HEADER HYDROLASE 02-JAN-24 8RLE TITLE SPNS2:SFGFP HETERO DIMER ASSEMBLED BY DI-GLUEBODY - SFGFP LOCAL TITLE 2 REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLUEBODY GBENHANCER; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: GLUEBODY GBC4; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_TAXID: 6100; SOURCE 4 GENE: GFP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 9 ORGANISM_TAXID: 9844; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 14 ORGANISM_TAXID: 9844; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA HELICASE, DI-GLUEBODY, HYDROLASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.YI,M.YE,D.MAMALIS,D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT REVDAT 2 24-DEC-25 8RLE 1 JRNL REVDAT 1 15-JAN-25 8RLE 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. 3.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3K1K REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 154.900 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) : 3.750 REMARK 3 NUMBER OF PARTICLES : 321178 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 8RLE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135660. 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 : LOCAL REFINEMENT OF GFP PART OF REMARK 245 THE SPNS2:SFGFP HETERODIMER REMARK 245 ASSEMBLED BY DI-GLUEBODY; GREEN REMARK 245 FLUORESCENT PROTEIN; DI-GLUEBODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.20 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 : GBENHANCER AND GBC4 WERE REMARK 245 ASSEMBLED VIA A DISULFIDE TO FORM A HETERO DI-GLUEBODY; GREEN REMARK 245 FLUORESCENT PROTEIN; GLUEBODY GBENHANCER AND GLUEBODY GBC4 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 8674 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) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, 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 MET B 1 REMARK 465 SER B 2 REMARK 465 LYS B 3 REMARK 465 GLY B 4 REMARK 465 GLU B 5 REMARK 465 GLU B 6 REMARK 465 LEU B 7 REMARK 465 GLY B 228 REMARK 465 ILE B 229 REMARK 465 THR B 230 REMARK 465 HIS B 231 REMARK 465 GLY B 232 REMARK 465 MET B 233 REMARK 465 ASP B 234 REMARK 465 GLU B 235 REMARK 465 LEU B 236 REMARK 465 TYR B 237 REMARK 465 LYS B 238 REMARK 465 SER C 0 REMARK 465 GLN C 1 REMARK 465 GLY C 2 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 VAL B 11 CG1 CG2 REMARK 470 VAL B 12 CG1 CG2 REMARK 470 PRO B 13 CG CD REMARK 470 ILE B 14 CG1 CG2 CD1 REMARK 470 LEU B 15 CG CD1 CD2 REMARK 470 VAL B 16 CG1 CG2 REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 LEU B 18 CG CD1 CD2 REMARK 470 ASP B 19 CG OD1 OD2 REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 156 CG CD CE NZ REMARK 470 GLN B 157 CG CD OE1 NE2 REMARK 470 LYS B 158 CG CD CE NZ REMARK 470 LYS B 214 CG CD CE NZ REMARK 470 LYS D 13 CG CD CE NZ REMARK 470 ARG D 56 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 75 CG CD NE CZ NH1 NH2 REMARK 470 MET D 82 CG SD CE REMARK 470 LYS D 83 CG CD CE NZ REMARK 470 GLU C 44 CG CD OE1 OE2 REMARK 470 LYS C 64 CG CD CE NZ REMARK 470 MET C 82 CG SD CE REMARK 470 LYS C 86 CG CD CE NZ REMARK 470 GLU C 88 CG CD OE1 OE2 REMARK 470 LYS C 111 CG CD CE NZ 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 ASP B 102 -2.21 76.76 REMARK 500 ASP B 133 -0.57 80.11 REMARK 500 ASN D 82A -128.14 60.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19340 RELATED DB: EMDB REMARK 900 SPNS2:SFGFP HETERO DIMER ASSEMBLED BY DI-GLUEBODY - SFGFP LOCAL REMARK 900 REFINEMENT DBREF1 8RLE B 1 238 UNP A0A059PIQ0_AEQVI DBREF2 8RLE B A0A059PIQ0 1 238 DBREF 8RLE D 1 110 PDB 8RLE 8RLE 1 110 DBREF 8RLE C 0 118 PDB 8RLE 8RLE 0 118 SEQADV 8RLE SER B 2 UNP A0A059PIQ ARG 2 CONFLICT SEQADV 8RLE ARG B 30 UNP A0A059PIQ SER 30 CONFLICT SEQADV 8RLE SER B 72 UNP A0A059PIQ ALA 72 CONFLICT SEQADV 8RLE ARG B 80 UNP A0A059PIQ GLN 80 CONFLICT SEQADV 8RLE VAL B 206 UNP A0A059PIQ ALA 206 CONFLICT SEQRES 1 B 238 MET SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO SEQRES 2 B 238 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 B 238 PHE SER VAL ARG GLY GLU GLY GLU GLY ASP ALA THR ASN SEQRES 4 B 238 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 B 238 LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR LEU THR SEQRES 6 B 238 TYR GLY VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET SEQRES 7 B 238 LYS ARG HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY SEQRES 8 B 238 TYR VAL GLN GLU ARG THR ILE SER PHE LYS ASP ASP GLY SEQRES 9 B 238 THR TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP SEQRES 10 B 238 THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE SEQRES 11 B 238 LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR SEQRES 12 B 238 ASN PHE ASN SER HIS ASN VAL TYR ILE THR ALA ASP LYS SEQRES 13 B 238 GLN LYS ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS SEQRES 14 B 238 ASN VAL GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR SEQRES 15 B 238 GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU SEQRES 16 B 238 PRO ASP ASN HIS TYR LEU SER THR GLN SER VAL LEU SER SEQRES 17 B 238 LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU SEQRES 18 B 238 GLU PHE VAL THR ALA ALA GLY ILE THR HIS GLY MET ASP SEQRES 19 B 238 GLU LEU TYR LYS SEQRES 1 D 114 GLN VAL GLN LEU VAL GLU ASN GLY GLY ALA CYS VAL LYS SEQRES 2 D 114 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 114 PHE PRO VAL ASN ARG TYR SER MET ARG TRP TYR ARG GLN SEQRES 4 D 114 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA GLY MET SER SEQRES 5 D 114 SER ALA GLY ASP ARG SER SER TYR GLU ASP SER VAL LYS SEQRES 6 D 114 GLY ARG PHE THR ILE SER ARG ASP ASP ALA ARG ASN THR SEQRES 7 D 114 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 114 ALA VAL TYR TYR CYS ASN VAL ASN VAL GLY PHE GLU TYR SEQRES 9 D 114 TRP GLY GLN GLY THR GLN VAL MET VAL SER SEQRES 1 C 119 SER GLN GLY GLN LEU VAL GLU ASN GLY GLY GLY CYS VAL SEQRES 2 C 119 LYS ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 C 119 GLN GLY THR LEU SER ASN LEU VAL THR GLY TRP PHE ARG SEQRES 4 C 119 ARG ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ASN ILE SEQRES 5 C 119 GLY ARG ASP GLY LEU THR VAL TYR SER ASN SER VAL LYS SEQRES 6 C 119 GLY ARG PHE THR ILE SER ARG ASP ARG ALA LYS ASN THR SEQRES 7 C 119 VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU ASP THR SEQRES 8 C 119 ALA VAL TYR TYR CYS ALA GLY ARG LEU SER ARG PHE PRO SEQRES 9 C 119 GLY GLU TYR ASP TYR TRP SER LYS GLY THR PRO VAL MET SEQRES 10 C 119 VAL SER HELIX 1 AA1 TRP B 57 TYR B 66 1 10 HELIX 2 AA2 PRO B 75 ARG B 80 1 6 HELIX 3 AA3 ALA B 87 GLU B 90 5 4 HELIX 4 AA4 GLY B 134 HIS B 139 1 6 HELIX 5 AA5 LYS D 83 ALA D 88 5 6 HELIX 6 AA6 ASN C 61 LYS C 64 5 4 HELIX 7 AA7 LYS C 86 THR C 90 5 5 SHEET 1 AA112 VAL B 11 VAL B 22 0 SHEET 2 AA112 HIS B 25 ASP B 36 -1 O GLY B 33 N ILE B 14 SHEET 3 AA112 LYS B 41 CYS B 48 -1 O THR B 43 N GLU B 34 SHEET 4 AA112 VAL B 219 ALA B 227 -1 O LEU B 220 N LEU B 44 SHEET 5 AA112 ASN B 198 SER B 208 -1 N SER B 208 O VAL B 219 SHEET 6 AA112 HIS B 148 ASP B 155 -1 N HIS B 148 O THR B 203 SHEET 7 AA112 GLY B 160 ASN B 170 -1 O LYS B 162 N THR B 153 SHEET 8 AA112 VAL B 176 PRO B 187 -1 O HIS B 181 N PHE B 165 SHEET 9 AA112 TYR B 92 SER B 99 -1 N GLU B 95 O GLN B 184 SHEET 10 AA112 THR B 105 GLU B 115 -1 O ALA B 110 N GLN B 94 SHEET 11 AA112 THR B 118 ILE B 128 -1 O VAL B 120 N LYS B 113 SHEET 12 AA112 VAL B 11 VAL B 22 1 N ASP B 21 O LEU B 125 SHEET 1 AA2 4 GLN D 3 ASN D 7 0 SHEET 2 AA2 4 ARG D 19 SER D 25 -1 O ALA D 23 N VAL D 5 SHEET 3 AA2 4 THR D 77 GLN D 81 -1 O VAL D 78 N CYS D 22 SHEET 4 AA2 4 SER D 70 ASP D 72 -1 N SER D 70 O TYR D 79 SHEET 1 AA3 4 SER D 57 TYR D 59 0 SHEET 2 AA3 4 GLU D 46 MET D 51 -1 N GLY D 50 O SER D 58 SHEET 3 AA3 4 MET D 34 GLN D 39 -1 N ARG D 38 O GLU D 46 SHEET 4 AA3 4 VAL D 89 ASN D 93 -1 O ASN D 93 N ARG D 35 SHEET 1 AA4 4 LEU C 4 ASN C 7 0 SHEET 2 AA4 4 ARG C 19 ALA C 24 -1 O ALA C 23 N VAL C 5 SHEET 3 AA4 4 THR C 77 MET C 82 -1 O LEU C 80 N LEU C 20 SHEET 4 AA4 4 PHE C 67 ASP C 72 -1 N THR C 68 O GLN C 81 SHEET 1 AA5 4 THR C 57 TYR C 59 0 SHEET 2 AA5 4 GLU C 46 ILE C 51 -1 N ASN C 50 O VAL C 58 SHEET 3 AA5 4 VAL C 33 ARG C 39 -1 N ARG C 38 O GLU C 46 SHEET 4 AA5 4 VAL C 92 ARG C 98 -1 O TYR C 94 N PHE C 37 SSBOND 1 CYS D 11 CYS C 11 1555 1555 2.03 SSBOND 2 CYS D 22 CYS D 92 1555 1555 2.03 SSBOND 3 CYS C 22 CYS C 95 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 3263 ALA B 227 TER 4923 SER D 110 TER 6621 SER C 118 CONECT 3409 5031 CONECT 3554 4649 CONECT 4649 3554 CONECT 5031 3409 CONECT 5187 6274 CONECT 6274 5187 MASTER 186 0 0 7 28 0 0 6 3428 3 6 38 END