10 20 30 40 50 60 70 80 1NYJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 12-FEB-03 1NYJ
TITLE THE CLOSED STATE STRUCTURE OF M2 PROTEIN H+ CHANNEL BY TITLE 2 SOLID STATE NMR 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 SOURCE 4 PHASE PEPTIDE SYNTHESIS. THIS SEQUENCE OCCURS NATURALLY IN SOURCE 5 THE INFLUENZA A VIRUS (UDORN/72).
KEYWDS INFLUENZA A VIRUS, MEMBRANE PROTEIN STRUCTURE, M2 PROTON KEYWDS 2 CHANNEL, SOLID STATE NMR, VIRAL PROTEIN
EXPDTA SOLID-STATE NMR
AUTHOR K.NISHIMURA,S.KIM,L.ZHANG,T.A.CROSS
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 JRNL TITL 2 COMBINING PRECISE ORIENTATIONAL AND DISTANCE JRNL TITL 3 RESTRAINTS FROM SOLID 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 REMARK 1 TITL 2 PROTEIN H+ 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: THE SYMMETRIC, TETRAMERIC BUNDLE REMARK 3 MODEL OF M2-TMP WAS CONSTRUCTED FROM THE MONOMER STRUCTURE REMARK 3 (1MP6). THE M2-TMP MONOMER COORDINATES WERE OBTAINED BY A REMARK 3 GEOMETRICAL SEARCH USING A SEARCH ALGORITHIM TO OBTAIN A REMARK 3 MINIMUM OF THE GLOBAL PENALTY FUNCTION THAT INCORPORATES ALL REMARK 3 THE ORIENTATIONAL RESTRAINTS AND THE CHARMM EMPIRICAL REMARK 3 FUNCTION. THE ORIENTATIONAL RESTRAINTS IMPOSED ON THE REMARK 3 STRUCTURE DURING REFINEMENT ARE 15 15N CHEMICAL SHIFTS AND 15 REMARK 3 15N-1H DIPOLAR COUPLINGS FROM PISEMA EXPERIMENTS. THE REMARK 3 REFINEMENT WAS CARRIED OUT IN VACUO WITH THE INITIAL REMARK 3 COORDINATES OF AN IDEAL A-HELIX STRUCTURE (3.6 RESIDUES PER REMARK 3 TURN) HAVING A RANGE OF TILT AND ROTATIONAL ORIENTATIONS WITH REMARK 3 RESPECT TO THE BILAYER SPANNING THE VALUES OBTAINED FROM THE REMARK 3 PISA WHEELS. THE RESULTING TETRAMERIC BUNDLE MODEL WAS USED TO REMARK 3 SEARCH THE SIDE CHAIN ORIENTATIONS IN ACCORD WITH THE REMARK 3 EXPERIMENTALLY MEASURED DISTANCE BETWEEN 15ND1 HIS37 AND 13CG REMARK 3 TRP41. BOTH CHI 1 AND CHI 2 ANGLES OF THE RESIDUES WERE REMARK 3 SEARCHED EXTENSIVELY USING 10 INCREMENTS TO DISCERN WHETHER REMARK 3 THE INTERACTION WAS INTRAMOLECULAR OR INTERMOLECULAR AND TO REMARK 3 FIND OUT WHICH RESIDUES ACCOUNTED FOR THE OBSERVED SPIN REMARK 3 INTERACTION BEFORE CHARACTERIZING THE ROTAMERIC STATES OF THE REMARK 3 SIDECHAINS. NOTE THAT WHILE THE HIS37 AND TRP41 SIDECHAIN REMARK 3 ROTAMERIC STATES ARE DEFINED BY THE DISTANCE RESTRAINT, THE REMARK 3 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-03. REMARK 100 THE RCSB ID CODE IS RCSB018352.
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 REMARK 210 (DMPC) IN A 1:16 MOLAR RATIO REMARK 210 WERE CO-SOLUBILIZED IN REMARK 210 TRIFLUOROETHANOL (TFE). AFTER REMARK 210 LYOPHILIZATION, THE WHITE REMARK 210 POWDER WAS HYDRATED BY ADDING REMARK 210 50% (BY TOTAL SAMPLE DRY REMARK 210 WEIGHT) PH 7.0, HPLC GRADE REMARK 210 WATER FOLLOWED BY INCUBATION REMARK 210 FOR 2 DAYS AT 42 OC. THE REMARK 210 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 REMARK 210 3 HOURS. AFTER EXCESS WATER REMARK 210 WAS REMOVED, THE PELLET WAS REMARK 210 TRANSFERRED TO AN EPPENDORF REMARK 210 TUBE, TIGHTLY SEALED TO REMARK 210 MAINTAIN THE SAME HYDRATION REMARK 210 LEVEL, AND THEN INCUBATED AT REMARK 210 45 OC FOR 2 DAYS. THEN, THE REMARK 210 SAMPLE WAS TRANSFERRED TO A REMARK 210 GLASS INSERT FOR A BRUKER 7 MM REMARK 210 SPINNER AND SEALED WITH EPOXY. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SOLID STATE NMR PISEMA AND REMARK 210 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- REMARK 210 STATE NMR ORIENTATIONAL DATA. REMARK 210 THE MONOMER STRUCTURE WAS THE REMARK 210 LOWEST ENERGY CONFORMER FROM REMARK 210 30 SIMULATED ANNEALING REMARK 210 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 REMARK 210 SOLID STATE NMR REDOR EXPERIMENTS. 13C-REDOR WAS PERFORMED ON REMARK 210 A DMX-300 WITH AN XY8-PULSE SEQUENCE FOR IRRADIATION OF 15N REMARK 210 NUCLEI TO COMPENSATE FOR ERRORS IN THE FLIP ANGLE, OFF REMARK 210 RESONANCE EFFECT, AND VARIATION IN THE H1 FIELD. THE SPINNING REMARK 210 SPEED WAS CONTROLLED AT 4000 1 HZ AND THE EXPERIMENTS WERE REMARK 210 PERFORMED AT 38 C. REDOR AND FULL ECHO SPECTRA WERE RECORDED REMARK 210 AT VARIOUS DIPOLAR EVOLUTION TIMES, NCTR, (WHERE NC AND TR ARE REMARK 210 THE ROTOR CYCLE NUMBER AND ROTOR PERIOD, RESPECTIVELY) FROM 2 REMARK 210 TO 16 MS TO OBSERVE REASONABLE DIPOLAR DEPHASING OF THE REMARK 210 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 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