HEADER PROTEIN FIBRIL 02-JUL-25 9PEF TITLE YG17 PEPTIDE - RIBBON COMPND MOL_ID: 1; COMPND 2 MOLECULE: YG17 PEPTIDE; COMPND 3 CHAIN: J, B, K, L, M, N, O, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NANOMATEIRAL, SHORT-PEPTIDES, CROSS-BETA, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR R.R.SONANI,H.E.DISTAFFEN,E.NIEDZIALKOWSKA,B.L.NILSSON,E.H.EGELMAN REVDAT 1 22-JUL-26 9PEF 0 JRNL AUTH R.R.SONANI,E.H.EGELMAN JRNL TITL YG17 PEPTIDE - RIBBON JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.70 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 168225 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 9PEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000297632. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HELICAL OLIGOMER OF YG17 REMARK 245 PEPTIDES 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 : 7.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: J, B, K, L, M, N, O, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE J 7 O - C - N ANGL. DEV. = -12.5 DEGREES REMARK 500 GLY B 8 C - N - CA ANGL. DEV. = 23.7 DEGREES REMARK 500 PHE K 7 CA - C - N ANGL. DEV. = 19.8 DEGREES REMARK 500 PHE K 7 O - C - N ANGL. DEV. = -24.8 DEGREES REMARK 500 GLY K 8 C - N - CA ANGL. DEV. = 12.9 DEGREES REMARK 500 PHE L 7 O - C - N ANGL. DEV. = -18.9 DEGREES REMARK 500 PHE M 7 CA - C - N ANGL. DEV. = 23.3 DEGREES REMARK 500 PHE M 7 O - C - N ANGL. DEV. = -24.7 DEGREES REMARK 500 GLY M 8 C - N - CA ANGL. DEV. = 27.4 DEGREES REMARK 500 GLY N 8 C - N - CA ANGL. DEV. = -24.7 DEGREES REMARK 500 PHE O 7 CA - C - N ANGL. DEV. = 16.7 DEGREES REMARK 500 PHE O 7 O - C - N ANGL. DEV. = -16.9 DEGREES REMARK 500 GLY C 8 C - N - CA ANGL. DEV. = 22.3 DEGREES 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 J 7 45.27 -73.73 REMARK 500 PHE B 7 29.42 -79.38 REMARK 500 PHE O 7 23.13 -65.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE J 7 -12.92 REMARK 500 PHE K 7 -18.46 REMARK 500 PHE L 7 21.39 REMARK 500 PHE M 7 10.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-71560 RELATED DB: EMDB REMARK 900 YG17 PEPTIDE - RIBBON DBREF 9PEF J 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF B 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF K 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF L 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF M 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF N 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF O 0 9 PDB 9PEF 9PEF 0 9 DBREF 9PEF C 0 9 PDB 9PEF 9PEF 0 9 SEQRES 1 J 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 B 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 K 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 L 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 M 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 N 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 O 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 SEQRES 1 C 10 ACE PHE LYS PHE GLU PHE LYS PHE GLY NH2 HET ACE J 0 3 HET NH2 J 9 1 HET ACE B 0 3 HET NH2 B 9 1 HET ACE K 0 3 HET NH2 K 9 1 HET ACE L 0 3 HET NH2 L 9 1 HET ACE M 0 3 HET NH2 M 9 1 HET ACE N 0 3 HET NH2 N 9 1 HET ACE O 0 3 HET NH2 O 9 1 HET ACE C 0 3 HET NH2 C 9 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 8(C2 H4 O) FORMUL 1 NH2 8(H2 N) SHEET 1 AA1 2 PHE J 3 PHE J 5 0 SHEET 2 AA1 2 PHE B 3 PHE B 5 1 O PHE B 5 N GLU J 4 SHEET 1 AA2 2 LYS K 2 LYS K 6 0 SHEET 2 AA2 2 LYS L 2 LYS L 6 -1 O LYS L 6 N LYS K 2 SHEET 1 AA3 2 LYS M 2 LYS M 6 0 SHEET 2 AA3 2 LYS N 2 LYS N 6 -1 O LYS N 2 N LYS M 6 SHEET 1 AA4 2 PHE O 3 LYS O 6 0 SHEET 2 AA4 2 PHE C 3 LYS C 6 1 O PHE C 5 N GLU O 4 LINK C ACE J 0 N PHE J 1 1555 1555 1.46 LINK C GLY J 8 N NH2 J 9 1555 1555 1.45 LINK C ACE B 0 N PHE B 1 1555 1555 1.46 LINK C GLY B 8 N NH2 B 9 1555 1555 1.45 LINK C ACE K 0 N PHE K 1 1555 1555 1.46 LINK C GLY K 8 N NH2 K 9 1555 1555 1.45 LINK C ACE L 0 N PHE L 1 1555 1555 1.46 LINK C GLY L 8 N NH2 L 9 1555 1555 1.45 LINK C ACE M 0 N PHE M 1 1555 1555 1.46 LINK C GLY M 8 N NH2 M 9 1555 1555 1.45 LINK C ACE N 0 N PHE N 1 1555 1555 1.46 LINK C GLY N 8 N NH2 N 9 1555 1555 1.45 LINK C ACE O 0 N PHE O 1 1555 1555 1.46 LINK C GLY O 8 N NH2 O 9 1555 1555 1.45 LINK C ACE C 0 N PHE C 1 1555 1555 1.46 LINK C GLY C 8 N NH2 C 9 1555 1555 1.45 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 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 77 79 CONECT 79 77 CONECT 81 82 83 84 CONECT 82 81 CONECT 83 81 CONECT 84 81 CONECT 157 159 CONECT 159 157 CONECT 161 162 163 164 CONECT 162 161 CONECT 163 161 CONECT 164 161 CONECT 237 239 CONECT 239 237 CONECT 241 242 243 244 CONECT 242 241 CONECT 243 241 CONECT 244 241 CONECT 317 319 CONECT 319 317 CONECT 321 322 323 324 CONECT 322 321 CONECT 323 321 CONECT 324 321 CONECT 397 399 CONECT 399 397 CONECT 401 402 403 404 CONECT 402 401 CONECT 403 401 CONECT 404 401 CONECT 477 479 CONECT 479 477 CONECT 481 482 483 484 CONECT 482 481 CONECT 483 481 CONECT 484 481 CONECT 557 559 CONECT 559 557 CONECT 561 562 563 564 CONECT 562 561 CONECT 563 561 CONECT 564 561 CONECT 637 639 CONECT 639 637 MASTER 168 0 16 0 8 0 0 6 632 8 48 8 END