HEADER PROTEIN FIBRIL 09-MAY-26 26PC TITLE OAT PROTEIN AMYLOID FIBRILS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 11S GLOBULIN; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AVENA SATIVA; SOURCE 3 ORGANISM_COMMON: OATS; SOURCE 4 ORGANISM_TAXID: 4498; SOURCE 5 GENE: GLAV1; SOURCE 6 EXPRESSION_SYSTEM: AVENA SATIVA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4498 KEYWDS PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,Q.CAO,Y.CAO REVDAT 1 16-SEP-26 26PC 0 JRNL AUTH S.LI,Q.CAO,Y.CAO JRNL TITL STRUCTURE OF OAT PROTEIN AMYLOID FIBRIL AT 2.94 ANGSTROMS JRNL TITL 2 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, 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 : 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) : 2.950 REMARK 3 NUMBER OF PARTICLES : 171776 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 26PC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300074022. 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 : PARTICLE REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : OAT STORAGE 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 : 2.00 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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) : 4000.00 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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: 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 ARG A 400 32.63 -143.51 REMARK 500 HIS A 427 31.46 -97.09 REMARK 500 ARG B 400 32.58 -143.48 REMARK 500 HIS B 427 31.51 -97.10 REMARK 500 ARG C 400 32.60 -143.49 REMARK 500 HIS C 427 31.53 -97.10 REMARK 500 ARG D 400 32.62 -143.45 REMARK 500 HIS D 427 31.52 -97.18 REMARK 500 ARG E 400 32.68 -143.49 REMARK 500 HIS E 427 31.52 -97.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-80803 RELATED DB: EMDB REMARK 900 OAT PROTEIN AMYLOID FIBRILS DBREF 26PC A 391 435 UNP Q38779 Q38779_AVESA 391 435 DBREF 26PC B 391 435 UNP Q38779 Q38779_AVESA 391 435 DBREF 26PC C 391 435 UNP Q38779 Q38779_AVESA 391 435 DBREF 26PC D 391 435 UNP Q38779 Q38779_AVESA 391 435 DBREF 26PC E 391 435 UNP Q38779 Q38779_AVESA 391 435 SEQRES 1 A 45 LEU ASN ILE VAL GLN MET SER ALA THR ARG VAL ASN LEU SEQRES 2 A 45 TYR GLN ASN ALA ILE LEU SER PRO PHE TRP ASN ILE ASN SEQRES 3 A 45 ALA HIS SER VAL ILE TYR MET ILE GLN GLY HIS ALA ARG SEQRES 4 A 45 VAL GLN VAL VAL ASN ASN SEQRES 1 B 45 LEU ASN ILE VAL GLN MET SER ALA THR ARG VAL ASN LEU SEQRES 2 B 45 TYR GLN ASN ALA ILE LEU SER PRO PHE TRP ASN ILE ASN SEQRES 3 B 45 ALA HIS SER VAL ILE TYR MET ILE GLN GLY HIS ALA ARG SEQRES 4 B 45 VAL GLN VAL VAL ASN ASN SEQRES 1 C 45 LEU ASN ILE VAL GLN MET SER ALA THR ARG VAL ASN LEU SEQRES 2 C 45 TYR GLN ASN ALA ILE LEU SER PRO PHE TRP ASN ILE ASN SEQRES 3 C 45 ALA HIS SER VAL ILE TYR MET ILE GLN GLY HIS ALA ARG SEQRES 4 C 45 VAL GLN VAL VAL ASN ASN SEQRES 1 D 45 LEU ASN ILE VAL GLN MET SER ALA THR ARG VAL ASN LEU SEQRES 2 D 45 TYR GLN ASN ALA ILE LEU SER PRO PHE TRP ASN ILE ASN SEQRES 3 D 45 ALA HIS SER VAL ILE TYR MET ILE GLN GLY HIS ALA ARG SEQRES 4 D 45 VAL GLN VAL VAL ASN ASN SEQRES 1 E 45 LEU ASN ILE VAL GLN MET SER ALA THR ARG VAL ASN LEU SEQRES 2 E 45 TYR GLN ASN ALA ILE LEU SER PRO PHE TRP ASN ILE ASN SEQRES 3 E 45 ALA HIS SER VAL ILE TYR MET ILE GLN GLY HIS ALA ARG SEQRES 4 E 45 VAL GLN VAL VAL ASN ASN SHEET 1 AA1 5 ASN A 392 MET A 396 0 SHEET 2 AA1 5 ASN B 392 MET B 396 1 O GLN B 395 N VAL A 394 SHEET 3 AA1 5 ASN C 392 MET C 396 1 O GLN C 395 N VAL B 394 SHEET 4 AA1 5 ASN D 392 MET D 396 1 O GLN D 395 N VAL C 394 SHEET 5 AA1 5 ASN E 392 MET E 396 1 O GLN E 395 N VAL D 394 SHEET 1 AA2 5 ALA A 407 ILE A 408 0 SHEET 2 AA2 5 ALA B 407 ILE B 408 1 O ALA B 407 N ILE A 408 SHEET 3 AA2 5 ALA C 407 ILE C 408 1 O ALA C 407 N ILE B 408 SHEET 4 AA2 5 ALA D 407 ILE D 408 1 O ALA D 407 N ILE C 408 SHEET 5 AA2 5 ALA E 407 ILE E 408 1 O ALA E 407 N ILE D 408 SHEET 1 AA3 5 ILE A 415 ASN A 416 0 SHEET 2 AA3 5 ILE B 415 ASN B 416 1 O ILE B 415 N ASN A 416 SHEET 3 AA3 5 ILE C 415 ASN C 416 1 O ILE C 415 N ASN B 416 SHEET 4 AA3 5 ILE D 415 ASN D 416 1 O ILE D 415 N ASN C 416 SHEET 5 AA3 5 ILE E 415 ASN E 416 1 O ILE E 415 N ASN D 416 SHEET 1 AA4 5 SER A 419 MET A 423 0 SHEET 2 AA4 5 SER B 419 MET B 423 1 O VAL B 420 N SER A 419 SHEET 3 AA4 5 SER C 419 MET C 423 1 O VAL C 420 N SER B 419 SHEET 4 AA4 5 SER D 419 MET D 423 1 O VAL D 420 N SER C 419 SHEET 5 AA4 5 SER E 419 MET E 423 1 O VAL E 420 N SER D 419 SHEET 1 AA5 5 ARG A 429 VAL A 433 0 SHEET 2 AA5 5 ARG B 429 VAL B 433 1 O VAL B 432 N VAL A 433 SHEET 3 AA5 5 ARG C 429 VAL C 433 1 O VAL C 432 N VAL B 433 SHEET 4 AA5 5 ARG D 429 VAL D 433 1 O VAL D 432 N VAL C 433 SHEET 5 AA5 5 ARG E 429 VAL E 433 1 O VAL E 432 N VAL D 433 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 126 0 0 0 25 0 0 6 1805 5 0 20 END