HEADER PROTEIN BINDING 26-MAY-24 9FGY TITLE CRYO-EM STRUCTURE OF LYSOZYME HOMO-DIMER ASSEMBLED BY HOMO DI-GLUEBODY TITLE 2 - LOCAL REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-LYSOZYME GLUEBODY; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LYSOZYME C; COMPND 7 CHAIN: D; COMPND 8 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 9 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 8 ORGANISM_COMMON: CHICKEN; SOURCE 9 ORGANISM_TAXID: 9031 KEYWDS GLUEBODY, NANOBODY, CRYO-EM SPA, SMALL PROTEIN, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR G.YI,M.YE,D.MAMALIS,L.CARRIQUE,M.FAIRHEAD,H.LI,K.DUERR,P.ZHANG, AUTHOR 2 D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT REVDAT 2 24-DEC-25 9FGY 1 JRNL REVDAT 1 11-JUN-25 9FGY 0 JRNL AUTH G.YI,D.MAMALIS,M.YE,L.CARRIQUE,M.FAIRHEAD,H.LI,K.L.DUERR, JRNL AUTH 2 P.ZHANG,D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT JRNL TITL COVALENTLY CONSTRAINED 'DI-GEMBODIES' ENABLE PARALLEL JRNL TITL 2 STRUCTURE SOLUTIONS BY CRYO-EM. JRNL REF NAT.CHEM.BIOL. 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40817135 JRNL DOI 10.1038/S41589-025-01972-7 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, UCSF CHIMERAX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6BJ2 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.160 REMARK 3 NUMBER OF PARTICLES : 233961 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9FGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1292138880. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : LYSOZYME HOMO-DIMER ASSEMBLED REMARK 245 BY HOMO DI-GLUEBODY GBLYSOZYME - REMARK 245 ONE COPY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 SER C 0 REMARK 465 SER C 127 REMARK 465 LYS D 1 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 LYS D 13 CG CD CE NZ REMARK 470 LYS D 33 CG CD CE NZ 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 TRP D 63 H CYS D 76 1.59 REMARK 500 O PHE C 37 H THR C 95 1.60 REMARK 500 OG1 THR C 35 OH TYR C 114 2.16 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 VAL C 48 -55.30 -123.22 REMARK 500 ASN D 74 57.29 36.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50433 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF LYSOZYME HOMO-DIMER ASSEMBLED BY HOMO DI- REMARK 900 GLUEBODY - LOCAL REFINEMENT DBREF 9FGY C 0 127 PDB 9FGY 9FGY 0 127 DBREF 9FGY D 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 C 128 SER ASP VAL GLN LEU VAL GLU ASN GLY GLY GLY CYS VAL SEQRES 2 C 128 LYS ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 C 128 GLY SER THR ASP SER ILE GLU TYR MET THR TRP PHE ARG SEQRES 4 C 128 GLN ALA PRO GLY LYS ALA ARG GLU GLY VAL ALA ALA LEU SEQRES 5 C 128 TYR THR HIS THR GLY ASN THR TYR TYR THR ASP SER VAL SEQRES 6 C 128 LYS GLY ARG PHE THR ILE SER GLN ASP LYS ALA LYS ASN SEQRES 7 C 128 MET ALA TYR LEU ARG MET ASP SER VAL LYS SER GLU ASP SEQRES 8 C 128 THR ALA ILE TYR THR CYS GLY ALA THR ARG LYS ALA VAL SEQRES 9 C 128 PRO VAL ARG PHE ALA LEU ASP GLN SER SER TYR ASP TYR SEQRES 10 C 128 TRP GLY GLN GLY THR GLN VAL MET VAL SER SER SEQRES 1 D 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 D 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 D 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 D 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 D 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 D 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 D 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 D 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 D 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 D 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET GOL C 201 8 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 HELIX 1 AA1 SER C 27 ILE C 31 5 5 HELIX 2 AA2 LYS C 87 THR C 91 5 5 HELIX 3 AA3 GLY D 4 HIS D 15 1 12 HELIX 4 AA4 SER D 24 ASN D 37 1 14 HELIX 5 AA5 PRO D 79 SER D 85 1 7 HELIX 6 AA6 ILE D 88 SER D 100 1 13 HELIX 7 AA7 ASN D 103 ALA D 107 5 5 HELIX 8 AA8 TRP D 108 ARG D 114 1 7 HELIX 9 AA9 ASP D 119 ARG D 125 5 7 SHEET 1 AA1 4 LEU C 4 ASN C 7 0 SHEET 2 AA1 4 LEU C 18 ALA C 24 -1 O SER C 21 N ASN C 7 SHEET 3 AA1 4 MET C 78 MET C 83 -1 O LEU C 81 N LEU C 20 SHEET 4 AA1 4 THR C 69 ASP C 73 -1 N THR C 69 O ARG C 82 SHEET 1 AA2 6 GLY C 10 CYS C 11 0 SHEET 2 AA2 6 THR C 121 MET C 124 1 O MET C 124 N GLY C 10 SHEET 3 AA2 6 ALA C 92 THR C 99 -1 N TYR C 94 O THR C 121 SHEET 4 AA2 6 TYR C 33 GLN C 39 -1 N PHE C 37 O THR C 95 SHEET 5 AA2 6 GLU C 46 TYR C 52 -1 O VAL C 48 N TRP C 36 SHEET 6 AA2 6 THR C 58 TYR C 60 -1 O TYR C 59 N ALA C 50 SHEET 1 AA3 3 ASN D 44 ARG D 45 0 SHEET 2 AA3 3 THR D 51 TYR D 53 -1 O ASP D 52 N ASN D 44 SHEET 3 AA3 3 ILE D 58 ASN D 59 -1 O ILE D 58 N TYR D 53 SSBOND 1 CYS C 22 CYS C 96 1555 1555 2.03 SSBOND 2 CYS D 6 CYS D 127 1555 1555 2.03 SSBOND 3 CYS D 30 CYS D 115 1555 1555 2.03 SSBOND 4 CYS D 64 CYS D 80 1555 1555 2.03 SSBOND 5 CYS D 76 CYS D 94 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 TER 1857 SER C 126 TER 3765 LEU D 129 HETATM 3766 C1 AGOL C 201 141.878 143.056 173.664 0.20 34.17 C HETATM 3767 O1 AGOL C 201 141.871 143.238 175.045 0.20 35.97 O HETATM 3768 C2 AGOL C 201 143.010 143.941 173.104 0.20 33.52 C HETATM 3769 O2 AGOL C 201 144.249 143.566 173.597 0.20 34.53 O HETATM 3770 C3 AGOL C 201 142.627 145.378 173.519 0.20 34.21 C HETATM 3771 O3 AGOL C 201 141.281 145.540 173.200 0.20 35.01 O HETATM 3772 H31AGOL C 201 142.826 145.506 174.460 0.20 34.78 H HETATM 3773 H32AGOL C 201 143.188 146.013 173.050 0.20 35.04 H CONECT 275 1402 CONECT 1402 275 CONECT 1930 3716 CONECT 2285 3534 CONECT 2792 3019 CONECT 2962 3206 CONECT 3019 2792 CONECT 3206 2962 CONECT 3534 2285 CONECT 3716 1930 CONECT 3766 3767 3768 CONECT 3767 3766 CONECT 3768 3766 3769 3770 CONECT 3769 3768 CONECT 3770 3768 3771 3772 3773 CONECT 3771 3770 CONECT 3772 3770 CONECT 3773 3770 MASTER 156 0 1 9 13 0 0 6 1947 2 18 20 END