HEADER SYNTHETIC PEPTIDE 07-OCT-14 3J89 TITLE STRUCTURAL PLASTICITY OF HELICAL NANOTUBES BASED ON COILED-COIL TITLE 2 ASSEMBLIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTHETIC PEPTIDE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS COILED-COIL, SYNTHETIC PEPTIDE, NANOTUBE, HELICAL FILAMENT EXPDTA ELECTRON MICROSCOPY AUTHOR E.H.EGELMAN,C.XU,F.DIMAIO,E.MAGNOTTI,C.MODLIN,X.YU,E.WRIGHT,D.BAKER, AUTHOR 2 V.P.CONTICELLO REVDAT 4 21-FEB-24 3J89 1 REMARK REVDAT 3 18-JUL-18 3J89 1 REMARK REVDAT 2 18-FEB-15 3J89 1 JRNL REVDAT 1 11-FEB-15 3J89 0 JRNL AUTH E.H.EGELMAN,C.XU,F.DIMAIO,E.MAGNOTTI,C.MODLIN,X.YU,E.WRIGHT, JRNL AUTH 2 D.BAKER,V.P.CONTICELLO JRNL TITL STRUCTURAL PLASTICITY OF HELICAL NANOTUBES BASED ON JRNL TITL 2 COILED-COIL ASSEMBLIES. JRNL REF STRUCTURE V. 23 280 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25620001 JRNL DOI 10.1016/J.STR.2014.12.008 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER 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) : 1.020 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.600 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: BOTH FSC AND COMPARISON WITH ATOMIC MODEL USED FOR REMARK 3 RESOLUTION DETERMINATION. REMARK 4 REMARK 4 3J89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000160375. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HELICAL NANOTUBE FORMED FROM A REMARK 245 29-RESIDUE PEPTIDE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO LIQUID ETHANE (FEI REMARK 245 VITROBOT MARK IV) REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : NULL REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-AUG-13 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4400.00 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) : 1000.00 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 300 REMARK: THIS PEPTIDE FORMS A HELICAL NANOTUBE OF INDETERMINATE REMARK 300 LENGTH. THE DESIGNATION "NONADECAMERIC" IN REMARK 350 IS AN REMARK 300 ARTIFACT OF THE PDB FORMAT AND CAN BE DISREGARDED. REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -87.10 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 2.20 ANGSTROMS 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: NONADECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L, M, N, O, P, Q, R, S 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 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 17 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG C 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG D 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG D 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG D 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG E 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG E 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG E 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG F 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG F 17 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG G 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG G 17 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG H 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG H 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG I 13 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG I 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG I 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG J 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG J 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG J 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG K 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG K 17 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG L 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG L 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG L 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG M 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG M 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG M 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG N 13 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG N 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG N 17 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG O 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG O 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG O 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG P 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG P 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG P 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG Q 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG Q 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG Q 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG R 13 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG R 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG R 17 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG S 13 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6123 RELATED DB: EMDB DBREF 3J89 A 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 B 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 C 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 D 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 E 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 F 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 G 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 H 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 I 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 J 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 K 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 L 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 M 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 N 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 O 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 P 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 Q 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 R 1 29 PDB 3J89 3J89 1 29 DBREF 3J89 S 1 29 PDB 3J89 3J89 1 29 SEQRES 1 A 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 A 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 A 29 ARG ALA GLN SEQRES 1 B 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 B 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 B 29 ARG ALA GLN SEQRES 1 C 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 C 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 C 29 ARG ALA GLN SEQRES 1 D 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 D 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 D 29 ARG ALA GLN SEQRES 1 E 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 E 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 E 29 ARG ALA GLN SEQRES 1 F 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 F 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 F 29 ARG ALA GLN SEQRES 1 G 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 G 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 G 29 ARG ALA GLN SEQRES 1 H 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 H 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 H 29 ARG ALA GLN SEQRES 1 I 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 I 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 I 29 ARG ALA GLN SEQRES 1 J 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 J 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 J 29 ARG ALA GLN SEQRES 1 K 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 K 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 K 29 ARG ALA GLN SEQRES 1 L 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 L 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 L 29 ARG ALA GLN SEQRES 1 M 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 M 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 M 29 ARG ALA GLN SEQRES 1 N 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 N 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 N 29 ARG ALA GLN SEQRES 1 O 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 O 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 O 29 ARG ALA GLN SEQRES 1 P 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 P 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 P 29 ARG ALA GLN SEQRES 1 Q 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 Q 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 Q 29 ARG ALA GLN SEQRES 1 R 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 R 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 R 29 ARG ALA GLN SEQRES 1 S 29 GLN ALA ARG ILE LEU GLU ALA ASP ALA GLU ILE LEU ARG SEQRES 2 S 29 ALA TYR ALA ARG ILE LEU GLU ALA HIS ALA GLU ILE LEU SEQRES 3 S 29 ARG ALA GLN HELIX 1 1 GLN A 1 GLN A 29 1 29 HELIX 2 2 ALA B 2 GLN B 29 1 28 HELIX 3 3 ALA C 2 GLN C 29 1 28 HELIX 4 4 ALA D 2 GLN D 29 1 28 HELIX 5 5 ALA E 2 GLN E 29 1 28 HELIX 6 6 ALA F 2 GLN F 29 1 28 HELIX 7 7 ALA G 2 GLN G 29 1 28 HELIX 8 8 ALA H 2 GLN H 29 1 28 HELIX 9 9 ALA I 2 GLN I 29 1 28 HELIX 10 10 ALA J 2 GLN J 29 1 28 HELIX 11 11 ALA K 2 GLN K 29 1 28 HELIX 12 12 ALA L 2 GLN L 29 1 28 HELIX 13 13 ALA M 2 GLN M 29 1 28 HELIX 14 14 ALA N 2 GLN N 29 1 28 HELIX 15 15 ALA O 2 GLN O 29 1 28 HELIX 16 16 ALA P 2 GLN P 29 1 28 HELIX 17 17 ALA Q 2 GLN Q 29 1 28 HELIX 18 18 ALA R 2 GLN R 29 1 28 HELIX 19 19 ALA S 2 GLN S 29 1 28 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