HEADER PROTEIN TRANSPORT 23-JUN-06 2HF6 TITLE SOLUTION STRUCTURE OF HUMAN ZETA-COP COMPND MOL_ID: 1; COMPND 2 MOLECULE: COATOMER SUBUNIT ZETA-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-149; COMPND 5 SYNONYM: ZETA-1 COAT PROTEIN, ZETA-1 COP, ZETA-COP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: COPZ1, COPZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS COP I, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.YU,C.JIN,B.XIA REVDAT 4 01-MAY-24 2HF6 1 REMARK REVDAT 3 30-NOV-11 2HF6 1 JRNL VERSN REVDAT 2 24-FEB-09 2HF6 1 VERSN REVDAT 1 12-JUN-07 2HF6 0 JRNL AUTH W.YU,J.LIN,C.JIN,B.XIA JRNL TITL SOLUTION STRUCTURE OF HUMAN ZETA-COP: DIRECT EVIDENCES FOR JRNL TITL 2 STRUCTURAL SIMILARITY BETWEEN COP I AND CLATHRIN-ADAPTOR JRNL TITL 3 COATS JRNL REF J.MOL.BIOL. V. 386 903 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19167404 JRNL DOI 10.1016/J.JMB.2008.12.083 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE CYANA 2.0, AMBER 7.0 REMARK 3 AUTHORS : F. DELAGLIO, S. GRZESIEK, G. W. VUISTER, G. ZHU, REMARK 3 J. PFEIFER AND A. BAX (NMRPIPE), DAVID A. CASE, REMARK 3 ET. AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TORSION ANGLE DYNAMICS PERFORMED BY REMARK 3 DYANA; SIMULATED ANNEALING PERFORMED BY AMBER REMARK 4 REMARK 4 2HF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038278. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM ZETA-COP, 20MM POTASSIUM REMARK 210 PHOSPHATE (PH 7.0), 50MM NACL, REMARK 210 1MM EDTA , 20MM DTT, 10MM PMSF, REMARK 210 0.01% SODIUM AZIDE, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB,CBCA(CO)NH; REMARK 210 HNCO,HN(CA)CO; HC(C)H COSY; HC(C) REMARK 210 H TOCSY; 3D_13C-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0, DIANA CYANA2.0, REMARK 210 XWINNMR 3.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 OD1 ASP A 32 HG1 THR A 34 1.57 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 5 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 15 ARG A 149 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 18 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 19 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 19 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 25 94.49 -67.58 REMARK 500 1 GLU A 58 -37.49 152.02 REMARK 500 1 ILE A 73 -69.27 57.59 REMARK 500 1 ASP A 74 19.84 -146.09 REMARK 500 1 GLU A 85 -12.87 -148.62 REMARK 500 2 LEU A 4 -31.53 -141.29 REMARK 500 2 ASN A 21 21.18 -69.18 REMARK 500 2 SER A 57 -177.62 67.69 REMARK 500 2 GLU A 58 -46.01 57.91 REMARK 500 2 ILE A 73 -87.65 49.53 REMARK 500 2 ASP A 74 26.00 -145.26 REMARK 500 2 TYR A 84 -167.11 50.23 REMARK 500 2 VAL A 109 45.13 -78.01 REMARK 500 2 SER A 137 17.26 -140.44 REMARK 500 3 ALA A 3 -92.40 40.59 REMARK 500 3 TYR A 11 123.87 74.94 REMARK 500 3 SER A 57 179.79 68.64 REMARK 500 3 GLU A 58 -50.95 56.94 REMARK 500 3 ILE A 73 -85.02 53.79 REMARK 500 3 ASP A 74 29.57 -146.60 REMARK 500 3 SER A 83 33.45 -77.01 REMARK 500 3 GLU A 85 26.62 -72.43 REMARK 500 4 GLU A 7 63.72 28.54 REMARK 500 4 ARG A 25 107.23 -59.66 REMARK 500 4 SER A 57 -174.52 141.89 REMARK 500 4 GLU A 58 -47.57 61.08 REMARK 500 4 ILE A 73 -84.27 65.00 REMARK 500 4 ASP A 74 21.07 -150.82 REMARK 500 4 TYR A 84 -143.59 48.98 REMARK 500 4 SER A 137 31.06 -143.93 REMARK 500 5 ALA A 3 -1.49 -141.82 REMARK 500 5 SER A 57 178.92 69.05 REMARK 500 5 GLU A 58 -46.56 55.96 REMARK 500 5 ILE A 73 -84.29 53.03 REMARK 500 5 ASP A 74 30.76 -149.85 REMARK 500 5 GLU A 85 -23.30 -147.33 REMARK 500 5 VAL A 109 38.95 -79.99 REMARK 500 5 SER A 137 38.69 -148.19 REMARK 500 6 SER A 57 143.51 77.77 REMARK 500 6 GLU A 58 -38.00 127.29 REMARK 500 6 GLU A 63 19.42 -66.89 REMARK 500 6 ILE A 73 -78.84 62.74 REMARK 500 6 ASP A 74 34.59 -156.90 REMARK 500 6 SER A 83 38.50 -74.46 REMARK 500 6 VAL A 109 46.73 -77.95 REMARK 500 6 SER A 137 -5.98 -143.60 REMARK 500 7 GLU A 58 -40.35 144.73 REMARK 500 7 GLU A 63 -2.25 61.34 REMARK 500 7 ILE A 73 -76.35 62.58 REMARK 500 7 ASP A 74 21.84 -143.39 REMARK 500 REMARK 500 THIS ENTRY HAS 174 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 9 ARG A 25 0.08 SIDE CHAIN REMARK 500 11 ARG A 25 0.10 SIDE CHAIN REMARK 500 12 ARG A 25 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2HF6 A 1 149 UNP P61923 COPZ1_HUMAN 1 149 SEQRES 1 A 149 MET GLU ALA LEU ILE LEU GLU PRO SER LEU TYR THR VAL SEQRES 2 A 149 LYS ALA ILE LEU ILE LEU ASP ASN ASP GLY ASP ARG LEU SEQRES 3 A 149 PHE ALA LYS TYR TYR ASP ASP THR TYR PRO SER VAL LYS SEQRES 4 A 149 GLU GLN LYS ALA PHE GLU LYS ASN ILE PHE ASN LYS THR SEQRES 5 A 149 HIS ARG THR ASP SER GLU ILE ALA LEU LEU GLU GLY LEU SEQRES 6 A 149 THR VAL VAL TYR LYS SER SER ILE ASP LEU TYR PHE TYR SEQRES 7 A 149 VAL ILE GLY SER SER TYR GLU ASN GLU LEU MET LEU MET SEQRES 8 A 149 ALA VAL LEU ASN CYS LEU PHE ASP SER LEU SER GLN MET SEQRES 9 A 149 LEU ARG LYS ASN VAL GLU LYS ARG ALA LEU LEU GLU ASN SEQRES 10 A 149 MET GLU GLY LEU PHE LEU ALA VAL ASP GLU ILE VAL ASP SEQRES 11 A 149 GLY GLY VAL ILE LEU GLU SER ASP PRO GLN GLN VAL VAL SEQRES 12 A 149 HIS ARG VAL ALA LEU ARG HELIX 1 1 SER A 37 HIS A 53 1 17 HELIX 2 2 GLU A 87 ARG A 106 1 20 HELIX 3 3 GLU A 110 GLU A 116 1 7 HELIX 4 4 ASN A 117 ILE A 128 1 12 HELIX 5 5 ASP A 138 ARG A 149 1 12 SHEET 1 A 5 ARG A 25 TYR A 30 0 SHEET 2 A 5 ALA A 15 ASP A 20 -1 N ILE A 18 O PHE A 27 SHEET 3 A 5 LEU A 75 GLY A 81 -1 O ILE A 80 N ALA A 15 SHEET 4 A 5 LEU A 65 SER A 72 -1 N LYS A 70 O PHE A 77 SHEET 5 A 5 ILE A 59 LEU A 62 -1 N LEU A 62 O LEU A 65 SHEET 1 B 2 VAL A 129 ASP A 130 0 SHEET 2 B 2 VAL A 133 ILE A 134 -1 O VAL A 133 N ASP A 130 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