Header list of 1nyj.pdb file
Complete list - 23 202 Bytes
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
Complete list - 23 202 Bytes