HEADER STRUCTURAL PROTEIN 02-MAY-24 9BNC TITLE COLLAGEN XVIII TRIMERIZATION DOMAIN WITH INTRODUCED INTER-CHAIN TITLE 2 DISULFIDE BOND, E31C-V37C COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN ALPHA-1(XVIII) CHAIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: TRIMERIZATION DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: COL18A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRIMER, DISULFIDE, BIOLOGIC SCAFFOLD, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YOUNG REVDAT 2 29-OCT-25 9BNC 1 JRNL REVDAT 1 27-AUG-25 9BNC 0 JRNL AUTH J.GONZALES,T.YOUNG,H.CHOI,M.PARK,Y.JEWEL,C.FAN,R.PUROHIT, JRNL AUTH 2 P.J.BJORKMAN,J.C.WILLIAMS JRNL TITL DEVELOPMENT OF AN ULTRAHIGH AFFINITY, TRIMERIC ACE2 BIOLOGIC JRNL TITL 2 AS A UNIVERSAL SARS-COV-2 ANTAGONIST. JRNL REF COMMUN BIOL V. 8 1428 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 41053501 JRNL DOI 10.1038/S42003-025-08819-W REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 29539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1427 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 32.0100 - 3.0200 1.00 3049 163 0.1663 0.1836 REMARK 3 2 3.0200 - 2.3900 1.00 2949 131 0.1808 0.2114 REMARK 3 3 2.3900 - 2.0900 1.00 2896 144 0.1577 0.1737 REMARK 3 4 2.0900 - 1.9000 1.00 2895 134 0.1637 0.1882 REMARK 3 5 1.9000 - 1.7600 1.00 2848 150 0.1777 0.2061 REMARK 3 6 1.7600 - 1.6600 1.00 2864 146 0.1746 0.2075 REMARK 3 7 1.6600 - 1.5800 1.00 2836 156 0.1773 0.2472 REMARK 3 8 1.5800 - 1.5100 1.00 2853 143 0.1791 0.1934 REMARK 3 9 1.5100 - 1.4500 0.93 2613 134 0.1851 0.2224 REMARK 3 10 1.4500 - 1.4000 0.81 2309 126 0.1934 0.2393 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.26 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 : 0.010 NULL REMARK 3 ANGLE : 1.094 NULL REMARK 3 CHIRALITY : 0.088 207 REMARK 3 PLANARITY : 0.014 251 REMARK 3 DIHEDRAL : 8.020 213 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 9BNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000281383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979338 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29542 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.05122 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21500 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 (%): 36.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M TRIS HCL, REMARK 280 PH 8.5, 25% (W/V) PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 19.18000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.63400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.03900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.63400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.03900 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 ARG A 54 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 LEU A 5 CG CD1 CD2 REMARK 470 ARG A 49 NE CZ NH1 NH2 REMARK 470 LEU A 52 CG CD1 CD2 REMARK 470 PRO A 53 CG CD REMARK 470 GLN B 30 CG CD OE1 NE2 REMARK 470 GLN C 10 CD OE1 NE2 REMARK 470 VAL C 16 CG1 CG2 REMARK 470 GLU C 29 CG CD OE1 OE2 REMARK 470 ARG C 36 NE CZ NH1 NH2 REMARK 470 GLN C 38 CG CD OE1 NE2 REMARK 470 ASN C 39 CG OD1 ND2 REMARK 470 ARG C 54 CG CD NE CZ NH1 NH2 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 SER A 1 -127.67 -125.06 REMARK 500 ASN A 39 48.43 -140.29 REMARK 500 SER B 1 -125.37 -119.26 REMARK 500 SER C 1 -127.70 -123.04 REMARK 500 GLN C 30 -3.38 86.59 REMARK 500 ASN C 39 10.74 82.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 9BNC A -2 54 UNP P39060 COIA1_HUMAN 1440 1496 DBREF 9BNC B -2 54 UNP P39060 COIA1_HUMAN 1440 1496 DBREF 9BNC C -2 54 UNP P39060 COIA1_HUMAN 1440 1496 SEQADV 9BNC GLY A -1 UNP P39060 ALA 1441 CONFLICT SEQADV 9BNC CYS A 31 UNP P39060 GLU 1473 ENGINEERED MUTATION SEQADV 9BNC CYS A 37 UNP P39060 VAL 1479 ENGINEERED MUTATION SEQADV 9BNC GLY B -1 UNP P39060 ALA 1441 CONFLICT SEQADV 9BNC CYS B 31 UNP P39060 GLU 1473 ENGINEERED MUTATION SEQADV 9BNC CYS B 37 UNP P39060 VAL 1479 ENGINEERED MUTATION SEQADV 9BNC GLY C -1 UNP P39060 ALA 1441 CONFLICT SEQADV 9BNC CYS C 31 UNP P39060 GLU 1473 ENGINEERED MUTATION SEQADV 9BNC CYS C 37 UNP P39060 VAL 1479 ENGINEERED MUTATION SEQRES 1 A 57 GLY GLY SER SER GLY VAL ARG LEU TRP ALA THR ARG GLN SEQRES 2 A 57 ALA MET LEU GLY GLN VAL HIS GLU VAL PRO GLU GLY TRP SEQRES 3 A 57 LEU ILE PHE VAL ALA GLU GLN CYS GLU LEU TYR VAL ARG SEQRES 4 A 57 CYS GLN ASN GLY PHE ARG LYS VAL GLN LEU GLU ALA ARG SEQRES 5 A 57 THR PRO LEU PRO ARG SEQRES 1 B 57 GLY GLY SER SER GLY VAL ARG LEU TRP ALA THR ARG GLN SEQRES 2 B 57 ALA MET LEU GLY GLN VAL HIS GLU VAL PRO GLU GLY TRP SEQRES 3 B 57 LEU ILE PHE VAL ALA GLU GLN CYS GLU LEU TYR VAL ARG SEQRES 4 B 57 CYS GLN ASN GLY PHE ARG LYS VAL GLN LEU GLU ALA ARG SEQRES 5 B 57 THR PRO LEU PRO ARG SEQRES 1 C 57 GLY GLY SER SER GLY VAL ARG LEU TRP ALA THR ARG GLN SEQRES 2 C 57 ALA MET LEU GLY GLN VAL HIS GLU VAL PRO GLU GLY TRP SEQRES 3 C 57 LEU ILE PHE VAL ALA GLU GLN CYS GLU LEU TYR VAL ARG SEQRES 4 C 57 CYS GLN ASN GLY PHE ARG LYS VAL GLN LEU GLU ALA ARG SEQRES 5 C 57 THR PRO LEU PRO ARG HET SO4 B 101 5 HET PEG C 101 17 HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 4 SO4 O4 S 2- FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *175(H2 O) HELIX 1 AA1 THR A 8 VAL A 16 1 9 HELIX 2 AA2 HIS A 17 VAL A 19 5 3 HELIX 3 AA3 THR B 8 GLY B 14 1 7 HELIX 4 AA4 GLN B 15 VAL B 19 5 5 HELIX 5 AA5 THR C 8 GLY C 14 1 7 HELIX 6 AA6 GLN C 15 VAL C 19 5 5 SHEET 1 AA1 5 GLY A -1 SER A 0 0 SHEET 2 AA1 5 VAL B 3 TRP B 6 -1 O LEU B 5 N GLY A -1 SHEET 3 AA1 5 LEU B 24 VAL B 27 1 O PHE B 26 N ARG B 4 SHEET 4 AA1 5 GLU B 32 CYS B 37 -1 O TYR B 34 N ILE B 25 SHEET 5 AA1 5 GLY B 40 LYS B 43 -1 O GLY B 40 N CYS B 37 SHEET 1 AA2 5 GLY A 40 LYS A 43 0 SHEET 2 AA2 5 GLU A 32 CYS A 37 -1 N CYS A 37 O GLY A 40 SHEET 3 AA2 5 LEU A 24 VAL A 27 -1 N ILE A 25 O TYR A 34 SHEET 4 AA2 5 VAL A 3 TRP A 6 1 N ARG A 4 O LEU A 24 SHEET 5 AA2 5 GLY C -1 SER C 0 -1 O GLY C -1 N LEU A 5 SHEET 1 AA3 5 GLY B -1 SER B 0 0 SHEET 2 AA3 5 VAL C 3 TRP C 6 -1 O LEU C 5 N GLY B -1 SHEET 3 AA3 5 LEU C 24 VAL C 27 1 O PHE C 26 N ARG C 4 SHEET 4 AA3 5 GLU C 32 CYS C 37 -1 O TYR C 34 N ILE C 25 SHEET 5 AA3 5 GLY C 40 LYS C 43 -1 O ARG C 42 N VAL C 35 SSBOND 1 CYS A 31 CYS C 37 1555 1555 2.05 SSBOND 2 CYS A 37 CYS B 31 1555 1555 2.04 SSBOND 3 CYS B 37 CYS C 31 1555 1555 2.03 CRYST1 38.360 58.078 67.268 90.00 90.00 90.00 P 21 21 21 12 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 0.026069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014866 0.00000 CONECT 550 2461 CONECT 551 2462 CONECT 681 1424 CONECT 1424 681 CONECT 1548 2358 CONECT 2358 1548 CONECT 2461 550 CONECT 2462 551 CONECT 2727 2728 2729 2730 2731 CONECT 2728 2727 CONECT 2729 2727 CONECT 2730 2727 CONECT 2731 2727 CONECT 2732 2733 2734 2739 2740 CONECT 2733 2732 2741 CONECT 2734 2732 2735 2742 2743 CONECT 2735 2734 2736 CONECT 2736 2735 2737 2744 2745 CONECT 2737 2736 2738 2746 2747 CONECT 2738 2737 2748 CONECT 2739 2732 CONECT 2740 2732 CONECT 2741 2733 CONECT 2742 2734 CONECT 2743 2734 CONECT 2744 2736 CONECT 2745 2736 CONECT 2746 2737 CONECT 2747 2737 CONECT 2748 2738 MASTER 251 0 2 6 15 0 0 6 1497 3 30 15 END