HEADER DE NOVO PROTEIN 18-DEC-23 8VE7 TITLE A DARPIN DISPLAYED ON A DESIGNED TETRAHEDRAL PROTEIN SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DARPIN PROTEIN SCAFFOLD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: WITH A HELICAL CONNECTION TO A CHAIN OF A DESIGNED COMPND 6 PROTEIN SCAFFOLD 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 KEYWDS SCAFFOLD, TETRAHEDRAL, DARPIN, SYMMETRICAL, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.S.SUDER,S.GONEN REVDAT 2 03-JUL-24 8VE7 1 JRNL REVDAT 1 05-JUN-24 8VE7 0 JRNL AUTH D.S.SUDER,S.GONEN JRNL TITL MITIGATING THE BLURRING EFFECT OF CRYOEM AVERAGING ON A JRNL TITL 2 FLEXIBLE AND HIGHLY SYMMETRIC PROTEIN COMPLEX THROUGH JRNL TITL 3 SUB-PARTICLE RECONSTRUCTION. JRNL REF INT J MOL SCI V. 25 2024 JRNL REFN ESSN 1422-0067 JRNL PMID 38891853 JRNL DOI 10.3390/IJMS25115665 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 287323 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: RESOLUTION RANGES DRASTICALLY ACROSS THE MAP, REMARK 3 THOUGH. REMARK 4 REMARK 4 8VE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279999. 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 : DARPIN WITH A HELICAL REMARK 245 CONNECTION TO A CHAIN OF A REMARK 245 DESIGNED PROTEIN SCAFFOLD 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 : 8.00 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 : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 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) : 3000.00 REMARK 245 ILLUMINATION MODE : OTHER 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: MONOMERIC 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 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 OG1 THR A 38 OE1 GLN A 60 2.14 REMARK 500 OG1 THR A 232 ND1 HIS A 235 2.14 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 LYS A 45 4.48 -68.37 REMARK 500 ASP A 49 -167.51 -77.72 REMARK 500 HIS A 219 33.24 -97.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 176 ASP A 177 -146.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8VDZ RELATED DB: PDB REMARK 900 RELATED ID: EMD-43157 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-43158 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-43159 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-43167 RELATED DB: EMDB REMARK 900 A DARPIN DISPLAYED ON A DESIGNED TETRAHEDRAL PROTEIN SCAFFOLD DBREF 8VE7 A 23 316 PDB 8VE7 8VE7 23 316 SEQRES 1 A 294 LYS ASP SER PRO ILE ILE GLU ALA ASN GLY THR LEU ASP SEQRES 2 A 294 GLU LEU THR SER PHE ILE GLY GLU ALA LYS HIS TYR VAL SEQRES 3 A 294 ASP GLU GLU MET LYS GLY ILE LEU GLU GLU ILE GLN ASN SEQRES 4 A 294 ASP ILE TYR LYS ILE MET GLY GLU ILE GLY SER LYS GLY SEQRES 5 A 294 LYS ILE GLU GLY ILE SER GLU GLU ARG ILE ALA TRP LEU SEQRES 6 A 294 LEU LYS LEU ILE LEU ARG TYR MET GLU MET VAL ASN LEU SEQRES 7 A 294 LYS SER PHE VAL LEU PRO GLY GLY THR LEU GLU SER ALA SEQRES 8 A 294 LYS LEU ASP VAL CYS ARG THR ILE ALA ARG ARG ALA LEU SEQRES 9 A 294 ARG LYS VAL LEU THR VAL THR ARG GLU PHE GLY ILE GLY SEQRES 10 A 294 ALA GLU ALA ALA ALA TYR LEU LEU ALA LEU SER ASP LEU SEQRES 11 A 294 LEU PHE LEU LEU ALA ARG VAL ILE GLU ILE GLU LEU GLY SEQRES 12 A 294 LYS LYS LEU LEU GLU ALA ALA ARG ALA GLY GLN ASP ASP SEQRES 13 A 294 GLU VAL ARG ILE LEU MET ALA ASN GLY ALA ASP VAL ASN SEQRES 14 A 294 ALA HIS ASP ASP GLN GLY SER THR PRO LEU HIS LEU ALA SEQRES 15 A 294 ALA TRP ILE GLY HIS PRO GLU ILE VAL GLU VAL LEU LEU SEQRES 16 A 294 LYS HIS GLY ALA ASP VAL ASN ALA ARG ASP THR ASP GLY SEQRES 17 A 294 TRP THR PRO LEU HIS LEU ALA ALA ASP ASN GLY HIS LEU SEQRES 18 A 294 GLU ILE VAL GLU VAL LEU LEU LYS TYR GLY ALA ASP VAL SEQRES 19 A 294 ASN ALA GLN ASP ALA TYR GLY LEU THR PRO LEU HIS LEU SEQRES 20 A 294 ALA ALA ASP ARG GLY HIS LEU GLU ILE VAL GLU VAL LEU SEQRES 21 A 294 LEU LYS HIS GLY ALA ASP VAL ASN ALA GLN ASP LYS PHE SEQRES 22 A 294 GLY LYS THR ALA PHE ASP ILE SER ILE ASP ASN GLY ASN SEQRES 23 A 294 GLU ASP LEU ALA GLU ILE LEU GLN HELIX 1 AA1 ASP A 24 LYS A 45 1 22 HELIX 2 AA2 ASP A 49 SER A 72 1 24 HELIX 3 AA3 SER A 80 MET A 97 1 18 HELIX 4 AA4 THR A 109 GLY A 137 1 29 HELIX 5 AA5 GLY A 139 GLY A 175 1 37 HELIX 6 AA6 GLN A 176 ASN A 186 1 11 HELIX 7 AA7 THR A 199 GLY A 208 1 10 HELIX 8 AA8 HIS A 209 HIS A 219 1 11 HELIX 9 AA9 THR A 232 ASN A 240 1 9 HELIX 10 AB1 HIS A 242 TYR A 252 1 11 HELIX 11 AB2 THR A 265 ARG A 273 1 9 HELIX 12 AB3 HIS A 275 HIS A 285 1 11 HELIX 13 AB4 THR A 298 GLY A 307 1 10 HELIX 14 AB5 ASN A 308 GLN A 316 1 9 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