HEADER FLUORESCENT PROTEIN 13-FEB-26 28QL TITLE GFP BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DARPIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 8 ORGANISM_TAXID: 6100; SOURCE 9 GENE: GFP; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GFP, DARPIN, SCAFFOLD, FLUORESCENT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,M.FAIRHEAD,O.GITTINS,F.VON DELFT, AUTHOR 2 J.ENDICOTT,M.MARTIN,A.C.W.PIKE,D.B.SAUER,L.S.DLAMINI REVDAT 1 04-MAR-26 28QL 0 JRNL AUTH D.S.M.FERREIRA,M.NOBLE,R.J.ROWLAND,O.GITTINS,M.MARTIN, JRNL AUTH 2 J.ENDICOTT,M.FAIRHEAD,F.VON DELFT,A.C.W.PIKE,D.B.SAUER, JRNL AUTH 3 L.S.DLAMINI JRNL TITL AN ENGINEERED SYMMETRICAL SCAFFOLD SYSTEM ENABLES HIGH JRNL TITL 2 RESOLUTION IMAGING OF SMALL CARGO PROTEINS BY CRYO-ELECTRON JRNL TITL 3 MICROSCOPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL 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) : 2.720 REMARK 3 NUMBER OF PARTICLES : 240603 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 28QL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1292153825. 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 : GFP BOUND TO DARPIN ON AN AHIR REMARK 245 DODECAMER SCAFFOLD SYSTEM.; REMARK 245 DARPIN; GREEN FLUORESCENT REMARK 245 PROTEIN 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5050.00 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 A 1 REMARK 465 SER A 2 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 GLN B 67 1.47 -64.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-56749 RELATED DB: EMDB REMARK 900 GFP BOUND TO DISTAL DARPIN (AHIR DODECAMER SCAFFOLD SYSTEM) DBREF 28QL A 1 163 PDB 28QL 28QL 1 163 DBREF1 28QL B 1 227 UNP A0A059PIQ0_AEQVI DBREF2 28QL B A0A059PIQ0 3 229 SEQADV 28QL ARG B 28 UNP A0A059PIQ SER 30 CONFLICT SEQADV 28QL SER B 70 UNP A0A059PIQ ALA 72 CONFLICT SEQADV 28QL ARG B 78 UNP A0A059PIQ GLN 80 CONFLICT SEQRES 1 A 163 MET SER ASP LEU GLY LYS LYS LEU LEU GLU ALA ALA ARG SEQRES 2 A 163 ALA GLY GLN ASP ASP GLU VAL ARG ILE LEU MET ALA ASN SEQRES 3 A 163 GLY ALA ASP VAL ASN ALA ALA ASP ASP VAL GLY VAL THR SEQRES 4 A 163 PRO LEU HIS LEU ALA ALA GLN ARG GLY HIS LEU GLU ILE SEQRES 5 A 163 VAL GLU VAL LEU LEU LYS TYR GLY ALA ASP VAL ASN ALA SEQRES 6 A 163 ALA ASP LEU TRP GLY GLN THR PRO LEU HIS LEU ALA ALA SEQRES 7 A 163 THR ALA GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS SEQRES 8 A 163 ASN GLY ALA ASP VAL ASN ALA ARG ASP ASN ILE GLY HIS SEQRES 9 A 163 THR PRO LEU HIS LEU ALA ALA TRP ALA GLY HIS LEU GLU SEQRES 10 A 163 ILE VAL GLU VAL LEU LEU LYS TYR GLY ALA ASP VAL ASN SEQRES 11 A 163 ALA GLN ASP LYS PHE GLY LYS THR PRO LYS ASP LEU ALA SEQRES 12 A 163 ARG ASP ASN GLY ASN GLU TRP ILE ARG GLU LEU LEU GLU SEQRES 13 A 163 LYS ALA GLU ARG LYS LEU LYS SEQRES 1 B 227 LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO ILE LEU SEQRES 2 B 227 VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS PHE SER SEQRES 3 B 227 VAL ARG GLY GLU GLY GLU GLY ASP ALA THR ASN GLY LYS SEQRES 4 B 227 LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS LEU PRO SEQRES 5 B 227 VAL PRO TRP PRO THR LEU VAL THR THR LEU THR TYR GLY SEQRES 6 B 227 VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET LYS ARG SEQRES 7 B 227 HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL SEQRES 8 B 227 GLN GLU ARG THR ILE SER PHE LYS ASP ASP GLY THR TYR SEQRES 9 B 227 LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU SEQRES 10 B 227 VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU SEQRES 11 B 227 ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN PHE SEQRES 12 B 227 ASN SER HIS ASN VAL TYR ILE THR ALA ASP LYS GLN LYS SEQRES 13 B 227 ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS ASN VAL SEQRES 14 B 227 GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR GLN GLN SEQRES 15 B 227 ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP SEQRES 16 B 227 ASN HIS TYR LEU SER THR GLN SER ALA LEU SER LYS ASP SEQRES 17 B 227 PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU PHE SEQRES 18 B 227 VAL THR ALA ALA GLY ILE HELIX 1 AA1 ASP A 3 GLY A 15 1 13 HELIX 2 AA2 GLN A 16 ASN A 26 1 11 HELIX 3 AA3 THR A 39 GLY A 48 1 10 HELIX 4 AA4 HIS A 49 TYR A 59 1 11 HELIX 5 AA5 THR A 72 GLY A 81 1 10 HELIX 6 AA6 HIS A 82 ASN A 92 1 11 HELIX 7 AA7 THR A 105 GLY A 114 1 10 HELIX 8 AA8 HIS A 115 TYR A 125 1 11 HELIX 9 AA9 THR A 138 GLY A 147 1 10 HELIX 10 AB1 ASN A 148 LYS A 163 1 16 HELIX 11 AB2 GLY B 2 THR B 7 5 6 HELIX 12 AB3 TRP B 55 TYR B 64 1 10 HELIX 13 AB4 VAL B 66 SER B 70 5 5 HELIX 14 AB5 PRO B 73 HIS B 79 5 7 HELIX 15 AB6 ASP B 80 ALA B 85 1 6 SHEET 1 AA112 VAL B 9 VAL B 20 0 SHEET 2 AA112 HIS B 23 ASP B 34 -1 O GLY B 33 N VAL B 10 SHEET 3 AA112 LYS B 39 CYS B 46 -1 O ILE B 45 N ARG B 28 SHEET 4 AA112 HIS B 215 ALA B 225 -1 O LEU B 218 N LEU B 42 SHEET 5 AA112 HIS B 197 SER B 206 -1 N SER B 200 O THR B 223 SHEET 6 AA112 HIS B 146 ASP B 153 -1 N HIS B 146 O THR B 201 SHEET 7 AA112 GLY B 158 ASN B 168 -1 O LYS B 160 N THR B 151 SHEET 8 AA112 VAL B 174 PRO B 185 -1 O GLN B 175 N HIS B 167 SHEET 9 AA112 TYR B 90 PHE B 98 -1 N VAL B 91 O THR B 184 SHEET 10 AA112 THR B 103 GLU B 113 -1 O VAL B 110 N TYR B 90 SHEET 11 AA112 THR B 116 ILE B 126 -1 O VAL B 118 N LYS B 111 SHEET 12 AA112 VAL B 9 VAL B 20 1 N GLU B 15 O ILE B 121 CISPEP 1 MET B 86 PRO B 87 0 0.63 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 MASTER 129 0 0 15 12 0 0 6 3025 2 0 31 END