HEADER PROTEIN BINDING 06-JUN-23 8T2M TITLE CRYSTAL STRUCTURE OF GABARAP IN COMPLEX WITH THE LIR OF NSS4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN S,GAMMA-AMINOBUTYRIC ACID RECEPTOR- COMPND 3 ASSOCIATED PROTEIN CHIMERA; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: GS IS THE REMAIN OF THE REMOVED EXPRESSION TAG. THE C COMPND 6 TERMINUS OF NSS 257-265 HAS BEEN FUSED WITH Q9H492 TO FACILITATE THE COMPND 7 CRYSTALIZATION. THE GG IS A SPACER BETWEEN NSS AND GABARAP PROTEIN.; COMPND 8 SYNONYM: NSS,GABA(A) RECEPTOR-ASSOCIATED PROTEIN,MM46; COMPND 9 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: NSS, GABARAP, FLC3B, HT004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RIFT VALLEY FEVER VIRUS, AUTOPHAGY, LC3, GABARAP, LIR, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.G.H.ALI,H.M.WAHBA,N.CYR,J.G.OMICHINSKI REVDAT 1 03-APR-24 8T2M 0 JRNL AUTH K.PETRACCIONE,M.G.H.ALI,N.CYR,H.M.WAHBA,T.STOCKER, JRNL AUTH 2 M.AKHRYMUK,I.AKHRYMUK,L.PANNY,N.BRACCI,R.CAFARO,D.SASTRE, JRNL AUTH 3 A.SILBERFARB,P.O'MAILLE,J.OMICHINSKI,K.KEHN-HALL JRNL TITL AN LIR MOTIF IN THE RIFT VALLEY FEVER VIRUS NSS PROTEIN IS JRNL TITL 2 CRITICAL FOR THE INTERACTION WITH LC3 FAMILY MEMBERS AND JRNL TITL 3 INHIBITION OF AUTOPHAGY. JRNL REF PLOS PATHOG. V. 20 12093 2024 JRNL REFN ESSN 1553-7374 JRNL PMID 38512999 JRNL DOI 10.1371/JOURNAL.PPAT.1012093 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 33688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 29.4500 - 3.0600 1.00 2539 159 0.1680 0.1733 REMARK 3 2 3.0600 - 2.4300 1.00 2429 153 0.1609 0.1761 REMARK 3 3 2.4300 - 2.1200 1.00 2386 151 0.1375 0.1392 REMARK 3 4 2.1200 - 1.9300 1.00 2363 149 0.1310 0.1684 REMARK 3 5 1.9300 - 1.7900 1.00 2369 150 0.1375 0.1482 REMARK 3 6 1.7900 - 1.6900 1.00 2360 148 0.1395 0.1862 REMARK 3 7 1.6900 - 1.6000 1.00 2346 148 0.1462 0.1811 REMARK 3 8 1.6000 - 1.5300 1.00 2343 148 0.1396 0.1820 REMARK 3 9 1.5300 - 1.4700 1.00 2329 147 0.1349 0.1888 REMARK 3 10 1.4700 - 1.4200 1.00 2336 148 0.1379 0.1679 REMARK 3 11 1.4200 - 1.3800 1.00 2333 146 0.1730 0.2085 REMARK 3 12 1.3800 - 1.3400 1.00 2330 148 0.2670 0.3452 REMARK 3 13 1.3400 - 1.3000 0.86 1999 126 0.3673 0.3615 REMARK 3 14 1.3000 - 1.2700 0.53 1228 77 0.4246 0.4969 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 1118 REMARK 3 ANGLE : 0.964 1509 REMARK 3 CHIRALITY : 0.078 155 REMARK 3 PLANARITY : 0.017 198 REMARK 3 DIHEDRAL : 14.032 427 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 8T2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000271804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18057 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 29.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE:HCL, PH 4.6, 8% REMARK 280 PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 16.37050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.67300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.55950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.67300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.37050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.55950 REMARK 290 SMTRY3 4 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 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. (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 -12 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 HE22 GLN A 93 O HOH A 202 1.51 REMARK 500 O HOH A 371 O HOH A 374 1.67 REMARK 500 O HOH A 277 O HOH A 353 1.87 REMARK 500 O HOH A 377 O HOH A 389 1.89 REMARK 500 O HOH A 417 O HOH A 419 1.92 REMARK 500 O HOH A 300 O HOH A 376 2.00 REMARK 500 O HOH A 357 O HOH A 400 2.03 REMARK 500 NZ LYS A 20 O HOH A 201 2.08 REMARK 500 NE2 GLN A 93 O HOH A 202 2.10 REMARK 500 O HOH A 211 O HOH A 222 2.11 REMARK 500 O HOH A 204 O HOH A 325 2.13 REMARK 500 O HOH A 347 O HOH A 401 2.15 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 215 O HOH A 362 3554 1.86 REMARK 500 O HOH A 318 O HOH A 362 3554 1.97 REMARK 500 O HOH A 355 O HOH A 356 3554 2.01 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 ARG A 14 0.08 SIDE CHAIN 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 A 419 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 420 DISTANCE = 6.63 ANGSTROMS DBREF 8T2M A -10 -2 UNP P21698 NSS_RVFVZ 257 265 DBREF 8T2M A 1 117 UNP O95166 GBRAP_HUMAN 1 117 SEQADV 8T2M GLY A -12 UNP P21698 EXPRESSION TAG SEQADV 8T2M SER A -11 UNP P21698 EXPRESSION TAG SEQADV 8T2M GLY A -1 UNP P21698 LINKER SEQADV 8T2M GLY A 0 UNP P21698 LINKER SEQRES 1 A 130 GLY SER ASP ASP ASP GLY PHE VAL GLU VAL ASP GLY GLY SEQRES 2 A 130 MET LYS PHE VAL TYR LYS GLU GLU HIS PRO PHE GLU LYS SEQRES 3 A 130 ARG ARG SER GLU GLY GLU LYS ILE ARG LYS LYS TYR PRO SEQRES 4 A 130 ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO LYS ALA SEQRES 5 A 130 ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU VAL PRO SEQRES 6 A 130 SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU ILE ARG SEQRES 7 A 130 LYS ARG ILE HIS LEU ARG ALA GLU ASP ALA LEU PHE PHE SEQRES 8 A 130 PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA THR MET SEQRES 9 A 130 GLY GLN LEU TYR GLN GLU HIS HIS GLU GLU ASP PHE PHE SEQRES 10 A 130 LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR GLY LEU FORMUL 2 HOH *220(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 LYS A 48 PRO A 52 0 SHEET 2 AA1 4 ARG A 28 LYS A 35 -1 N VAL A 31 O TYR A 49 SHEET 3 AA1 4 LEU A 105 SER A 110 1 O ILE A 107 N ILE A 32 SHEET 4 AA1 4 PHE A 77 PHE A 79 -1 N PHE A 79 O ALA A 108 CRYST1 32.741 59.119 67.346 90.00 90.00 90.00 P 21 21 21 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 0.030543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014849 0.00000