HEADER PROTEIN BINDING 09-DEC-19 6TNO TITLE CRYSTAL STRUCTURE OF THE HUMAN ARC N-LOBE BOUND TO STARGAZIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARC_C DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, C, E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CHAINS: B,D,F; COMPND 7 CHAIN: B, D, F; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: PEPTIDE FROM STARGAZIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FELIS CATUS; SOURCE 3 ORGANISM_COMMON: DOMESTIC CAT; SOURCE 4 ORGANISM_TAXID: 9685; SOURCE 5 GENE: ARC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS ARC, CAPSID HOMOLOGY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR E.I.HALLIN,C.R.BRAMHAM,P.KURSULA REVDAT 3 24-JAN-24 6TNO 1 REMARK REVDAT 2 07-APR-21 6TNO 1 JRNL REVDAT 1 16-DEC-20 6TNO 0 JRNL AUTH E.I.HALLIN,C.R.BRAMHAM,P.KURSULA JRNL TITL STRUCTURAL PROPERTIES AND PEPTIDE LIGAND BINDING OF THE JRNL TITL 2 CAPSID HOMOLOGY DOMAINS OF HUMAN ARC. JRNL REF BIOCHEM BIOPHYS REP V. 26 00975 2021 JRNL REFN ESSN 2405-5808 JRNL PMID 33732907 JRNL DOI 10.1016/J.BBREP.2021.100975 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 17109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL 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) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.87 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 : 0.005 2042 REMARK 3 ANGLE : 0.885 2751 REMARK 3 CHIRALITY : 0.047 247 REMARK 3 PLANARITY : 0.006 357 REMARK 3 DIHEDRAL : 20.922 1180 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 6TNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105763. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38600 REMARK 200 FOR SHELL : 2.900 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: 4X3H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M TRISODIUM CITRATE, PH 7.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 14.88500 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, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 203 REMARK 465 ALA A 204 REMARK 465 MET A 205 REMARK 465 GLY A 206 REMARK 465 PRO A 207 REMARK 465 GLY A 208 REMARK 465 VAL A 209 REMARK 465 ASP A 210 REMARK 465 ARG B 225 REMARK 465 GLY C 203 REMARK 465 ALA C 204 REMARK 465 MET C 205 REMARK 465 GLY C 206 REMARK 465 PRO C 207 REMARK 465 GLY C 208 REMARK 465 VAL C 209 REMARK 465 ASP C 210 REMARK 465 ARG D 225 REMARK 465 GLY E 203 REMARK 465 ALA E 204 REMARK 465 MET E 205 REMARK 465 GLY E 206 REMARK 465 PRO E 207 REMARK 465 GLY E 208 REMARK 465 VAL E 209 REMARK 465 ASP E 210 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 O GLU E 276 O HOH E 301 2.11 REMARK 500 OE2 GLU C 226 O HOH C 301 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6TNO A 206 277 UNP A0A2I2UQ80_FELCA DBREF2 6TNO A A0A2I2UQ80 206 277 DBREF 6TNO B 225 232 PDB 6TNO 6TNO 225 232 DBREF1 6TNO C 206 277 UNP A0A2I2UQ80_FELCA DBREF2 6TNO C A0A2I2UQ80 206 277 DBREF 6TNO D 225 232 PDB 6TNO 6TNO 225 232 DBREF1 6TNO E 206 277 UNP A0A2I2UQ80_FELCA DBREF2 6TNO E A0A2I2UQ80 206 277 DBREF 6TNO F 225 232 PDB 6TNO 6TNO 225 232 SEQADV 6TNO GLY A 203 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO ALA A 204 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO MET A 205 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO GLY C 203 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO ALA C 204 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO MET C 205 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO GLY E 203 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO ALA E 204 UNP A0A2I2UQ8 EXPRESSION TAG SEQADV 6TNO MET E 205 UNP A0A2I2UQ8 EXPRESSION TAG SEQRES 1 A 75 GLY ALA MET GLY PRO GLY VAL ASP THR GLN ILE PHE GLU SEQRES 2 A 75 ASP PRO ARG GLU PHE LEU SER HIS LEU GLU GLU TYR LEU SEQRES 3 A 75 ARG GLN VAL GLY GLY SER GLU GLU TYR TRP LEU SER GLN SEQRES 4 A 75 ILE GLN ASN HIS MET ASN GLY PRO ALA LYS LYS TRP TRP SEQRES 5 A 75 GLU PHE LYS GLN GLY SER VAL LYS ASN TRP VAL GLU PHE SEQRES 6 A 75 LYS LYS GLU PHE LEU GLN TYR SER GLU GLY SEQRES 1 B 8 ARG ILE PRO SER TYR ARG TYR ARG SEQRES 1 C 75 GLY ALA MET GLY PRO GLY VAL ASP THR GLN ILE PHE GLU SEQRES 2 C 75 ASP PRO ARG GLU PHE LEU SER HIS LEU GLU GLU TYR LEU SEQRES 3 C 75 ARG GLN VAL GLY GLY SER GLU GLU TYR TRP LEU SER GLN SEQRES 4 C 75 ILE GLN ASN HIS MET ASN GLY PRO ALA LYS LYS TRP TRP SEQRES 5 C 75 GLU PHE LYS GLN GLY SER VAL LYS ASN TRP VAL GLU PHE SEQRES 6 C 75 LYS LYS GLU PHE LEU GLN TYR SER GLU GLY SEQRES 1 D 8 ARG ILE PRO SER TYR ARG TYR ARG SEQRES 1 E 75 GLY ALA MET GLY PRO GLY VAL ASP THR GLN ILE PHE GLU SEQRES 2 E 75 ASP PRO ARG GLU PHE LEU SER HIS LEU GLU GLU TYR LEU SEQRES 3 E 75 ARG GLN VAL GLY GLY SER GLU GLU TYR TRP LEU SER GLN SEQRES 4 E 75 ILE GLN ASN HIS MET ASN GLY PRO ALA LYS LYS TRP TRP SEQRES 5 E 75 GLU PHE LYS GLN GLY SER VAL LYS ASN TRP VAL GLU PHE SEQRES 6 E 75 LYS LYS GLU PHE LEU GLN TYR SER GLU GLY SEQRES 1 F 8 ARG ILE PRO SER TYR ARG TYR ARG FORMUL 7 HOH *107(H2 O) HELIX 1 AA1 ASP A 216 GLY A 232 1 17 HELIX 2 AA2 SER A 234 ILE A 242 1 9 HELIX 3 AA3 GLN A 243 ASN A 247 5 5 HELIX 4 AA4 GLY A 248 GLN A 258 1 11 HELIX 5 AA5 GLY A 259 VAL A 261 5 3 HELIX 6 AA6 ASN A 263 GLY A 277 1 15 HELIX 7 AA7 ASP C 216 GLY C 232 1 17 HELIX 8 AA8 SER C 234 ILE C 242 1 9 HELIX 9 AA9 GLY C 248 GLN C 258 1 11 HELIX 10 AB1 ASN C 263 GLU C 276 1 14 HELIX 11 AB2 ASP E 216 GLY E 232 1 17 HELIX 12 AB3 SER E 234 ILE E 242 1 9 HELIX 13 AB4 GLY E 248 GLN E 258 1 11 HELIX 14 AB5 GLY E 259 VAL E 261 5 3 HELIX 15 AB6 ASN E 263 GLU E 276 1 14 SHEET 1 AA1 2 GLN A 212 PHE A 214 0 SHEET 2 AA1 2 PRO B 227 TYR B 229 1 O SER B 228 N PHE A 214 SHEET 1 AA2 3 GLN C 212 PHE C 214 0 SHEET 2 AA2 3 PRO D 227 ARG D 230 1 O SER D 228 N PHE C 214 SHEET 3 AA2 3 MET C 246 ASN C 247 1 N ASN C 247 O TYR D 229 SHEET 1 AA3 3 GLN E 212 PHE E 214 0 SHEET 2 AA3 3 PRO F 227 ARG F 230 1 O SER F 228 N PHE E 214 SHEET 3 AA3 3 MET E 246 ASN E 247 1 N ASN E 247 O TYR F 229 CRYST1 51.390 29.770 71.790 90.00 92.51 90.00 P 1 21 1 6 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 0.019459 0.000000 0.000853 0.00000 SCALE2 0.000000 0.033591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013943 0.00000