HEADER HYDROLASE 02-JAN-24 8RLB TITLE RECQL5: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 G5-006; COMPND 11 CHAIN: K; 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 RECQL5, DI-GLUEBODY, HYDROLASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.YI,M.YE,D.MAMALIS,M.FAIRHEAD,D.B.SAUER,F.VON DELFT,B.G.DAVIS, AUTHOR 2 R.J.C.GILBERT REVDAT 1 15-JAN-25 8RLB 0 JRNL AUTH G.YI,D.MAMALIS,M.YE,L.CARRIQUE,M.FAIRHEAD,H.LI,K.DUERR, JRNL AUTH 2 P.ZHANG,D.B.SAUER,F.VON DELFT,B.G.DAVIS,R.J.C.GILBERT JRNL TITL DI-GLUEBODIES: RIGID MODULAR NANOBODY PROTEIN ASSEMBLIES JRNL TITL 2 ENABLING SIMULTANEOUS DETERMINATION OF HIGH-RESOLUTION JRNL TITL 3 CRYO-EM STRUCTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, 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 : 103.600 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 359811 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 8RLB 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_1292135657. 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 THE SFGFP REMARK 245 PART OF THE RECQL5:SFGFP REMARK 245 HETERODIMER ASSEMBLED BY THE DI- REMARK 245 GLUEBODY; GREEN FLUORESCENT REMARK 245 PROTEIN; DI-GLUEBODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.10 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 G5-006 WERE REMARK 245 ASSEMBLED VIA A DISULFIDE TO FORM A HETERO DI-GLUEBODY; GREEN REMARK 245 FLUORESCENT PROTEIN; GLUEBODY GBENHANCER AND GLUEBODY G5-006 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10102 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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) : 4200.00 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, K 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 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 K -2 REMARK 465 MET K -1 REMARK 465 ALA K 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 LYS B 52 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 ARG D 56 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 75 CG CD NE CZ NH1 NH2 REMARK 470 VAL K 5 CG1 CG2 REMARK 470 VAL K 12 CG1 CG2 REMARK 470 LYS K 13 CG CD CE NZ REMARK 470 SER K 17 OG REMARK 470 LEU K 20 CG CD1 CD2 REMARK 470 CYS K 22 SG REMARK 470 GLU K 44 CG CD OE1 OE2 REMARK 470 GLU K 46 CG CD OE1 OE2 REMARK 470 SER K 56 OG REMARK 470 ASN K 73 CG OD1 ND2 REMARK 470 CYS K 95 SG REMARK 470 ASP K 112 CG OD1 OD2 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 ASN B 144 146.67 -170.13 REMARK 500 ASN D 82A -126.75 52.60 REMARK 500 PHE D 98 -121.69 56.04 REMARK 500 ARG K 33 141.63 -170.75 REMARK 500 ASN K 76 42.56 35.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19337 RELATED DB: EMDB REMARK 900 RECQL5:SFGFP HETERO DIMER ASSEMBLED BY DI-GLUEBODY - SFGFP LOCAL REMARK 900 REFINEMENT DBREF1 8RLB B 1 238 UNP A0A059PIQ0_AEQVI DBREF2 8RLB B A0A059PIQ0 1 238 DBREF 8RLB D 1 110 PDB 8RLB 8RLB 1 110 DBREF 8RLB K -2 124 PDB 8RLB 8RLB -2 124 SEQADV 8RLB SER B 2 UNP A0A059PIQ ARG 2 CONFLICT SEQADV 8RLB ARG B 30 UNP A0A059PIQ SER 30 CONFLICT SEQADV 8RLB SER B 72 UNP A0A059PIQ ALA 72 CONFLICT SEQADV 8RLB ARG B 80 UNP A0A059PIQ GLN 80 CONFLICT SEQADV 8RLB 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 K 127 SER MET ALA GLN VAL GLN LEU VAL GLU ASN GLY GLY GLY SEQRES 2 K 127 CYS VAL LYS ALA GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 K 127 ALA SER GLY SER ILE PHE SER ILE ASN ARG MET THR TRP SEQRES 4 K 127 TYR ARG GLN ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA SEQRES 5 K 127 ALA ILE THR SER GLY GLY SER THR ASN TYR ALA ASP SER SEQRES 6 K 127 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA GLU SEQRES 7 K 127 ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 K 127 ASP THR ALA VAL TYR TYR CYS GLU ALA TYR GLY THR TYR SEQRES 9 K 127 THR LEU ALA PRO THR GLY GLU GLY GLU TYR ASP ASP TYR SEQRES 10 K 127 TRP GLY GLN GLY THR GLN VAL MET VAL SER HELIX 1 AA1 GLU B 5 THR B 9 5 5 HELIX 2 AA2 PRO B 56 THR B 65 1 10 HELIX 3 AA3 MET B 78 HIS B 81 5 4 HELIX 4 AA4 ASP B 82 MET B 88 1 7 HELIX 5 AA5 LYS D 83 ALA D 88 5 6 SHEET 1 AA112 VAL B 12 VAL B 22 0 SHEET 2 AA112 HIS B 25 ASP B 36 -1 O GLY B 31 N VAL B 16 SHEET 3 AA112 LYS B 41 CYS B 48 -1 O ILE B 47 N ARG B 30 SHEET 4 AA112 VAL B 219 ALA B 227 -1 O LEU B 220 N LEU B 44 SHEET 5 AA112 HIS B 199 SER B 208 -1 N SER B 202 O THR B 225 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 TYR B 106 N ILE B 98 SHEET 11 AA112 THR B 118 ILE B 128 -1 O THR B 118 N GLU B 115 SHEET 12 AA112 VAL B 12 VAL B 22 1 N GLU B 17 O ASN B 121 SHEET 1 AA2 4 GLN D 3 ASN D 7 0 SHEET 2 AA2 4 LEU D 20 SER D 25 -1 O ALA D 23 N VAL D 5 SHEET 3 AA2 4 THR D 77 LEU D 80 -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 MET D 34 O MET D 51 SHEET 4 AA3 4 VAL D 89 ASN D 93 -1 O ASN D 93 N ARG D 35 SHEET 1 AA4 4 LEU K 4 ASN K 7 0 SHEET 2 AA4 4 ARG K 19 ALA K 24 -1 O ALA K 23 N VAL K 5 SHEET 3 AA4 4 THR K 77 MET K 82 -1 O LEU K 80 N LEU K 20 SHEET 4 AA4 4 PHE K 67 ASP K 72 -1 N SER K 70 O TYR K 79 SHEET 1 AA5 5 SER K 30 ILE K 31 0 SHEET 2 AA5 5 VAL K 92 LEU K 103 -1 O TYR K 101 N SER K 30 SHEET 3 AA5 5 ARG K 33 GLN K 39 -1 N GLN K 39 O VAL K 92 SHEET 4 AA5 5 GLU K 46 THR K 52 -1 O VAL K 48 N TRP K 36 SHEET 5 AA5 5 THR K 57 TYR K 59 -1 O ASN K 58 N ALA K 50 SHEET 1 AA6 3 SER K 30 ILE K 31 0 SHEET 2 AA6 3 VAL K 92 LEU K 103 -1 O TYR K 101 N SER K 30 SHEET 3 AA6 3 GLY K 109 TRP K 115 -1 O GLU K 110 N THR K 102 SSBOND 1 CYS D 11 CYS K 11 1555 1555 2.03 SSBOND 2 CYS D 22 CYS D 92 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