HEADER VIRAL PROTEIN 26-SEP-25 9WYG TITLE CRYSTAL STRUCTURE OF HASTV8 SPIKE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN VP27; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ASTROVIRUS-8; SOURCE 3 ORGANISM_COMMON: HASTV-8; SOURCE 4 ORGANISM_TAXID: 43358; SOURCE 5 GENE: ORF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN ASTROVIRUS (HASTV), SPIKE PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.WANG,Y.XU,S.J.ZHANG REVDAT 1 11-FEB-26 9WYG 0 JRNL AUTH W.WANG,Y.XU,S.J.ZHANG JRNL TITL CRYSTAL STRUCTURE OF HASTV8 SPIKE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.44 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37035 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 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 33.3800 - 3.3900 1.00 2896 155 0.1538 0.1724 REMARK 3 2 3.3900 - 2.6900 1.00 2783 120 0.1582 0.2033 REMARK 3 3 2.6900 - 2.3500 1.00 2754 133 0.1706 0.2173 REMARK 3 4 2.3500 - 2.1400 1.00 2719 145 0.1457 0.1975 REMARK 3 5 2.1400 - 1.9800 1.00 2713 137 0.1471 0.1834 REMARK 3 6 1.9800 - 1.8700 1.00 2678 143 0.1483 0.2007 REMARK 3 7 1.8700 - 1.7700 1.00 2729 116 0.1480 0.2204 REMARK 3 8 1.7700 - 1.7000 1.00 2686 148 0.1725 0.2337 REMARK 3 9 1.7000 - 1.6300 1.00 2684 123 0.1867 0.2440 REMARK 3 10 1.6300 - 1.5700 1.00 2672 145 0.1873 0.2232 REMARK 3 11 1.5700 - 1.5300 1.00 2668 131 0.2168 0.2819 REMARK 3 12 1.5300 - 1.4800 1.00 2680 148 0.2839 0.3209 REMARK 3 13 1.4800 - 1.4400 0.98 2613 116 0.3786 0.3721 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 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 : 0.004 1805 REMARK 3 ANGLE : 0.725 2486 REMARK 3 CHIRALITY : 0.081 282 REMARK 3 PLANARITY : 0.005 318 REMARK 3 DIHEDRAL : 6.170 249 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 9WYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300064142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-25 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 443248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.96 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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 (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 30% W/V REMARK 280 POLYETHYLENE GLYCOL 1,000, LIQUID DIFFUSION, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 33.37850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.85450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.37850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.85450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: 3510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1011 LIES ON A SPECIAL POSITION. 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 475 REMARK 465 ALA A 476 REMARK 465 THR A 477 REMARK 465 PRO A 478 REMARK 465 MET A 479 REMARK 465 THR A 480 REMARK 465 PHE A 481 REMARK 465 GLY A 482 REMARK 465 ARG A 483 REMARK 465 SER A 484 REMARK 465 ILE A 485 REMARK 465 PRO A 486 REMARK 465 GLU A 487 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 490 CD OE1 OE2 REMARK 470 MET A 502 SD CE REMARK 470 ASN A 508 CG OD1 ND2 REMARK 470 LEU A 532 CG CD1 CD2 REMARK 470 GLU A 533 CD OE1 OE2 REMARK 470 GLU A 545 CD OE1 OE2 REMARK 470 PHE A 554 CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 558 OD1 OD2 REMARK 470 ASP A 633 CG OD1 OD2 REMARK 470 ARG A 678 NE CZ NH1 NH2 REMARK 470 GLU A 699 CD OE1 OE2 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 HOH A 946 O HOH A 953 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 693 -4.01 80.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 9WYG A 475 706 UNP Q9IFX1 CAPSD_HASV8 415 646 SEQADV 9WYG LEU A 707 UNP Q9IFX1 EXPRESSION TAG SEQRES 1 A 233 GLY ALA THR PRO MET THR PHE GLY ARG SER ILE PRO GLU SEQRES 2 A 233 PRO GLY GLU GLN PHE ARG VAL LEU LEU THR VAL GLY PRO SEQRES 3 A 233 PRO MET ALA PRO ASN THR ALA ASN SER GLN ASN TRP VAL SEQRES 4 A 233 ASN LYS THR ILE VAL PRO PRO GLU ASN GLN TYR THR VAL SEQRES 5 A 233 LYS ILE GLY ILE ASP LEU GLU HIS TYR THR THR MET GLN SEQRES 6 A 233 GLY PHE THR PRO VAL GLU SER VAL SER TRP TYR THR ALA SEQRES 7 A 233 ASP PHE GLN PRO SER ASP GLU PRO SER PRO ILE PRO GLY SEQRES 8 A 233 LEU TYR ALA ARG VAL ASN ASN THR LYS LYS ALA ASP VAL SEQRES 9 A 233 TYR GLY VAL GLN GLN PHE LYS SER SER HIS THR ASN ASN SEQRES 10 A 233 ARG HIS GLN ILE THR SER VAL PHE LEU VAL ARG VAL THR SEQRES 11 A 233 THR SER PHE GLN VAL ILE ASN TYR THR SER TYR PHE ILE SEQRES 12 A 233 ARG GLY ALA GLU SER GLY SER ASN VAL SER ASN LEU LYS SEQRES 13 A 233 ILE ARG ASP GLN THR TYR HIS THR PRO LEU GLN PHE THR SEQRES 14 A 233 GLN GLY LYS TRP TYR LEU LEU THR SER THR VAL MET HIS SEQRES 15 A 233 ASP GLY PRO THR SER SER GLY TRP VAL TRP MET ASN GLN SEQRES 16 A 233 GLU LEU THR ASN ASN ILE ALA TYR ARG VAL ASP PRO GLY SEQRES 17 A 233 MET MET TYR LEU ILE THR PRO PRO PRO ALA ALA SER GLN SEQRES 18 A 233 LEU TYR PHE GLU LEU HIS THR VAL LEU PRO GLN LEU FORMUL 2 HOH *231(H2 O) SHEET 1 AA1 8 TYR A 535 THR A 537 0 SHEET 2 AA1 8 VAL A 526 GLY A 529 -1 N ILE A 528 O THR A 536 SHEET 3 AA1 8 TYR A 567 VAL A 570 -1 O ARG A 569 N LYS A 527 SHEET 4 AA1 8 THR A 573 SER A 587 -1 O LYS A 575 N ALA A 568 SHEET 5 AA1 8 ARG A 592 VAL A 603 -1 O LEU A 600 N TYR A 579 SHEET 6 AA1 8 TRP A 647 ASP A 657 -1 O SER A 652 N SER A 597 SHEET 7 AA1 8 GLY A 540 THR A 551 -1 N THR A 542 O LEU A 649 SHEET 8 AA1 8 PRO A 556 SER A 557 -1 O SER A 557 N TRP A 549 SHEET 1 AA2 9 TYR A 535 THR A 537 0 SHEET 2 AA2 9 VAL A 526 GLY A 529 -1 N ILE A 528 O THR A 536 SHEET 3 AA2 9 TYR A 567 VAL A 570 -1 O ARG A 569 N LYS A 527 SHEET 4 AA2 9 THR A 573 SER A 587 -1 O LYS A 575 N ALA A 568 SHEET 5 AA2 9 ARG A 592 VAL A 603 -1 O LEU A 600 N TYR A 579 SHEET 6 AA2 9 TRP A 647 ASP A 657 -1 O SER A 652 N SER A 597 SHEET 7 AA2 9 GLY A 540 THR A 551 -1 N THR A 542 O LEU A 649 SHEET 8 AA2 9 PHE A 492 VAL A 498 -1 N THR A 497 O GLU A 545 SHEET 9 AA2 9 GLN A 695 LEU A 700 -1 O LEU A 696 N LEU A 496 SHEET 1 AA3 3 VAL A 513 ASN A 514 0 SHEET 2 AA3 3 PHE A 607 SER A 614 -1 O SER A 614 N VAL A 513 SHEET 3 AA3 3 TYR A 636 PHE A 642 -1 O LEU A 640 N VAL A 609 SHEET 1 AA4 2 PHE A 616 ILE A 617 0 SHEET 2 AA4 2 LYS A 630 ILE A 631 -1 O LYS A 630 N ILE A 617 CISPEP 1 ALA A 503 PRO A 504 0 9.35 CRYST1 66.757 53.709 56.303 90.00 90.00 90.00 P 21 21 2 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 0.014980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017761 0.00000 MASTER 287 0 0 0 22 0 0 6 1957 1 0 18 END