HEADER SIGNALING PROTEIN 10-AUG-18 6HB9 TITLE CRYSTAL STRUCTURE OF THE GABARAP IN COMPLEX WITH THE UBA5 LIR MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GABA(A) RECEPTOR-ASSOCIATED PROTEIN,MM46; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN COMPND 7 (GABARAP) RESIDUES 3-116 N-TERMINALLY FUSED TO THE HUMAN UBA5 LIR COMPND 8 MOTIF (RESIDUES 340-351, EWGIELVSEVSE) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GABARAP, FLC3B, HT004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GABARAP, UBA5 LIR MOTIF, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HUBER,V.ROGOV,M.AKUTSU REVDAT 4 15-MAY-24 6HB9 1 REMARK REVDAT 3 29-JAN-20 6HB9 1 JRNL REVDAT 2 08-MAY-19 6HB9 1 JRNL REVDAT 1 01-MAY-19 6HB9 0 JRNL AUTH J.HUBER,M.OBATA,J.GRUBER,M.AKUTSU,F.LOHR,N.ROGOVA,P.GUNTERT, JRNL AUTH 2 I.DIKIC,V.KIRKIN,M.KOMATSU,V.DOTSCH,V.V.ROGOV JRNL TITL AN ATYPICAL LIR MOTIF WITHIN UBA5 (UBIQUITIN LIKE MODIFIER JRNL TITL 2 ACTIVATING ENZYME 5) INTERACTS WITH GABARAP PROTEINS AND JRNL TITL 3 MEDIATES MEMBRANE LOCALIZATION OF UBA5. JRNL REF AUTOPHAGY V. 16 256 2020 JRNL REFN ESSN 1554-8635 JRNL PMID 30990354 JRNL DOI 10.1080/15548627.2019.1606637 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 32909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1666 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 33.3383 - 2.9756 0.98 2696 159 0.1613 0.2097 REMARK 3 2 2.9756 - 2.3620 0.99 2700 151 0.1956 0.1791 REMARK 3 3 2.3620 - 2.0635 0.98 2651 141 0.1733 0.1995 REMARK 3 4 2.0635 - 1.8749 0.99 2686 141 0.1681 0.1795 REMARK 3 5 1.8749 - 1.7405 0.99 2660 150 0.1777 0.2308 REMARK 3 6 1.7405 - 1.6379 0.98 2634 144 0.1849 0.2064 REMARK 3 7 1.6379 - 1.5558 0.98 2642 149 0.1897 0.2138 REMARK 3 8 1.5558 - 1.4881 0.97 2612 121 0.2478 0.2615 REMARK 3 9 1.4881 - 1.4308 0.94 2537 130 0.2815 0.2952 REMARK 3 10 1.4308 - 1.3815 0.94 2538 127 0.2825 0.2681 REMARK 3 11 1.3815 - 1.3383 0.93 2449 141 0.2755 0.2960 REMARK 3 12 1.3383 - 1.3000 0.91 2438 112 0.2796 0.3001 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.83 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1123 REMARK 3 ANGLE : 1.111 1519 REMARK 3 CHIRALITY : 0.050 156 REMARK 3 PLANARITY : 0.006 198 REMARK 3 DIHEDRAL : 13.395 426 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HB9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM PHOSPHATE, 0.1 M HEPES, REMARK 280 PH7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.00500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 GLU A -12 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 27 O HOH A 201 1.89 REMARK 500 O HOH A 215 O HOH A 274 2.02 REMARK 500 O HOH A 204 O HOH A 284 2.03 REMARK 500 O HOH A 204 O HOH A 228 2.12 REMARK 500 O HOH A 290 O HOH A 306 2.12 REMARK 500 OD2 ASP A 111 O HOH A 202 2.13 REMARK 500 O HOH A 204 O HOH A 256 2.15 REMARK 500 O HOH A 233 O HOH A 269 2.16 REMARK 500 NZ LYS A 66 O HOH A 203 2.18 REMARK 500 NE2 HIS A 99 O HOH A 204 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 289 O HOH A 303 1455 1.99 REMARK 500 O HOH A 204 O HOH A 264 1655 2.07 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 ARG A 40 59.91 -103.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6H8C RELATED DB: PDB REMARK 900 STRUCTURE OF THE HUMAN GABARAPL2 PROTEIN IN COMPLEX WITH THE UBA5 REMARK 900 LIR MOTIF DBREF 6HB9 A 3 116 UNP O95166 GBRAP_HUMAN 3 116 SEQADV 6HB9 GLU A -12 UNP O95166 EXPRESSION TAG SEQADV 6HB9 TRP A -11 UNP O95166 EXPRESSION TAG SEQADV 6HB9 GLY A -10 UNP O95166 EXPRESSION TAG SEQADV 6HB9 ILE A -9 UNP O95166 EXPRESSION TAG SEQADV 6HB9 GLU A -8 UNP O95166 EXPRESSION TAG SEQADV 6HB9 LEU A -7 UNP O95166 EXPRESSION TAG SEQADV 6HB9 VAL A -6 UNP O95166 EXPRESSION TAG SEQADV 6HB9 SER A -5 UNP O95166 EXPRESSION TAG SEQADV 6HB9 GLU A -4 UNP O95166 EXPRESSION TAG SEQADV 6HB9 VAL A -3 UNP O95166 EXPRESSION TAG SEQADV 6HB9 SER A -2 UNP O95166 EXPRESSION TAG SEQADV 6HB9 GLU A -1 UNP O95166 EXPRESSION TAG SEQADV 6HB9 ALA A 0 UNP O95166 EXPRESSION TAG SEQADV 6HB9 MET A 1 UNP O95166 EXPRESSION TAG SEQADV 6HB9 GLY A 2 UNP O95166 EXPRESSION TAG SEQRES 1 A 129 GLU TRP GLY ILE GLU LEU VAL SER GLU VAL SER GLU ALA SEQRES 2 A 129 MET GLY PHE VAL TYR LYS GLU GLU HIS PRO PHE GLU LYS SEQRES 3 A 129 ARG ARG SER GLU GLY GLU LYS ILE ARG LYS LYS TYR PRO SEQRES 4 A 129 ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO LYS ALA SEQRES 5 A 129 ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU VAL PRO SEQRES 6 A 129 SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU ILE ARG SEQRES 7 A 129 LYS ARG ILE HIS LEU ARG ALA GLU ASP ALA LEU PHE PHE SEQRES 8 A 129 PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA THR MET SEQRES 9 A 129 GLY GLN LEU TYR GLN GLU HIS HIS GLU GLU ASP PHE PHE SEQRES 10 A 129 LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR GLY FORMUL 2 HOH *137(H2 O) HELIX 1 AA1 PHE A 3 HIS A 9 1 7 HELIX 2 AA2 PRO A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 ILE A 68 1 13 HELIX 4 AA4 THR A 90 HIS A 99 1 10 SHEET 1 AA1 4 TYR A 49 PRO A 52 0 SHEET 2 AA1 4 ARG A 28 LYS A 35 -1 N VAL A 29 O VAL A 51 SHEET 3 AA1 4 LEU A 105 SER A 110 1 O LEU A 105 N ILE A 32 SHEET 4 AA1 4 PHE A 77 PHE A 79 -1 N PHE A 77 O SER A 110 CRYST1 33.776 58.010 36.421 90.00 99.35 90.00 P 1 21 1 2 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 0.029607 0.000000 0.004874 0.00000 SCALE2 0.000000 0.017238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027826 0.00000