HEADER PROTEIN TRANSPORT 18-JUN-10 2KZK TITLE SOLUTION STRUCTURE OF ALPHA-MANNOSIDASE BINDING DOMAIN OF ATG34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YOL083W; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ALPHA-MANNOSIDASE BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: YOL083W, O0957; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS SELECTIVE AUTOPHAGY, ATG34, ALPHA-MANNOSIDASE, ATG19, PROTEIN KEYWDS 2 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WATANABE,N.NODA,H.KUMETA,K.SUZUKI,Y.OHSUMI,F.INAGAKI REVDAT 4 14-JUN-23 2KZK 1 REMARK REVDAT 3 26-FEB-20 2KZK 1 REMARK SEQADV REVDAT 2 12-MAR-14 2KZK 1 JRNL VERSN REVDAT 1 21-JUL-10 2KZK 0 JRNL AUTH Y.WATANABE,N.N.NODA,H.KUMETA,K.SUZUKI,Y.OHSUMI,F.INAGAKI JRNL TITL SELECTIVE TRANSPORT OF ALPHA-MANNOSIDASE BY AUTOPHAGIC JRNL TITL 2 PATHWAYS: STRUCTURAL BASIS FOR CARGO RECOGNITION BY ATG19 JRNL TITL 3 AND ATG34. JRNL REF J.BIOL.CHEM. V. 285 30026 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20659891 JRNL DOI 10.1074/JBC.M110.143545 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000101770. 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 : 25 MM SODIUM PHOSPHATE-1, 100 MM REMARK 210 SODIUM CHLORIDE-2, 2 MM DTT-3, REMARK 210 0.7 MM [U-99% 13C; U-99% 15N] REMARK 210 ALPHA-MANNOSIDASE BINDING DOMAIN REMARK 210 OF ATG34-4, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HN(CO)CA; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HN(CO)HA; 3D REMARK 210 HBHA(CO)NH; 2D 1H-13C HSQC; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 1H-15N NOESY; 2D (HB)CB(CGCD)HD; REMARK 210 2D (HB)CB(CGCDCE)HE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRPIPE, SPARKY, VNMR REMARK 210 METHOD USED : NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 242 REMARK 465 PRO A 243 REMARK 465 HIS A 244 REMARK 465 MET A 245 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 ASP A 247 132.81 65.15 REMARK 500 1 SER A 260 -167.11 -165.28 REMARK 500 1 HIS A 262 95.28 -163.20 REMARK 500 1 THR A 269 175.16 -48.00 REMARK 500 1 GLU A 280 101.61 -176.73 REMARK 500 1 SER A 283 -173.97 -178.45 REMARK 500 1 ILE A 298 -76.07 -105.77 REMARK 500 1 SER A 311 174.73 178.44 REMARK 500 1 LEU A 316 57.79 -109.80 REMARK 500 1 ASN A 318 2.63 83.19 REMARK 500 1 MET A 321 64.63 28.59 REMARK 500 1 ASN A 325 -165.56 -101.04 REMARK 500 1 CYS A 336 76.62 48.23 REMARK 500 1 LYS A 345 -76.84 -98.06 REMARK 500 1 SER A 346 142.06 159.84 REMARK 500 1 PRO A 347 -80.27 -74.99 REMARK 500 2 ASP A 247 87.73 52.96 REMARK 500 2 ASN A 256 82.30 60.82 REMARK 500 2 SER A 260 -173.94 176.27 REMARK 500 2 ASN A 276 50.73 70.27 REMARK 500 2 GLU A 280 65.69 -152.70 REMARK 500 2 SER A 286 -173.16 -52.70 REMARK 500 2 GLU A 287 172.78 -46.50 REMARK 500 2 ILE A 298 -79.90 -65.28 REMARK 500 2 SER A 311 131.15 169.74 REMARK 500 2 LEU A 316 60.12 -102.36 REMARK 500 2 THR A 320 -64.92 -107.81 REMARK 500 2 MET A 321 35.72 34.09 REMARK 500 2 CYS A 336 71.72 45.68 REMARK 500 2 SER A 339 148.72 -178.95 REMARK 500 2 SER A 346 158.19 158.98 REMARK 500 3 ASP A 247 101.37 -167.93 REMARK 500 3 ASN A 256 67.52 60.48 REMARK 500 3 SER A 260 -176.70 -174.21 REMARK 500 3 HIS A 262 103.76 -160.49 REMARK 500 3 ASN A 267 96.60 -68.38 REMARK 500 3 ILE A 271 172.95 -54.61 REMARK 500 3 GLU A 280 89.92 -171.68 REMARK 500 3 SER A 286 -167.10 -55.61 REMARK 500 3 ILE A 298 -79.49 -92.56 REMARK 500 3 ILE A 300 -86.08 -53.66 REMARK 500 3 LEU A 306 73.79 -161.27 REMARK 500 3 PHE A 309 157.34 -37.63 REMARK 500 3 SER A 311 144.95 176.13 REMARK 500 3 MET A 321 68.52 31.19 REMARK 500 3 CYS A 336 76.00 49.14 REMARK 500 3 SER A 339 141.33 179.43 REMARK 500 3 SER A 346 145.91 159.70 REMARK 500 3 PRO A 347 -81.62 -75.03 REMARK 500 4 LEU A 249 141.80 -39.88 REMARK 500 REMARK 500 THIS ENTRY HAS 344 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17007 RELATED DB: BMRB DBREF 2KZK A 246 348 UNP Q12292 YO083_YEAST 246 348 SEQADV 2KZK GLY A 242 UNP Q12292 EXPRESSION TAG SEQADV 2KZK PRO A 243 UNP Q12292 EXPRESSION TAG SEQADV 2KZK HIS A 244 UNP Q12292 EXPRESSION TAG SEQADV 2KZK MET A 245 UNP Q12292 EXPRESSION TAG SEQRES 1 A 107 GLY PRO HIS MET ASN ASP PRO LEU LEU HIS VAL GLU VAL SEQRES 2 A 107 SER ASN GLU ASP ASN SER LEU HIS PHE ILE LEU TYR ASN SEQRES 3 A 107 LYS THR ASN ILE ILE ILE PRO GLY ASN CYS THR PHE GLU SEQRES 4 A 107 PHE SER SER GLN ILE SER GLU VAL PHE SER ILE LYS MET SEQRES 5 A 107 GLY PRO HIS GLU ILE GLY ILE LYS GLY GLN LYS GLU LEU SEQRES 6 A 107 TRP PHE PHE PRO SER LEU PRO THR PRO LEU SER ASN TYR SEQRES 7 A 107 THR MET LYS VAL VAL ASN GLN ASP GLY GLU THR ILE LEU SEQRES 8 A 107 VAL GLY LYS CYS ALA ASP SER ASN GLU ILE THR LEU LYS SEQRES 9 A 107 SER PRO LEU SHEET 1 A 3 HIS A 251 VAL A 254 0 SHEET 2 A 3 PHE A 263 TYR A 266 -1 O TYR A 266 N HIS A 251 SHEET 3 A 3 GLN A 303 GLU A 305 -1 O LYS A 304 N LEU A 265 SHEET 1 B 3 THR A 278 GLU A 280 0 SHEET 2 B 3 LYS A 322 VAL A 324 -1 O VAL A 324 N THR A 278 SHEET 3 B 3 THR A 330 VAL A 333 -1 O ILE A 331 N VAL A 323 CISPEP 1 PHE A 309 PRO A 310 1 -0.05 CISPEP 2 THR A 314 PRO A 315 1 -0.04 CISPEP 3 PHE A 309 PRO A 310 2 0.02 CISPEP 4 THR A 314 PRO A 315 2 -0.02 CISPEP 5 PHE A 309 PRO A 310 3 -0.03 CISPEP 6 THR A 314 PRO A 315 3 -0.01 CISPEP 7 PHE A 309 PRO A 310 4 0.01 CISPEP 8 THR A 314 PRO A 315 4 0.02 CISPEP 9 PHE A 309 PRO A 310 5 0.01 CISPEP 10 THR A 314 PRO A 315 5 0.02 CISPEP 11 PHE A 309 PRO A 310 6 0.01 CISPEP 12 THR A 314 PRO A 315 6 -0.01 CISPEP 13 PHE A 309 PRO A 310 7 -0.01 CISPEP 14 THR A 314 PRO A 315 7 0.06 CISPEP 15 PHE A 309 PRO A 310 8 0.03 CISPEP 16 THR A 314 PRO A 315 8 0.08 CISPEP 17 PHE A 309 PRO A 310 9 0.01 CISPEP 18 THR A 314 PRO A 315 9 -0.05 CISPEP 19 PHE A 309 PRO A 310 10 -0.01 CISPEP 20 THR A 314 PRO A 315 10 0.06 CISPEP 21 PHE A 309 PRO A 310 11 0.04 CISPEP 22 THR A 314 PRO A 315 11 -0.04 CISPEP 23 PHE A 309 PRO A 310 12 0.04 CISPEP 24 THR A 314 PRO A 315 12 0.04 CISPEP 25 PHE A 309 PRO A 310 13 0.05 CISPEP 26 THR A 314 PRO A 315 13 -0.03 CISPEP 27 PHE A 309 PRO A 310 14 0.08 CISPEP 28 THR A 314 PRO A 315 14 0.02 CISPEP 29 PHE A 309 PRO A 310 15 0.00 CISPEP 30 THR A 314 PRO A 315 15 -0.14 CISPEP 31 PHE A 309 PRO A 310 16 -0.10 CISPEP 32 THR A 314 PRO A 315 16 0.01 CISPEP 33 PHE A 309 PRO A 310 17 -0.05 CISPEP 34 THR A 314 PRO A 315 17 -0.05 CISPEP 35 PHE A 309 PRO A 310 18 0.00 CISPEP 36 THR A 314 PRO A 315 18 0.04 CISPEP 37 PHE A 309 PRO A 310 19 0.03 CISPEP 38 THR A 314 PRO A 315 19 -0.07 CISPEP 39 PHE A 309 PRO A 310 20 -0.01 CISPEP 40 THR A 314 PRO A 315 20 -0.07 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