV. = -5.3 DEGREES REMARK 500 4 TYR A 23 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 PHE A 31 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 PHE A 16 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 5 TYR A 23 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ALA A 25 N - CA - CB ANGL. DEV. = 10.4 DEGREES REMARK 500 6 TYR A 11 CB - CG - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 6 TYR A 11 CB - CG - CD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 6 TYR A 23 CB - CG - CD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 6 TYR A 23 CG - CD2 - CE2 ANGL. DEV. = -6.1 DEGREES REMARK 500 7 TYR A 11 CG - CD1 - CE1 ANGL. DEV. = -5.8 DEGREES REMARK 500 7 PHE A 16 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 7 PHE A 16 CB - CG - CD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 8 PHE A 7 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 TYR A 11 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 8 PHE A 16 CB - CG - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 8 PHE A 16 CG - CD2 - CE2 ANGL. DEV. = -6.6 DEGREES REMARK 500 8 TYR A 23 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 9 TYR A 11 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 MET A 22 CG - SD - CE ANGL. DEV. = -10.8 DEGREES REMARK 500 9 ILE A 26 CA - CB - CG2 ANGL. DEV. = 12.4 DEGREES REMARK 500 9 PHE A 31 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 10 PHE A 16 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 10 PHE A 16 CB - CG - CD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 10 PHE A 31 CB - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 10 PHE A 31 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES 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 2 TYR A 11 0.09 SIDE CHAIN REMARK 500 2 TYR A 23 0.07 SIDE CHAIN REMARK 500 3 TYR A 23 0.09 SIDE CHAIN REMARK 500 8 PHE A 8 0.10 SIDE CHAIN REMARK 500 8 TYR A 11 0.10 SIDE CHAIN REMARK 500 9 PHE A 16 0.09 SIDE CHAIN REMARK 500 10 TYR A 23 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30076 RELATED DB: BMRB DBREF 5JR0 A 4 31 UNP P15390 SCN4A_RAT 1567 1594 SEQADV 5JR0 LYS A 1 UNP P15390 EXPRESSION TAG SEQADV 5JR0 LYS A 2 UNP P15390 EXPRESSION TAG SEQADV 5JR0 LYS A 3 UNP P15390 EXPRESSION TAG SEQADV 5JR0 LYS A 32 UNP P15390 EXPRESSION TAG SEQADV 5JR0 LYS A 33 UNP P15390 EXPRESSION TAG SEQADV 5JR0 LYS A 34 UNP P15390 EXPRESSION TAG SEQADV 5JR0 NH2 A 35 UNP P15390 AMIDATION SEQRES 1 A 35 LYS LYS LYS GLY ILE CYS PHE PHE CYS SER TYR ILE ILE SEQRES 2 A 35 ILE SER PHE LEU ILE VAL VAL ASN MET TYR ILE ALA ILE SEQRES 3 A 35 ILE LEU GLU ASN PHE LYS LYS LYS NH2 HET NH2 A 35 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 AA1 ILE A 5 LYS A 34 1 30 LINK C LYS A 34 N NH2 A 35 1555 1555 1.35 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