HEADER BIOSYNTHETIC PROTEIN 15-MAY-24 9FCK TITLE 3D CRYO-EM REVEALS THE STRUCTURE OF A 3-FMOC ZIPPER MOTIF ENSURING THE TITLE 2 SELF-ASSEMBLY OF TRIPEPTIDE NANOFIBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: FMO-PHE-PHE-TYR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NANOFIBER, BIOSYNTHETIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.F.ESTROZI,L.JIERRY REVDAT 2 13-NOV-24 9FCK 1 JRNL REVDAT 1 06-NOV-24 9FCK 0 JRNL AUTH A.BIGO-SIMON,L.F.ESTROZI,A.CHAUMONT,R.SCHURHAMMER,G.SCHOEHN, JRNL AUTH 2 J.COMBET,M.SCHMUTZ,P.SCHAAF,L.JIERRY JRNL TITL 3D CRYO-ELECTRON MICROSCOPY REVEALS THE STRUCTURE OF A JRNL TITL 2 3-FLUORENYLMETHYLOXYCARBONYL ZIPPER MOTIF ENSURING THE JRNL TITL 3 SELF-ASSEMBLY OF TRIPEPTIDE NANOFIBERS. JRNL REF ACS NANO V. 18 30448 2024 JRNL REFN ESSN 1936-086X JRNL PMID 39441741 JRNL DOI 10.1021/ACSNANO.4C08043 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, SERIALEM, CTFFIND, RELION, REMARK 3 RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 650000 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 9FCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292138625. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : FMOC-FFY 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 : 9.30 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2182 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 4000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 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 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 H7 VP1 A 201 H9 VP1 B 201 0.83 REMARK 500 H5 VP1 B 201 HE1 PHE B 203 1.16 REMARK 500 H7 VP1 A 201 C13 VP1 B 201 1.53 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 PHE A 203 17.93 86.29 REMARK 500 PHE B 203 10.58 97.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50318 RELATED DB: EMDB REMARK 900 3D CRYO-EM REVEALS THE STRUCTURE OF A 3-FMOC ZIPPER MOTIF ENSURING REMARK 900 THE SELF-ASSEMBLY OF TRIPEPTIDE NANOFIBER DBREF 9FCK A 201 204 PDB 9FCK 9FCK 201 204 DBREF 9FCK B 201 204 PDB 9FCK 9FCK 201 204 SEQRES 1 A 4 VP1 PHE PHE TYR SEQRES 1 B 4 VP1 PHE PHE TYR HET VP1 A 201 28 HET VP1 B 201 28 HETNAM VP1 FLUORENYLMETHYLOXYCARBONYL CHLORIDE FORMUL 1 VP1 2(C15 H11 CL O2) LINK C01 VP1 A 201 N PHE A 202 1555 1555 1.34 LINK C01 VP1 B 201 N PHE B 202 1555 1555 1.34 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 HETATM 1 C01 VP1 A 201 3.050 13.455 5.981 1.00 0.00 C HETATM 2 C04 VP1 A 201 2.514 11.912 7.811 1.00 0.00 C HETATM 3 C05 VP1 A 201 2.191 10.807 6.890 1.00 0.00 C HETATM 4 C06 VP1 A 201 2.843 9.414 6.910 1.00 0.00 C HETATM 5 C07 VP1 A 201 4.145 9.108 6.625 1.00 0.00 C HETATM 6 C08 VP1 A 201 4.434 7.765 6.277 1.00 0.00 C HETATM 7 C09 VP1 A 201 3.489 6.730 6.365 1.00 0.00 C HETATM 8 C10 VP1 A 201 2.184 7.063 6.772 1.00 0.00 C HETATM 9 C11 VP1 A 201 1.893 8.394 6.950 1.00 0.00 C HETATM 10 C12 VP1 A 201 0.780 10.360 7.017 1.00 0.00 C HETATM 11 C13 VP1 A 201 -0.393 11.108 7.042 1.00 0.00 C HETATM 12 C14 VP1 A 201 -1.629 10.468 7.185 1.00 0.00 C HETATM 13 C15 VP1 A 201 -1.622 9.074 7.365 1.00 0.00 C HETATM 14 C16 VP1 A 201 -0.474 8.342 7.266 1.00 0.00 C HETATM 15 C17 VP1 A 201 0.661 8.999 7.116 1.00 0.00 C HETATM 16 O02 VP1 A 201 2.708 12.814 5.046 1.00 0.00 O HETATM 17 O03 VP1 A 201 3.222 12.985 7.260 1.00 0.00 O HETATM 18 H2 VP1 A 201 1.591 12.225 8.299 1.00 0.00 H HETATM 19 H3 VP1 A 201 3.115 11.460 8.601 1.00 0.00 H HETATM 20 H4 VP1 A 201 2.431 11.307 5.952 1.00 0.00 H HETATM 21 H5 VP1 A 201 4.911 9.854 6.473 1.00 0.00 H HETATM 22 H6 VP1 A 201 5.430 7.501 5.948 1.00 0.00 H HETATM 23 H7 VP1 A 201 3.669 5.697 6.101 1.00 0.00 H HETATM 24 H8 VP1 A 201 1.450 6.276 6.858 1.00 0.00 H HETATM 25 H9 VP1 A 201 -0.354 12.186 7.021 1.00 0.00 H HETATM 26 H10 VP1 A 201 -2.520 11.080 7.217 1.00 0.00 H HETATM 27 H11 VP1 A 201 -2.580 8.602 7.527 1.00 0.00 H HETATM 28 H12 VP1 A 201 -0.455 7.275 7.450 1.00 0.00 H TER 91 TYR A 204 HETATM 92 C01 VP1 B 201 8.100 3.838 6.940 1.00 0.00 C HETATM 93 C04 VP1 B 201 5.973 3.572 8.135 1.00 0.00 C HETATM 94 C05 VP1 B 201 5.262 2.575 7.315 1.00 0.00 C HETATM 95 C06 VP1 B 201 4.907 1.146 7.762 1.00 0.00 C HETATM 96 C07 VP1 B 201 5.777 0.126 8.026 1.00 0.00 C HETATM 97 C08 VP1 B 201 5.259 -1.195 7.992 1.00 0.00 C HETATM 98 C09 VP1 B 201 3.890 -1.476 7.857 1.00 0.00 C HETATM 99 C10 VP1 B 201 3.009 -0.393 7.701 1.00 0.00 C HETATM 100 C11 VP1 B 201 3.554 0.863 7.579 1.00 0.00 C HETATM 101 C12 VP1 B 201 3.886 3.011 6.965 1.00 0.00 C HETATM 102 C13 VP1 B 201 3.441 4.227 6.450 1.00 0.00 C HETATM 103 C14 VP1 B 201 2.076 4.425 6.203 1.00 0.00 C HETATM 104 C15 VP1 B 201 1.195 3.389 6.556 1.00 0.00 C HETATM 105 C16 VP1 B 201 1.647 2.176 6.991 1.00 0.00 C HETATM 106 C17 VP1 B 201 2.946 2.041 7.191 1.00 0.00 C HETATM 107 O02 VP1 B 201 7.671 4.301 5.936 1.00 0.00 O HETATM 108 O03 VP1 B 201 7.371 3.540 8.064 1.00 0.00 O HETATM 109 H2 VP1 B 201 5.566 4.555 7.902 1.00 0.00 H HETATM 110 H3 VP1 B 201 5.668 3.370 9.161 1.00 0.00 H HETATM 111 H4 VP1 B 201 5.956 2.532 6.476 1.00 0.00 H HETATM 112 H5 VP1 B 201 6.849 0.255 8.074 1.00 0.00 H HETATM 113 H6 VP1 B 201 5.929 -2.035 8.099 1.00 0.00 H HETATM 114 H7 VP1 B 201 3.458 -2.467 7.819 1.00 0.00 H HETATM 115 H8 VP1 B 201 1.952 -0.593 7.609 1.00 0.00 H HETATM 116 H9 VP1 B 201 4.131 5.043 6.301 1.00 0.00 H HETATM 117 H10 VP1 B 201 1.762 5.385 5.820 1.00 0.00 H HETATM 118 H11 VP1 B 201 0.143 3.579 6.410 1.00 0.00 H HETATM 119 H12 VP1 B 201 0.974 1.391 7.309 1.00 0.00 H TER 182 TYR B 204 CONECT 1 16 17 29 CONECT 2 3 17 18 19 CONECT 3 2 4 10 20 CONECT 4 3 5 9 CONECT 5 4 6 21 CONECT 6 5 7 22 CONECT 7 6 8 23 CONECT 8 7 9 24 CONECT 9 4 8 15 CONECT 10 3 11 15 CONECT 11 10 12 25 CONECT 12 11 13 26 CONECT 13 12 14 27 CONECT 14 13 15 28 CONECT 15 9 10 14 CONECT 16 1 CONECT 17 1 2 CONECT 18 2 CONECT 19 2 CONECT 20 3 CONECT 21 5 CONECT 22 6 CONECT 23 7 CONECT 24 8 CONECT 25 11 CONECT 26 12 CONECT 27 13 CONECT 28 14 CONECT 29 1 CONECT 92 107 108 120 CONECT 93 94 108 109 110 CONECT 94 93 95 101 111 CONECT 95 94 96 100 CONECT 96 95 97 112 CONECT 97 96 98 113 CONECT 98 97 99 114 CONECT 99 98 100 115 CONECT 100 95 99 106 CONECT 101 94 102 106 CONECT 102 101 103 116 CONECT 103 102 104 117 CONECT 104 103 105 118 CONECT 105 104 106 119 CONECT 106 100 101 105 CONECT 107 92 CONECT 108 92 93 CONECT 109 93 CONECT 110 93 CONECT 111 94 CONECT 112 96 CONECT 113 97 CONECT 114 98 CONECT 115 99 CONECT 116 102 CONECT 117 103 CONECT 118 104 CONECT 119 105 CONECT 120 92 MASTER 130 0 2 0 0 0 0 6 104 2 58 2 END