HEADER PROTEIN BINDING 24-MAR-22 7XCE TITLE CRYSTAL STRUCTURE OF ANKYRIN G IN COMPLEX WITH NEUROFASCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROFASCIN,ANKYRIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANK-3,ANKYRIN-G; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FUSION PROTEIN OF NEUROFASCIN, LINKER, AND COMPND 7 ANKYRIN-3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: NFASC, ANK3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL ADHESION, STRUCTURAL PROTEIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.HE,J.LI,C.WANG REVDAT 2 29-NOV-23 7XCE 1 REMARK REVDAT 1 21-SEP-22 7XCE 0 JRNL AUTH L.HE,W.JIANG,J.LI,C.WANG JRNL TITL CRYSTAL STRUCTURE OF ANKYRIN-G IN COMPLEX WITH A FRAGMENT OF JRNL TITL 2 NEUROFASCIN REVEALS BINDING MECHANISMS REQUIRED FOR JRNL TITL 3 INTEGRITY OF THE AXON INITIAL SEGMENT. JRNL REF J.BIOL.CHEM. V. 298 02272 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35850303 JRNL DOI 10.1016/J.JBC.2022.102272 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.18.2 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 744 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 34.6000 - 4.2800 0.99 3060 173 0.1713 0.2108 REMARK 3 2 4.2800 - 3.4000 1.00 2948 139 0.1776 0.2145 REMARK 3 3 3.4000 - 2.9700 1.00 2900 148 0.2189 0.2695 REMARK 3 4 2.9700 - 2.7000 1.00 2888 139 0.2367 0.2765 REMARK 3 5 2.7000 - 2.5000 1.00 2871 145 0.2497 0.2974 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.95 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7XCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15440 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.91300 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: 5Y4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 (PH 5.5), 17% W/V POLYETHYLENE GLYCOL 10000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.55050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.93850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.93850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.27525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.93850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.93850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.82575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.93850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.93850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.27525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.93850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.93850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 66.82575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.55050 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 233 REMARK 465 PRO A 234 REMARK 465 GLY A 235 REMARK 465 SER A 236 REMARK 465 GLU A 237 REMARK 465 PHE A 238 REMARK 465 SER A 239 REMARK 465 ASP A 240 REMARK 465 ASP A 241 REMARK 465 SER A 242 REMARK 465 LEU A 243 REMARK 465 VAL A 244 REMARK 465 ASP A 245 REMARK 465 TYR A 246 REMARK 465 GLY A 247 REMARK 465 GLU A 248 REMARK 465 GLY A 249 REMARK 465 GLY A 250 REMARK 465 GLY A 497 REMARK 465 ALA A 498 REMARK 465 GLN A 499 REMARK 465 VAL A 500 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 251 CG CD OE1 OE2 REMARK 470 LEU A 269 CG CD1 CD2 REMARK 470 VAL A 270 CG1 CG2 REMARK 470 ARG A 272 CG CD NE CZ NH1 NH2 REMARK 470 SER A 274 OG REMARK 470 ASN A 275 CG OD1 ND2 REMARK 470 ARG A 307 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 397 CG CD CE NZ REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 ARG A 473 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 483 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 491 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 495 CG CD OE1 NE2 DBREF 7XCE A 239 266 UNP P97685 NFASC_RAT 1187 1214 DBREF 7XCE A 275 500 UNP O70511 ANK3_RAT 275 500 SEQADV 7XCE GLY A 233 UNP P97685 EXPRESSION TAG SEQADV 7XCE PRO A 234 UNP P97685 EXPRESSION TAG SEQADV 7XCE GLY A 235 UNP P97685 EXPRESSION TAG SEQADV 7XCE SER A 236 UNP P97685 EXPRESSION TAG SEQADV 7XCE GLU A 237 UNP P97685 EXPRESSION TAG SEQADV 7XCE PHE A 238 UNP P97685 EXPRESSION TAG SEQADV 7XCE GLY A 267 UNP P97685 LINKER SEQADV 7XCE SER A 268 UNP P97685 LINKER SEQADV 7XCE LEU A 269 UNP P97685 LINKER SEQADV 7XCE VAL A 270 UNP P97685 LINKER SEQADV 7XCE PRO A 271 UNP P97685 LINKER SEQADV 7XCE ARG A 272 UNP P97685 LINKER SEQADV 7XCE GLY A 273 UNP P97685 LINKER SEQADV 7XCE SER A 274 UNP P97685 LINKER SEQRES 1 A 268 GLY PRO GLY SER GLU PHE SER ASP ASP SER LEU VAL ASP SEQRES 2 A 268 TYR GLY GLU GLY GLY GLU GLY GLN PHE ASN GLU ASP GLY SEQRES 3 A 268 SER PHE ILE GLY GLN TYR THR VAL GLY SER LEU VAL PRO SEQRES 4 A 268 ARG GLY SER ASN ASP ILE THR PRO LEU HIS VAL ALA SER SEQRES 5 A 268 LYS ARG GLY ASN ALA ASN MET VAL LYS LEU LEU LEU ASP SEQRES 6 A 268 ARG GLY ALA LYS ILE ASP ALA LYS THR ARG ASP GLY LEU SEQRES 7 A 268 THR PRO LEU HIS CYS GLY ALA ARG SER GLY HIS GLU GLN SEQRES 8 A 268 VAL VAL GLU MET LEU LEU ASP ARG ALA ALA PRO ILE LEU SEQRES 9 A 268 SER LYS THR LYS ASN GLY LEU SER PRO LEU HIS MET ALA SEQRES 10 A 268 THR GLN GLY ASP HIS LEU ASN CYS VAL GLN LEU LEU LEU SEQRES 11 A 268 GLN HIS ASN VAL PRO VAL ASP ASP VAL THR ASN ASP TYR SEQRES 12 A 268 LEU THR ALA LEU HIS VAL ALA ALA HIS CYS GLY HIS TYR SEQRES 13 A 268 LYS VAL ALA LYS VAL LEU LEU ASP LYS LYS ALA ASN PRO SEQRES 14 A 268 ASN ALA LYS ALA LEU ASN GLY PHE THR PRO LEU HIS ILE SEQRES 15 A 268 ALA CYS LYS LYS ASN ARG ILE ARG VAL MET GLU LEU LEU SEQRES 16 A 268 LEU LYS HIS GLY ALA SER ILE GLN ALA VAL THR GLU SER SEQRES 17 A 268 GLY LEU THR PRO ILE HIS VAL ALA ALA PHE MET GLY HIS SEQRES 18 A 268 VAL ASN ILE VAL SER GLN LEU MET HIS HIS GLY ALA SER SEQRES 19 A 268 PRO ASN THR THR ASN VAL ARG GLY GLU THR ALA LEU HIS SEQRES 20 A 268 MET ALA ALA ARG SER GLY GLN ALA GLU VAL VAL ARG TYR SEQRES 21 A 268 LEU VAL GLN ASP GLY ALA GLN VAL HET SO4 A 601 5 HET GOL A 602 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *30(H2 O) HELIX 1 AA1 GLU A 251 ASN A 255 5 5 HELIX 2 AA2 THR A 278 GLY A 287 1 10 HELIX 3 AA3 ASN A 288 ARG A 298 1 11 HELIX 4 AA4 THR A 311 SER A 319 1 9 HELIX 5 AA5 HIS A 321 ARG A 331 1 11 HELIX 6 AA6 SER A 344 GLY A 352 1 9 HELIX 7 AA7 HIS A 354 HIS A 364 1 11 HELIX 8 AA8 THR A 377 GLY A 386 1 10 HELIX 9 AA9 HIS A 387 LYS A 397 1 11 HELIX 10 AB1 THR A 410 LYS A 418 1 9 HELIX 11 AB2 ARG A 420 HIS A 430 1 11 HELIX 12 AB3 THR A 443 GLY A 452 1 10 HELIX 13 AB4 HIS A 453 HIS A 463 1 11 HELIX 14 AB5 THR A 476 GLY A 485 1 10 HELIX 15 AB6 GLN A 486 ASP A 496 1 11 CRYST1 97.877 97.877 89.101 90.00 90.00 90.00 P 41 21 2 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 0.010217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011223 0.00000