PDB Short entry for 1NYJ HEADER VIRAL PROTEIN 12-FEB-03 1NYJ TITLE THE CLOSED STATE STRUCTURE OF M2 PROTEIN H+ CHANNEL BY SOLID STATE NMR TITLE 2 SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN M2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: TRANSMEMBRANE PEPTIDE (RESIDUE 22-46); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS SYNTHESIZED USING SOLID PHASE PEPTIDE SOURCE 4 SYNTHESIS. THIS SEQUENCE OCCURS NATURALLY IN THE INFLUENZA A VIRUS SOURCE 5 (UDORN/72). KEYWDS INFLUENZA A VIRUS, MEMBRANE PROTEIN STRUCTURE, M2 PROTON CHANNEL, KEYWDS 2 SOLID STATE NMR, VIRAL PROTEIN EXPDTA SOLID-STATE NMR AUTHOR K.NISHIMURA,S.KIM,L.ZHANG,T.A.CROSS REVDAT 3 23-FEB-22 1NYJ 1 REMARK REVDAT 2 24-FEB-09 1NYJ 1 VERSN REVDAT 1 25-MAR-03 1NYJ 0 JRNL AUTH K.NISHIMURA,S.KIM,L.ZHANG,T.A.CROSS JRNL TITL THE CLOSED STATE OF A H+ CHANNEL HELICAL BUNDLE COMBINING JRNL TITL 2 PRECISE ORIENTATIONAL AND DISTANCE RESTRAINTS FROM SOLID JRNL TITL 3 STATE NMR JRNL REF BIOCHEMISTRY V. 41 13170 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12403618 JRNL DOI 10.1021/BI0262799 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.WANG,S.KIM,F.KOVACS,T.A.CROSS REMARK 1 TITL STRUCTURE OF THE TRANSMEMBRANE REGION OF THE M2 PROTEIN H+ REMARK 1 TITL 2 CHANNEL REMARK 1 REF PROTEIN SCI. V. 10 2241 2001 REMARK 1 REFN ISSN 0961-8368 REMARK 1 DOI 10.1110/PS.17901 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TORC V5.4 REMARK 3 AUTHORS : KETCHEM, ROUX, CROSS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE SYMMETRIC, TETRAMERIC BUNDLE MODEL OF M2-TMP WAS CONSTRUCTED REMARK 3 FROM THE MONOMER STRUCTURE (1MP6). THE M2-TMP MONOMER COORDINATES REMARK 3 WERE OBTAINED BY A GEOMETRICAL SEARCH USING A SEARCH ALGORITHIM TO REMARK 3 OBTAIN A MINIMUM OF THE GLOBAL PENALTY FUNCTION THAT INCORPORATES REMARK 3 ALL THE ORIENTATIONAL RESTRAINTS AND THE CHARMM EMPIRICAL REMARK 3 FUNCTION. THE ORIENTATIONAL RESTRAINTS IMPOSED ON THE STRUCTURE REMARK 3 DURING REFINEMENT ARE 15 15N CHEMICAL SHIFTS AND 15 15N-1H DIPOLAR REMARK 3 COUPLINGS FROM PISEMA EXPERIMENTS. THE REFINEMENT WAS CARRIED OUT REMARK 3 IN VACUO WITH THE INITIAL COORDINATES OF AN IDEAL A-HELIX REMARK 3 STRUCTURE (3.6 RESIDUES PER TURN) HAVING A RANGE OF TILT AND REMARK 3 ROTATIONAL ORIENTATIONS WITH RESPECT TO THE BILAYER SPANNING THE REMARK 3 VALUES OBTAINED FROM THE PISA WHEELS. REMARK 3 REMARK 3 THE RESULTING TETRAMERIC BUNDLE MODEL WAS USED TO SEARCH THE SIDE REMARK 3 CHAIN ORIENTATIONS IN ACCORD WITH THE EXPERIMENTALLY MEASURED REMARK 3 DISTANCE BETWEEN 15ND1 HIS37 AND 13CG TRP41. BOTH CHI 1 AND CHI 2 REMARK 3 ANGLES OF THE RESIDUES WERE SEARCHED EXTENSIVELY USING 10 REMARK 3 INCREMENTS TO DISCERN WHETHER THE INTERACTION WAS INTRAMOLECULAR REMARK 3 OR INTERMOLECULAR AND TO FIND OUT WHICH RESIDUES ACCOUNTED FOR THE REMARK 3 OBSERVED SPIN INTERACTION BEFORE CHARACTERIZING THE ROTAMERIC REMARK 3 STATES OF THE SIDECHAINS. NOTE THAT WHILE THE HIS37 AND TRP41 REMARK 3 SIDECHAIN ROTAMERIC STATES ARE DEFINED BY THE DISTANCE RESTRAINT, REMARK 3 THE ROTAMERIC STATES OF OTHER RESIDUES ARE TAKEN FROM THE BACKBONE REMARK 3 DEPENDENT SIDECHAIN ROTAMER LIBRARY. REMARK 4 REMARK 4 1NYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018352. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NONE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : TO PREPARE AN UNORIENTED REMARK 210 HYDRATED LIPID BILAYER SAMPLE, REMARK 210 M2-TMP AND REMARK 210 DIMYRISTOYLPHOSPHATIDYLCHOLINE (D REMARK 210 MPC) IN A 1:16 MOLAR RATIO WERE REMARK 210 CO-SOLUBILIZED IN REMARK 210 TRIFLUOROETHANOL (TFE). AFTER REMARK 210 LYOPHILIZATION, THE WHITE POWDER REMARK 210 WAS HYDRATED BY ADDING 50% (BY REMARK 210 TOTAL SAMPLE DRY WEIGHT) PH 7.0, REMARK 210 HPLC GRADE WATER FOLLOWED BY REMARK 210 INCUBATION FOR 2 DAYS AT 42 OC. REMARK 210 THE SAMPLE WAS THEN DISPERSED IN REMARK 210 30 ML OF 20 MM CITRIC/NA2HPO4 REMARK 210 BUFFER AT PH 7.0 AND INCUBATED REMARK 210 AT 45 OC FOR 2 HOURS BEFORE REMARK 210 CENTRIFUGING AT 20000 X G FOR 3 REMARK 210 HOURS. AFTER EXCESS WATER WAS REMARK 210 REMOVED, THE PELLET WAS REMARK 210 TRANSFERRED TO AN EPPENDORF TUBE, REMARK 210 TIGHTLY SEALED TO MAINTAIN THE REMARK 210 SAME HYDRATION LEVEL, AND THEN REMARK 210 INCUBATED AT 45 OC FOR 2 DAYS. REMARK 210 THEN, THE SAMPLE WAS TRANSFERRED REMARK 210 TO A GLASS INSERT FOR A BRUKER 7 REMARK 210 MM SPINNER AND SEALED WITH EPOXY. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SOLID STATE NMR PISEMA AND REDOR REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 300 MHZ REMARK 210 SPECTROMETER MODEL : CHEMAGNETICS; DMX-300 REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE TETRAMERIC OLIGOMER REMARK 210 CONFORMATION OF M2-TMP WAS REMARK 210 CONSTRUCTED USING THE MONOMER REMARK 210 STRUCTURE REFINED BY SOLID-STATE REMARK 210 NMR ORIENTATIONAL DATA. THE REMARK 210 MONOMER STRUCTURE WAS THE LOWEST REMARK 210 ENERGY CONFORMER FROM 30 REMARK 210 SIMULATED ANNEALING ATTEMPTS. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE HETERONUCLEAR DISTANCE WAS OBTAINED BY MEANS OF SOLID REMARK 210 STATE NMR REDOR EXPERIMENTS. 13C-REDOR WAS PERFORMED ON A DMX- REMARK 210 300 WITH AN XY8-PULSE SEQUENCE FOR IRRADIATION OF 15N NUCLEI TO REMARK 210 COMPENSATE FOR ERRORS IN THE FLIP ANGLE, OFF RESONANCE EFFECT, REMARK 210 AND VARIATION IN THE H1 FIELD. THE SPINNING SPEED WAS CONTROLLED REMARK 210 AT 4000 1 HZ AND THE EXPERIMENTS WERE PERFORMED AT 38 C. REDOR REMARK 210 AND FULL ECHO SPECTRA WERE RECORDED AT VARIOUS DIPOLAR EVOLUTION REMARK 210 TIMES, NCTR, (WHERE NC AND TR ARE THE ROTOR CYCLE NUMBER AND REMARK 210 ROTOR PERIOD, RESPECTIVELY) FROM 2 TO 16 MS TO OBSERVE REMARK 210 REASONABLE DIPOLAR DEPHASING OF THE SIGNALS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 CD1 TRP C 20 NE2 HIS D 16 1.58 REMARK 500 CD1 TRP B 20 NE2 HIS C 16 1.66 REMARK 500 CD1 TRP A 20 NE2 HIS B 16 1.67 REMARK 500 NE2 HIS A 16 CD1 TRP D 20 1.67 REMARK 500 CD1 LEU B 17 CB HIS C 16 1.73 REMARK 500 CD1 LEU C 17 CB HIS D 16 1.76 REMARK 500 CD2 LEU C 17 CA GLY D 13 1.77 REMARK 500 CB HIS A 16 CD1 LEU D 17 1.78 REMARK 500 CD1 LEU A 17 CB HIS B 16 1.80 REMARK 500 CD1 ILE B 14 O ALA C 9 1.84 REMARK 500 CD2 LEU B 17 CA GLY C 13 1.84 REMARK 500 CA GLY A 13 CD2 LEU D 17 1.86 REMARK 500 CD2 LEU A 17 CA GLY B 13 1.87 REMARK 500 O ALA A 9 CD1 ILE D 14 1.87 REMARK 500 CD1 ILE C 14 O ALA D 9 1.92 REMARK 500 CD1 ILE A 14 O ALA B 9 1.93 REMARK 500 CD2 LEU B 17 N GLY C 13 1.95 REMARK 500 N GLY A 13 CD2 LEU D 17 1.97 REMARK 500 CD2 LEU C 17 N GLY D 13 1.99 REMARK 500 CD2 LEU A 17 N GLY B 13 1.99 REMARK 500 CD1 LEU C 17 ND1 HIS D 16 2.04 REMARK 500 CD1 ILE B 14 C ALA C 9 2.06 REMARK 500 CD1 LEU A 17 ND1 HIS B 16 2.08 REMARK 500 C ALA A 9 CD1 ILE D 14 2.08 REMARK 500 ND1 HIS A 16 CD1 LEU D 17 2.09 REMARK 500 CD1 LEU B 17 ND1 HIS C 16 2.10 REMARK 500 CD1 ILE A 14 C ALA B 9 2.14 REMARK 500 CD1 ILE C 14 C ALA D 9 2.16 REMARK 500 CD1 LEU C 17 CG HIS D 16 2.19 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 ASP A 3 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 23 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 23 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 3 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP B 23 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP B 23 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG B 24 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP C 3 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP C 23 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP C 23 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG C 24 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP D 3 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP D 23 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP D 23 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG D 24 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MP6 RELATED DB: PDB DBREF 1NYJ A 1 25 UNP P35938 VMT2_IAUSS 22 46 DBREF 1NYJ B 1 25 UNP P35938 VMT2_IAUSS 22 46 DBREF 1NYJ C 1 25 UNP P35938 VMT2_IAUSS 22 46 DBREF 1NYJ D 1 25 UNP P35938 VMT2_IAUSS 22 46 SEQRES 1 A 25 SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE GLY SEQRES 2 A 25 ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 1 B 25 SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE GLY SEQRES 2 B 25 ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 1 C 25 SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE GLY SEQRES 2 C 25 ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU SEQRES 1 D 25 SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE GLY SEQRES 2 D 25 ILE LEU HIS LEU ILE LEU TRP ILE LEU ASP ARG LEU HELIX 1 1 SER A 1 LEU A 25 1 25 HELIX 2 2 SER B 1 LEU B 25 1 25 HELIX 3 3 SER C 1 LEU C 25 1 25 HELIX 4 4 SER D 1 LEU D 25 1 25 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