HEADER STRUCTURAL PROTEIN 24-AUG-22 8AU0 TITLE CRYSTAL STRUCTURE OF THE A1 LUMINAL COILED-COIL DOMAIN OF SUN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUN DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PROTEIN UNC-84 HOMOLOG A,SAD1/UNC-84 PROTEIN-LIKE 1; COMPND 5 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: SUN1, KIAA0810, UNC84A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LINC COMPLEX, NUCLEAR STRUCTURE, MICROTUBULES, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GURUSARAN,O.R.DAVIES REVDAT 2 01-MAY-24 8AU0 1 REMARK REVDAT 1 19-JUL-23 8AU0 0 JRNL AUTH M.GURUSARAN,J.J.BIEMANS,C.W.WOOD,O.R.DAVIES JRNL TITL MOLECULAR INSIGHTS INTO LINC COMPLEX ARCHITECTURE THROUGH JRNL TITL 2 THE CRYSTAL STRUCTURE OF A LUMINAL TRIMERIC COILED-COIL JRNL TITL 3 DOMAIN OF SUN1. JRNL REF FRONT CELL DEV BIOL V. 11 44277 2023 JRNL REFN ESSN 2296-634X JRNL PMID 37416798 JRNL DOI 10.3389/FCELL.2023.1144277 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 5183 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.520 REMARK 3 FREE R VALUE TEST SET COUNT : 286 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 30.3100 - 2.6100 0.96 2799 173 0.2289 0.2464 REMARK 3 2 2.6100 - 2.0700 0.73 2098 113 0.2741 0.2751 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.826 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.98 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 : 0.006 960 REMARK 3 ANGLE : 0.788 1285 REMARK 3 CHIRALITY : 0.032 147 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 15.731 364 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 361 THROUGH 400 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1767 1.5854 9.0464 REMARK 3 T TENSOR REMARK 3 T11: 0.1221 T22: 0.0887 REMARK 3 T33: 0.1227 T12: 0.0184 REMARK 3 T13: 0.0127 T23: -0.0259 REMARK 3 L TENSOR REMARK 3 L11: 3.4806 L22: 0.5768 REMARK 3 L33: 2.6853 L12: -0.0745 REMARK 3 L13: -2.5079 L23: -0.0637 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: 0.0694 S13: -0.0565 REMARK 3 S21: -0.1123 S22: -0.0985 S23: -0.0690 REMARK 3 S31: 0.1202 S32: 0.0372 S33: 0.1089 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 361 THROUGH 401 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7742 8.1208 13.4248 REMARK 3 T TENSOR REMARK 3 T11: 0.0797 T22: 0.1273 REMARK 3 T33: 0.0926 T12: -0.0154 REMARK 3 T13: -0.0346 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 3.4019 L22: 1.0533 REMARK 3 L33: 5.5928 L12: 0.8724 REMARK 3 L13: -3.7348 L23: -0.9954 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: 0.0215 S13: -0.0228 REMARK 3 S21: -0.1171 S22: 0.0673 S23: -0.1174 REMARK 3 S31: -0.0594 S32: 0.2392 S33: -0.0375 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 361 THROUGH 401 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9782 10.3919 7.9716 REMARK 3 T TENSOR REMARK 3 T11: 0.0149 T22: 0.0083 REMARK 3 T33: 0.0015 T12: 0.0289 REMARK 3 T13: 0.0142 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.0014 L22: -0.0006 REMARK 3 L33: 0.0011 L12: -0.0007 REMARK 3 L13: 0.0011 L23: -0.0002 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: 0.0144 S13: 0.0027 REMARK 3 S21: 0.0019 S22: 0.0047 S23: 0.0015 REMARK 3 S31: -0.0054 S32: 0.0064 S33: -0.0137 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 8AU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292125148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-19 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5986 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.069 REMARK 200 RESOLUTION RANGE LOW (A) : 30.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 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: ARCIMBOLDO REMARK 200 STARTING MODEL: IDEAL HELICES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M SODIUM NITRATE, 0.09M DISODIUM REMARK 280 PHOSPHATE, 0.09M AMMONIUM SULFATE, 0.1M IMIDAZOLE PH 6.5, 0.1M REMARK 280 MES (ACID), 37.5% MPD (RACEMIC), 37.5% PEG 1K, 37.5% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING 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 17.99300 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 360 REMARK 465 GLU A 401 REMARK 465 GLY B 360 REMARK 465 GLY C 360 DBREF 8AU0 A 362 401 UNP O94901 SUN1_HUMAN 362 401 DBREF 8AU0 B 362 401 UNP O94901 SUN1_HUMAN 362 401 DBREF 8AU0 C 362 401 UNP O94901 SUN1_HUMAN 362 401 SEQADV 8AU0 GLY A 360 UNP O94901 EXPRESSION TAG SEQADV 8AU0 SER A 361 UNP O94901 EXPRESSION TAG SEQADV 8AU0 GLY B 360 UNP O94901 EXPRESSION TAG SEQADV 8AU0 SER B 361 UNP O94901 EXPRESSION TAG SEQADV 8AU0 GLY C 360 UNP O94901 EXPRESSION TAG SEQADV 8AU0 SER C 361 UNP O94901 EXPRESSION TAG SEQRES 1 A 42 GLY SER MET SER GLY VAL GLU GLN GLN VAL ALA SER LEU SEQRES 2 A 42 SER GLY GLN CYS HIS HIS HIS GLY GLU ASN LEU ARG GLU SEQRES 3 A 42 LEU THR THR LEU LEU GLN LYS LEU GLN ALA ARG VAL ASP SEQRES 4 A 42 GLN MET GLU SEQRES 1 B 42 GLY SER MET SER GLY VAL GLU GLN GLN VAL ALA SER LEU SEQRES 2 B 42 SER GLY GLN CYS HIS HIS HIS GLY GLU ASN LEU ARG GLU SEQRES 3 B 42 LEU THR THR LEU LEU GLN LYS LEU GLN ALA ARG VAL ASP SEQRES 4 B 42 GLN MET GLU SEQRES 1 C 42 GLY SER MET SER GLY VAL GLU GLN GLN VAL ALA SER LEU SEQRES 2 C 42 SER GLY GLN CYS HIS HIS HIS GLY GLU ASN LEU ARG GLU SEQRES 3 C 42 LEU THR THR LEU LEU GLN LYS LEU GLN ALA ARG VAL ASP SEQRES 4 C 42 GLN MET GLU HET 2CO B 376 8 HETNAM 2CO S-HYDROPEROXYCYSTEINE FORMUL 2 2CO C3 H7 N O4 S FORMUL 4 HOH *55(H2 O) HELIX 1 AA1 SER A 361 MET A 400 1 40 HELIX 2 AA2 MET B 362 GLU B 401 1 40 HELIX 3 AA3 MET C 362 GLU C 401 1 40 LINK C GLN B 375 N B2CO B 376 1555 1555 1.32 LINK C B2CO B 376 N HIS B 377 1555 1555 1.33 CRYST1 31.313 35.986 46.095 90.00 104.54 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 0.031936 0.000000 0.008283 0.00000 SCALE2 0.000000 0.027789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022412 0.00000