HEADER IMMUNE SYSTEM 25-MAY-21 7ON5 TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 NEUTRALIZING NANOBODY RE5D06 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY RE5D06; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS NEUTRALIZING VHH, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.AKSU,T.GUTTLER,D.GORLICH REVDAT 3 31-JAN-24 7ON5 1 REMARK REVDAT 2 13-OCT-21 7ON5 1 JRNL REVDAT 1 11-AUG-21 7ON5 0 JRNL AUTH T.GUTTLER,M.AKSU,A.DICKMANNS,K.M.STEGMANN,K.GREGOR,R.REES, JRNL AUTH 2 W.TAXER,O.RYMARENKO,J.SCHUNEMANN,C.DIENEMANN,P.GUNKEL, JRNL AUTH 3 B.MUSSIL,J.KRULL,U.TEICHMANN,U.GROSS,V.C.CORDES, JRNL AUTH 4 M.DOBBELSTEIN,D.GORLICH JRNL TITL NEUTRALIZATION OF SARS-COV-2 BY HIGHLY POTENT, JRNL TITL 2 HYPERTHERMOSTABLE, AND MUTATION-TOLERANT NANOBODIES. JRNL REF EMBO J. V. 40 07985 2021 JRNL REFN ESSN 1460-2075 JRNL PMID 34302370 JRNL DOI 10.15252/EMBJ.2021107985 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41179 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2058 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 42.6200 - 3.0800 1.00 2881 152 0.1602 0.1692 REMARK 3 2 3.0800 - 2.4500 1.00 2710 142 0.1634 0.1787 REMARK 3 3 2.4500 - 2.1400 1.00 2651 140 0.1535 0.1614 REMARK 3 4 2.1400 - 1.9400 1.00 2637 138 0.1341 0.1531 REMARK 3 5 1.9400 - 1.8000 1.00 2624 138 0.1383 0.1657 REMARK 3 6 1.8000 - 1.7000 1.00 2618 139 0.1322 0.1549 REMARK 3 7 1.7000 - 1.6100 1.00 2598 135 0.1187 0.1524 REMARK 3 8 1.6100 - 1.5400 1.00 2577 136 0.1141 0.1537 REMARK 3 9 1.5400 - 1.4800 1.00 2605 138 0.1164 0.1501 REMARK 3 10 1.4800 - 1.4300 1.00 2581 136 0.1239 0.1728 REMARK 3 11 1.4300 - 1.3900 1.00 2580 136 0.1267 0.1670 REMARK 3 12 1.3900 - 1.3500 1.00 2557 134 0.1300 0.1599 REMARK 3 13 1.3500 - 1.3100 1.00 2560 135 0.1388 0.1839 REMARK 3 14 1.3100 - 1.2800 0.98 2521 132 0.1555 0.2073 REMARK 3 15 1.2800 - 1.2500 0.94 2421 127 0.1944 0.2412 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.66 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 7ON5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292114036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 42.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 23.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05427 REMARK 200 FOR THE DATA SET : 38.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 14.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39710 REMARK 200 FOR SHELL : 7.600 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: 7OLZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES: PH 6.0, 200 MM ZINC REMARK 280 ACETATE, 15% (V/V) ETHANOL, VAPOR DIFFUSION, TEMPERATURE 291K 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 72.07750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.30550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.30550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.03875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.30550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.30550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 108.11625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.30550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.30550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.03875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.30550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.30550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 108.11625 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 72.07750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 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 A 458 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 GLU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 GLN A 1 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 96 CB CYS A 96 SG -0.096 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ON5 A -2 127 PDB 7ON5 7ON5 -2 127 SEQRES 1 A 130 GLU GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 A 130 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 A 130 ALA SER GLY ILE THR LEU ASP TYR TYR ALA ILE GLY TRP SEQRES 4 A 130 PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SER SEQRES 5 A 130 ARG ILE ARG SER SER ASP GLY SER THR ASN TYR ALA ASP SEQRES 6 A 130 SER VAL LYS GLY ARG PHE THR MET SER ARG ASP ASN ALA SEQRES 7 A 130 LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 8 A 130 GLU ASP THR ALA VAL TYR TYR CYS ALA TYR GLY PRO LEU SEQRES 9 A 130 THR LYS TYR GLY SER SER TRP TYR TRP PRO TYR GLU TYR SEQRES 10 A 130 ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HET EDO A 201 4 HET EOH A 202 3 HETNAM EDO 1,2-ETHANEDIOL HETNAM EOH ETHANOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 EOH C2 H6 O FORMUL 4 HOH *204(H2 O) HELIX 1 AA1 ASN A 74 LYS A 76 5 3 HELIX 2 AA2 LYS A 87 THR A 91 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 121 VAL A 125 1 O THR A 124 N VAL A 12 SHEET 3 AA2 6 ALA A 92 PRO A 100 -1 N TYR A 94 O THR A 121 SHEET 4 AA2 6 TYR A 32 GLN A 39 -1 N ALA A 33 O GLY A 99 SHEET 5 AA2 6 GLU A 46 ARG A 52 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O ASN A 59 N ARG A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 121 VAL A 125 1 O THR A 124 N VAL A 12 SHEET 3 AA3 4 ALA A 92 PRO A 100 -1 N TYR A 94 O THR A 121 SHEET 4 AA3 4 TYR A 116 TRP A 117 -1 O TYR A 116 N TYR A 98 SHEET 1 AA4 2 THR A 102 TYR A 104 0 SHEET 2 AA4 2 SER A 107 TYR A 109 -1 O TYR A 109 N THR A 102 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.06 CRYST1 44.611 44.611 144.155 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 0.022416 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006937 0.00000