HEADER PROTEIN TRANSPORT 27-JAN-14 4CO7 TITLE CRYSTAL STRUCTURE OF HUMAN GATE-16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GABA(A) RECEPTOR-ASSOCIATED PROTEIN-LIKE 2, GANGLIOSIDE COMPND 5 EXPRESSION FACTOR 2, GEF-2, GENERAL PROTEIN TRANSPORT FACTOR P16, COMPND 6 GOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KDA, GATE-16, MAP1 LIGHT CHAIN COMPND 7 3-RELATED PROTEIN; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-2 KEYWDS PROTEIN TRANSPORT, AUTOPHAGY, BETA-GRASP FOLD, UBIQUITIN SUPERFAMILY EXPDTA X-RAY DIFFRACTION AUTHOR O.H.WEIERGRAEBER,P.MA,D.WILLBOLD REVDAT 3 20-DEC-23 4CO7 1 REMARK REVDAT 2 11-NOV-15 4CO7 1 JRNL REVDAT 1 14-JAN-15 4CO7 0 JRNL AUTH P.MA,O.SCHILLINGER,M.SCHWARTEN,J.LECHER,R.HARTMANN,M.STOLDT, JRNL AUTH 2 J.MOHRLUDER,O.OLUBIYI,B.STRODEL,D.WILLBOLD,O.H.WEIERGRABER JRNL TITL CONFORMATIONAL POLYMORPHISM IN AUTOPHAGY-RELATED PROTEIN JRNL TITL 2 GATE-16. JRNL REF BIOCHEMISTRY V. 54 5469 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26284781 JRNL DOI 10.1021/ACS.BIOCHEM.5B00366 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 14392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1051 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.8088 - 3.8232 0.83 1855 136 0.1374 0.1691 REMARK 3 2 3.8232 - 3.0362 0.88 1904 143 0.1544 0.2058 REMARK 3 3 3.0362 - 2.6528 0.89 1949 144 0.1939 0.2225 REMARK 3 4 2.6528 - 2.4105 0.89 1895 143 0.2206 0.2235 REMARK 3 5 2.4105 - 2.2378 0.89 1939 147 0.2337 0.2400 REMARK 3 6 2.2378 - 2.1059 0.89 1929 140 0.2430 0.2959 REMARK 3 7 2.1059 - 2.0005 0.88 1913 139 0.2796 0.2949 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.4900 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1966 REMARK 3 ANGLE : 0.817 2649 REMARK 3 CHIRALITY : 0.039 286 REMARK 3 PLANARITY : 0.004 335 REMARK 3 DIHEDRAL : 12.825 743 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4CO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1290059588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0092 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1EO6 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM PHOSPHATE PH 7.0, 50 MM REMARK 280 POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.72000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 GLY B -1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 0 CB OG REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 SER B 0 CB OG REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 GLN B 86 CG CD OE1 NE2 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 ILE A 41 150.76 -47.30 REMARK 500 LYS A 82 -2.45 63.39 REMARK 500 ILE B 41 157.76 -48.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2031 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B2003 DISTANCE = 5.93 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 PURIFIED PROTEIN CONTAINS CLONING ARTIFACT (GS) AT N- REMARK 999 TERMINUS DBREF 4CO7 A 1 117 UNP P60520 GBRL2_HUMAN 1 117 DBREF 4CO7 B 1 117 UNP P60520 GBRL2_HUMAN 1 117 SEQADV 4CO7 GLY A -1 UNP P60520 EXPRESSION TAG SEQADV 4CO7 SER A 0 UNP P60520 EXPRESSION TAG SEQADV 4CO7 GLY B -1 UNP P60520 EXPRESSION TAG SEQADV 4CO7 SER B 0 UNP P60520 EXPRESSION TAG SEQRES 1 A 119 GLY SER MET LYS TRP MET PHE LYS GLU ASP HIS SER LEU SEQRES 2 A 119 GLU HIS ARG CYS VAL GLU SER ALA LYS ILE ARG ALA LYS SEQRES 3 A 119 TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS VAL SER SEQRES 4 A 119 GLY SER GLN ILE VAL ASP ILE ASP LYS ARG LYS TYR LEU SEQRES 5 A 119 VAL PRO SER ASP ILE THR VAL ALA GLN PHE MET TRP ILE SEQRES 6 A 119 ILE ARG LYS ARG ILE GLN LEU PRO SER GLU LYS ALA ILE SEQRES 7 A 119 PHE LEU PHE VAL ASP LYS THR VAL PRO GLN SER SER LEU SEQRES 8 A 119 THR MET GLY GLN LEU TYR GLU LYS GLU LYS ASP GLU ASP SEQRES 9 A 119 GLY PHE LEU TYR VAL ALA TYR SER GLY GLU ASN THR PHE SEQRES 10 A 119 GLY PHE SEQRES 1 B 119 GLY SER MET LYS TRP MET PHE LYS GLU ASP HIS SER LEU SEQRES 2 B 119 GLU HIS ARG CYS VAL GLU SER ALA LYS ILE ARG ALA LYS SEQRES 3 B 119 TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS VAL SER SEQRES 4 B 119 GLY SER GLN ILE VAL ASP ILE ASP LYS ARG LYS TYR LEU SEQRES 5 B 119 VAL PRO SER ASP ILE THR VAL ALA GLN PHE MET TRP ILE SEQRES 6 B 119 ILE ARG LYS ARG ILE GLN LEU PRO SER GLU LYS ALA ILE SEQRES 7 B 119 PHE LEU PHE VAL ASP LYS THR VAL PRO GLN SER SER LEU SEQRES 8 B 119 THR MET GLY GLN LEU TYR GLU LYS GLU LYS ASP GLU ASP SEQRES 9 B 119 GLY PHE LEU TYR VAL ALA TYR SER GLY GLU ASN THR PHE SEQRES 10 B 119 GLY PHE FORMUL 3 HOH *151(H2 O) HELIX 1 1 TRP A 3 HIS A 9 1 7 HELIX 2 2 SER A 10 TYR A 25 1 16 HELIX 3 3 THR A 56 ILE A 68 1 13 HELIX 4 4 THR A 90 LYS A 99 1 10 HELIX 5 5 TRP B 3 HIS B 9 1 7 HELIX 6 6 SER B 10 TYR B 25 1 16 HELIX 7 7 THR B 56 ILE B 68 1 13 HELIX 8 8 THR B 90 LYS B 99 1 10 SHEET 1 AA 4 LYS A 48 PRO A 52 0 SHEET 2 AA 4 ARG A 28 LYS A 35 -1 O VAL A 29 N VAL A 51 SHEET 3 AA 4 LEU A 105 SER A 110 1 O LEU A 105 N ILE A 32 SHEET 4 AA 4 PHE A 77 PHE A 79 -1 O PHE A 77 N SER A 110 SHEET 1 BA 4 LYS B 48 PRO B 52 0 SHEET 2 BA 4 ARG B 28 LYS B 35 -1 O VAL B 29 N VAL B 51 SHEET 3 BA 4 LEU B 105 SER B 110 1 O LEU B 105 N ILE B 32 SHEET 4 BA 4 PHE B 77 PHE B 79 -1 O PHE B 77 N SER B 110 CRYST1 28.730 67.440 58.720 90.00 90.00 90.00 P 1 21 1 4 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 0.034807 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017030 0.00000 MTRIX1 1 -0.999800 -0.016690 0.008549 38.28000 1 MTRIX2 1 0.016550 -0.999700 -0.016620 74.79000 1 MTRIX3 1 0.008824 -0.016480 0.999800 29.62000 1