HEADER SIGNALING PROTEIN 24-APR-20 6YTU TITLE ATOMIC-RESOLUTION STRUCTURE OF THE COILED-COIL DIMERISATION DOMAIN OF TITLE 2 HUMAN ARC COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIVITY-REGULATED CYTOSKELETON-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HARC,ACTIVITY-REGULATED GENE 3.1 PROTEIN HOMOLOG,ARG3.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ARC, OLIGOMERISATION, COILED COIL, DIMER, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.I.HALLIN,C.TOUMA,C.R.BRAMHAM,P.KURSULA REVDAT 2 12-MAY-21 6YTU 1 JRNL REVDAT 1 03-MAR-21 6YTU 0 JRNL AUTH M.S.ERIKSEN,O.NIKOLAIENKO,E.I.HALLIN,S.GRODEM,H.J.BUSTAD, JRNL AUTH 2 M.I.FLYDAL,I.MERSKI,T.HOSOKAWA,D.LASCU,S.AKERKAR,J.CUELLAR, JRNL AUTH 3 J.J.CHAMBERS,R.O'CONNELL,G.MURUGANANDAM,R.LORIS,C.TOUMA, JRNL AUTH 4 T.KANHEMA,Y.HAYASHI,M.M.STRATTON,J.M.VALPUESTA,P.KURSULA, JRNL AUTH 5 A.MARTINEZ,C.R.BRAMHAM JRNL TITL ARC SELF-ASSOCIATION AND FORMATION OF VIRUS-LIKE CAPSIDS ARE JRNL TITL 2 MEDIATED BY AN N-TERMINAL HELICAL COIL MOTIF. JRNL REF FEBS J. V. 288 2930 2021 JRNL REFN ISSN 1742-464X JRNL PMID 33175445 JRNL DOI 10.1111/FEBS.15618 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 44785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.104 REMARK 3 R VALUE (WORKING SET) : 0.103 REMARK 3 FREE R VALUE : 0.124 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2242 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) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.41 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 : 0.019 803 REMARK 3 ANGLE : 1.708 1093 REMARK 3 CHIRALITY : 0.129 103 REMARK 3 PLANARITY : 0.015 143 REMARK 3 DIHEDRAL : 16.528 328 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 6YTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9796 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44960 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.28200 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% MPD, 0.1 M TRIS-HCL (PH 7.5), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281K 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 13.42200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.67500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.27800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.67500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.42200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.27800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 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 SER B 132 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 HE21 GLN B 99 O HOH B 302 1.54 REMARK 500 O HOH A 353 O HOH A 362 1.93 REMARK 500 OE1 GLU B 118 O HOH B 301 2.08 REMARK 500 O HOH A 310 O HOH A 353 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 111 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 111 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 LEU B 130 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE B 98 and GLN B REMARK 800 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE B 98 and GLN B REMARK 800 99 DBREF 6YTU A 99 132 UNP Q7LC44 ARC_HUMAN 99 132 DBREF 6YTU B 99 132 UNP Q7LC44 ARC_HUMAN 99 132 SEQADV 6YTU ACE A 98 UNP Q7LC44 ACETYLATION SEQADV 6YTU ACE B 98 UNP Q7LC44 ACETYLATION SEQRES 1 A 35 ACE GLN GLU THR ILE ALA ASN LEU GLU ARG TRP VAL LYS SEQRES 2 A 35 ARG GLU MET HIS VAL TRP ARG GLU VAL PHE TYR ARG LEU SEQRES 3 A 35 GLU ARG TRP ALA ASP ARG LEU GLU SER SEQRES 1 B 35 ACE GLN GLU THR ILE ALA ASN LEU GLU ARG TRP VAL LYS SEQRES 2 B 35 ARG GLU MET HIS VAL TRP ARG GLU VAL PHE TYR ARG LEU SEQRES 3 B 35 GLU ARG TRP ALA ASP ARG LEU GLU SER HET ACE A 98 3 HET ACE B 98 3 HET MPD A 201 22 HET CL A 202 1 HET MPD B 201 22 HETNAM ACE ACETYL GROUP HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CL CHLORIDE ION FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 MPD 2(C6 H14 O2) FORMUL 4 CL CL 1- FORMUL 6 HOH *114(H2 O) HELIX 1 AA1 GLN A 99 GLU A 131 1 33 HELIX 2 AA2 GLN B 99 LEU B 130 1 32 LINK C ACE A 98 N AGLN A 99 1555 1555 1.35 LINK C ACE A 98 N BGLN A 99 1555 1555 1.29 LINK C ACE B 98 N AGLN B 99 1555 1555 1.29 LINK C ACE B 98 N BGLN B 99 1555 1555 1.38 SITE 1 AC1 7 ASN A 104 ARG A 125 TRP A 126 HOH A 324 SITE 2 AC1 7 HOH A 332 ARG B 107 HOH B 345 SITE 1 AC2 3 ARG A 122 HOH A 344 ARG B 111 SITE 1 AC3 9 HOH A 334 HOH A 351 ASN B 104 LEU B 105 SITE 2 AC3 9 TRP B 108 TRP B 126 ARG B 129 LEU B 130 SITE 3 AC3 9 HOH B 323 SITE 1 AC4 15 LEU A 130 GLU A 131 SER A 132 HOH A 304 SITE 2 AC4 15 HOH A 320 GLU B 100 THR B 101 ILE B 102 SITE 3 AC4 15 ALA B 103 ARG B 125 HOH B 302 HOH B 322 SITE 4 AC4 15 HOH B 327 HOH B 330 HOH B 342 SITE 1 AC5 15 LEU A 130 GLU A 131 SER A 132 HOH A 304 SITE 2 AC5 15 HOH A 320 GLU B 100 THR B 101 ILE B 102 SITE 3 AC5 15 ALA B 103 ARG B 125 HOH B 302 HOH B 322 SITE 4 AC5 15 HOH B 327 HOH B 330 HOH B 342 CRYST1 26.844 42.556 67.350 90.00 90.00 90.00 P 21 21 21 8 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 0.037252 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014848 0.00000 HETATM 1 C ACE A 98 -6.307 9.791 13.351 1.00 10.32 C ANISOU 1 C ACE A 98 1068 1532 1322 8 -245 9 C HETATM 2 O ACE A 98 -6.049 9.927 14.540 1.00 10.39 O ANISOU 2 O ACE A 98 1139 1607 1200 -176 -228 14 O HETATM 3 CH3 ACE A 98 -7.244 10.707 12.599 1.00 15.03 C ANISOU 3 CH3 ACE A 98 1516 2203 1990 50 -630 227 C