HEADER MEMBRANE PROTEIN 17-NOV-98 1P23 TITLE STRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION, NMR, TITLE 2 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEIN TMP21 PRECURSOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN; COMPND 5 SYNONYM: INTEGRAL MEMBRANE PROTEIN P23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS TRANSPORT, PROTEIN TRANSPORT, TRANSMEMBRANE, GLYCOPROTEIN, VESICULAR KEYWDS 2 TRANSPORT, COP, COATOMER, GOLGI STACK, SOLUTION STRUCTURE, P24 KEYWDS 3 FAMILY, INTEGRAL MEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.WEIDLER,C.REINHARD,F.T.WIELAND,P.ROESCH REVDAT 4 23-FEB-22 1P23 1 REMARK REVDAT 3 24-FEB-09 1P23 1 VERSN REVDAT 2 01-APR-03 1P23 1 JRNL REVDAT 1 07-JUN-00 1P23 0 JRNL AUTH M.WEIDLER,C.REINHARD,G.FRIEDRICH,F.T.WIELAND,P.ROSCH JRNL TITL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF P23 IN SOLUTION: JRNL TITL 2 IMPLICATIONS FOR THE FORMATION OF COPI VESICLES. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 271 401 2000 JRNL REFN ISSN 0006-291X JRNL PMID 10799309 JRNL DOI 10.1006/BBRC.2000.2511 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRATEGY USED FOR NMR STRUCTURE REMARK 3 CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE REMARK 3 CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS -PEAKS REMARK 3 WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. REMARK 3 SUBSEQUENTLY, THE PROTON-PROTON DISTANCES IN THE CALCULATED REMARK 3 STRUCTURES WERE DETERMINED USING THE PROGRAM 'BACKCALC_DB 2.0' REMARK 3 (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH REMARK 3 THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY REMARK 3 DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE REMARK 3 DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE REMARK 3 CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN REMARK 3 FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED REMARK 3 SEVERAL TIMES, LEADING TO A TOTAL OF 223 INTRARESIDUAL AND 249 REMARK 3 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURE CALCULATIONS REMARK 3 STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB REMARK 3 INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X- REMARK 3 PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING REMARK 3 ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR REMARK 3 NON- BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE REMARK 3 EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN REMARK 3 IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE REMARK 3 PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO REMARK 3 AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE REMARK 3 STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 REMARK 3 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE REMARK 3 CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL REMARK 3 ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION. REMARK 4 REMARK 4 1P23 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175553. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280.00 REMARK 210 PH : 3.60 REMARK 210 IONIC STRENGTH : 650 MM REMARK 210 PRESSURE : 10E+5 PA ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; CLEAN-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX 600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NDEE 2.0, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, AGREEMENT WITH REMARK 210 EXPERIMENTAL DATA 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: 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 O LEU A 3 H PHE A 7 1.43 REMARK 500 O LEU B 3 H PHE B 7 1.50 REMARK 500 O LYS C 10 H ILE C 13 1.51 REMARK 500 O LYS B 10 H ILE B 13 1.53 REMARK 500 O LEU D 3 H PHE D 7 1.55 REMARK 500 O LYS A 10 H ILE A 13 1.56 REMARK 500 O LYS D 10 H ILE D 13 1.58 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 ARG A 4 -38.88 -39.85 REMARK 500 1 ILE A 13 46.74 -144.49 REMARK 500 1 ILE B 13 49.20 -150.98 REMARK 500 1 TYR C 2 -36.15 -172.26 REMARK 500 1 ILE C 13 46.04 -143.60 REMARK 500 1 TYR D 2 -35.41 -173.49 REMARK 500 1 ILE D 13 47.30 -148.95 REMARK 500 2 TYR A 2 -33.11 177.47 REMARK 500 2 ILE A 13 47.54 -147.29 REMARK 500 2 TYR C 2 -154.00 -163.44 REMARK 500 2 LEU C 3 -69.57 63.86 REMARK 500 2 ILE C 13 43.65 -142.23 REMARK 500 2 ILE D 13 46.79 -146.21 REMARK 500 3 ILE A 13 41.57 -142.97 REMARK 500 3 TYR B 2 -34.24 -172.38 REMARK 500 3 ILE B 13 46.92 -146.13 REMARK 500 3 ILE C 13 45.81 -147.94 REMARK 500 3 LEU D 3 -64.64 62.30 REMARK 500 3 ILE D 13 46.58 -148.89 REMARK 500 4 TYR A 2 -32.69 -178.31 REMARK 500 4 ILE A 13 43.88 -144.08 REMARK 500 4 TYR B 2 -14.69 82.76 REMARK 500 4 TYR C 2 -152.52 -159.64 REMARK 500 4 LEU C 3 -77.85 58.37 REMARK 500 4 TYR D 2 -34.27 176.57 REMARK 500 4 ILE D 13 47.06 -149.28 REMARK 500 5 ILE A 13 46.41 -147.38 REMARK 500 5 TYR B 2 -30.34 179.95 REMARK 500 5 ILE B 13 47.80 -161.79 REMARK 500 5 TYR C 2 -151.17 -149.88 REMARK 500 5 LEU C 3 -73.96 60.21 REMARK 500 5 ILE C 13 47.46 -145.60 REMARK 500 5 LYS D 11 -33.28 -38.99 REMARK 500 5 ILE D 13 -32.93 -146.59 REMARK 500 6 TYR A 2 -43.33 174.67 REMARK 500 6 ILE A 13 48.35 -146.42 REMARK 500 6 ILE B 13 46.60 -146.10 REMARK 500 6 TYR C 2 -31.92 -172.32 REMARK 500 6 PHE C 6 -62.97 -92.29 REMARK 500 6 ILE C 13 44.80 -144.54 REMARK 500 6 TYR D 2 -39.72 177.36 REMARK 500 6 ILE D 13 49.90 -150.23 REMARK 500 7 TYR A 2 -99.71 -163.50 REMARK 500 7 ILE A 13 44.00 -142.54 REMARK 500 7 ILE B 13 45.25 -151.02 REMARK 500 7 TYR C 2 -30.55 176.12 REMARK 500 7 ILE C 13 46.98 -146.64 REMARK 500 7 TYR D 2 -32.14 175.88 REMARK 500 7 ILE D 13 44.21 -143.81 REMARK 500 8 ILE A 13 45.20 -140.14 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. 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 1 ARG A 4 0.26 SIDE CHAIN REMARK 500 1 ARG A 5 0.21 SIDE CHAIN REMARK 500 1 ARG B 4 0.23 SIDE CHAIN REMARK 500 1 ARG B 5 0.26 SIDE CHAIN REMARK 500 1 ARG C 4 0.31 SIDE CHAIN REMARK 500 1 ARG D 4 0.23 SIDE CHAIN REMARK 500 1 ARG D 5 0.20 SIDE CHAIN REMARK 500 2 ARG A 4 0.27 SIDE CHAIN REMARK 500 2 ARG A 5 0.23 SIDE CHAIN REMARK 500 2 ARG B 4 0.17 SIDE CHAIN REMARK 500 2 ARG B 5 0.23 SIDE CHAIN REMARK 500 2 ARG C 4 0.24 SIDE CHAIN REMARK 500 2 ARG C 5 0.32 SIDE CHAIN REMARK 500 2 ARG D 4 0.21 SIDE CHAIN REMARK 500 2 ARG D 5 0.31 SIDE CHAIN REMARK 500 3 ARG B 4 0.32 SIDE CHAIN REMARK 500 3 ARG B 5 0.19 SIDE CHAIN REMARK 500 3 ARG C 4 0.12 SIDE CHAIN REMARK 500 3 ARG C 5 0.20 SIDE CHAIN REMARK 500 3 ARG D 4 0.32 SIDE CHAIN REMARK 500 3 ARG D 5 0.27 SIDE CHAIN REMARK 500 4 ARG A 5 0.31 SIDE CHAIN REMARK 500 4 ARG B 4 0.32 SIDE CHAIN REMARK 500 4 ARG B 5 0.23 SIDE CHAIN REMARK 500 4 ARG C 4 0.30 SIDE CHAIN REMARK 500 4 ARG D 4 0.19 SIDE CHAIN REMARK 500 4 ARG D 5 0.32 SIDE CHAIN REMARK 500 5 ARG A 4 0.32 SIDE CHAIN REMARK 500 5 ARG A 5 0.13 SIDE CHAIN REMARK 500 5 ARG B 4 0.22 SIDE CHAIN REMARK 500 5 ARG B 5 0.26 SIDE CHAIN REMARK 500 5 ARG C 4 0.31 SIDE CHAIN REMARK 500 5 ARG C 5 0.31 SIDE CHAIN REMARK 500 5 ARG D 4 0.12 SIDE CHAIN REMARK 500 5 ARG D 5 0.20 SIDE CHAIN REMARK 500 6 ARG A 4 0.26 SIDE CHAIN REMARK 500 6 ARG A 5 0.32 SIDE CHAIN REMARK 500 6 ARG B 4 0.18 SIDE CHAIN REMARK 500 6 ARG B 5 0.28 SIDE CHAIN REMARK 500 6 ARG C 4 0.09 SIDE CHAIN REMARK 500 6 ARG C 5 0.25 SIDE CHAIN REMARK 500 6 ARG D 4 0.23 SIDE CHAIN REMARK 500 6 ARG D 5 0.18 SIDE CHAIN REMARK 500 7 ARG A 4 0.24 SIDE CHAIN REMARK 500 7 ARG A 5 0.24 SIDE CHAIN REMARK 500 7 ARG B 4 0.31 SIDE CHAIN REMARK 500 7 ARG B 5 0.30 SIDE CHAIN REMARK 500 7 ARG C 4 0.09 SIDE CHAIN REMARK 500 7 ARG C 5 0.26 SIDE CHAIN REMARK 500 7 ARG D 4 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 72 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1P23 A 2 14 UNP Q28735 TMP21_RABIT 207 219 DBREF 1P23 B 2 14 UNP Q28735 TMP21_RABIT 207 219 DBREF 1P23 C 2 14 UNP Q28735 TMP21_RABIT 207 219 DBREF 1P23 D 2 14 UNP Q28735 TMP21_RABIT 207 219 SEQRES 1 A 14 CYS TYR LEU ARG ARG PHE PHE LYS ALA LYS LYS LEU ILE SEQRES 2 A 14 GLU SEQRES 1 B 14 CYS TYR LEU ARG ARG PHE PHE LYS ALA LYS LYS LEU ILE SEQRES 2 B 14 GLU SEQRES 1 C 14 CYS TYR LEU ARG ARG PHE PHE LYS ALA LYS LYS LEU ILE SEQRES 2 C 14 GLU SEQRES 1 D 14 CYS TYR LEU ARG ARG PHE PHE LYS ALA LYS LYS LEU ILE SEQRES 2 D 14 GLU HELIX 1 1 LEU A 3 LYS A 10 1 8 HELIX 2 2 LEU B 3 LYS B 10 1 8 HELIX 3 3 LEU C 3 LYS C 11 1 9 HELIX 4 4 LEU D 3 LYS D 10 1 8 SSBOND 1 CYS A 1 CYS B 1 1555 1555 2.02 SSBOND 2 CYS C 1 CYS D 1 1555 1555 2.02 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