HEADER PROTEIN FIBRIL 29-MAR-23 8OKR TITLE VIRUS ENHANCING AMYLOID FIBRIL FORMED BY CKFKFQF COMPND MOL_ID: 1; COMPND 2 MOLECULE: PNF-18; COMPND 3 CHAIN: S, T, U, V, W, X, M, N, O, P, Q, R, G, H, I, J, K, L, A, B, C, COMPND 4 D, E, F; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HIV WHOLE-GENOME VECTOR AA1305#18; SOURCE 4 ORGANISM_TAXID: 672471 KEYWDS VIRUS ENHANCING AMYLOID FIBRIL, PROTEIN FIBRIL, PRION EXPDTA ELECTRON MICROSCOPY AUTHOR T.HEERDE,M.SCHMIDT,M.FAENDRICH REVDAT 1 02-AUG-23 8OKR 0 JRNL AUTH T.HEERDE,D.SCHUTZ,Y.J.LIN,J.MUNCH,M.SCHMIDT,M.FANDRICH JRNL TITL CRYO-EM STRUCTURE AND POLYMORPHIC MATURATION OF A VIRAL JRNL TITL 2 TRANSDUCTION ENHANCING AMYLOID FIBRIL. JRNL REF NAT COMMUN V. 14 4293 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37464004 JRNL DOI 10.1038/S41467-023-40042-1 REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, GCTF, COOT, PHENIX, RELION, REMARK 3 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 : BACKBONE TRACE REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT 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) : 2.860 REMARK 3 NUMBER OF PARTICLES : 25550 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 8OKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129166. 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 : VIRUS ENHANCING AMYLOID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4500.00 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: 24-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, T, U, V, W, X, M, N, O, P, REMARK 350 AND CHAINS: Q, R, G, H, I, J, K, L, A, REMARK 350 AND CHAINS: B, C, D, E, F 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 NZ LYS Q 4 O PHE J 7 1.49 REMARK 500 NZ LYS N 4 O PHE G 7 1.49 REMARK 500 NZ LYS T 4 O PHE M 7 1.49 REMARK 500 NZ LYS W 4 O PHE P 7 1.49 REMARK 500 NZ LYS H 4 O PHE A 7 1.49 REMARK 500 NZ LYS K 4 O PHE D 7 1.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16930 RELATED DB: EMDB REMARK 900 VIRUS ENHANCING AMYLOID FIBRIL FORMED BY CKFKFQF DBREF 8OKR S 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR T 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR U 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR V 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR W 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR X 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR M 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR N 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR O 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR P 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR Q 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR R 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR G 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR H 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR I 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR J 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR K 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR L 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR A 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR B 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR C 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR D 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR E 1 7 PDB 8OKR 8OKR 1 7 DBREF 8OKR F 1 7 PDB 8OKR 8OKR 1 7 SEQRES 1 S 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 T 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 U 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 V 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 W 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 X 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 M 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 N 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 O 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 P 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 Q 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 R 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 G 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 H 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 I 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 J 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 K 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 L 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 A 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 B 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 C 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 D 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 E 7 CYS LYS PHE LYS PHE GLN PHE SEQRES 1 F 7 CYS LYS PHE LYS PHE GLN PHE SHEET 1 AA1 4 PHE S 3 GLN S 6 0 SHEET 2 AA1 4 PHE M 3 GLN M 6 1 O PHE M 5 N GLN S 6 SHEET 3 AA1 4 PHE G 3 GLN G 6 1 O PHE G 5 N GLN M 6 SHEET 4 AA1 4 PHE A 3 GLN A 6 1 O PHE A 5 N GLN G 6 SHEET 1 AA2 4 PHE T 3 GLN T 6 0 SHEET 2 AA2 4 PHE N 3 GLN N 6 1 O PHE N 5 N LYS T 4 SHEET 3 AA2 4 PHE H 3 GLN H 6 1 O PHE H 5 N LYS N 4 SHEET 4 AA2 4 PHE B 3 GLN B 6 1 O PHE B 5 N LYS H 4 SHEET 1 AA3 4 PHE U 3 GLN U 6 0 SHEET 2 AA3 4 PHE O 3 GLN O 6 1 O PHE O 5 N LYS U 4 SHEET 3 AA3 4 PHE I 3 GLN I 6 1 O PHE I 5 N LYS O 4 SHEET 4 AA3 4 PHE C 3 GLN C 6 1 O PHE C 5 N LYS I 4 SHEET 1 AA4 4 PHE V 3 GLN V 6 0 SHEET 2 AA4 4 PHE P 3 GLN P 6 1 O PHE P 5 N GLN V 6 SHEET 3 AA4 4 PHE J 3 GLN J 6 1 O PHE J 5 N GLN P 6 SHEET 4 AA4 4 PHE D 3 GLN D 6 1 O PHE D 5 N GLN J 6 SHEET 1 AA5 4 PHE W 3 GLN W 6 0 SHEET 2 AA5 4 PHE Q 3 GLN Q 6 1 O PHE Q 5 N LYS W 4 SHEET 3 AA5 4 PHE K 3 GLN K 6 1 O PHE K 5 N LYS Q 4 SHEET 4 AA5 4 PHE E 3 GLN E 6 1 O PHE E 5 N LYS K 4 SHEET 1 AA6 4 PHE X 3 GLN X 6 0 SHEET 2 AA6 4 PHE R 3 GLN R 6 1 O PHE R 5 N LYS X 4 SHEET 3 AA6 4 PHE L 3 GLN L 6 1 O PHE L 5 N LYS R 4 SHEET 4 AA6 4 PHE F 3 GLN F 6 1 O PHE F 5 N LYS L 4 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