HEADER RNA 30-NOV-21 7QDU TITLE TWIST-CORRECTED RNA ORIGAMI 5-HELIX TILE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: Q; COMPND 3 CHAIN: Q; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: IN VITRO TRANSCRIBED RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, ORIGAMI, NANOSTRUCTURE EXPDTA ELECTRON MICROSCOPY AUTHOR E.K.S.MCRAE,E.S.ANDERSEN REVDAT 4 13-DEC-23 7QDU 1 REMARK REVDAT 3 02-AUG-23 7QDU 1 JRNL REVDAT 2 29-MAR-23 7QDU 1 JRNL REVDAT 1 14-DEC-22 7QDU 0 JRNL AUTH E.K.S.MCRAE,H.O.RASMUSSEN,J.LIU,A.BOGGILD,M.T.A.NGUYEN, JRNL AUTH 2 N.SAMPEDRO VALLINA,T.BOESEN,J.S.PEDERSEN,G.REN,C.GEARY, JRNL AUTH 3 E.S.ANDERSEN JRNL TITL STRUCTURE, FOLDING AND FLEXIBILITY OF CO-TRANSCRIPTIONAL RNA JRNL TITL 2 ORIGAMI. JRNL REF NAT NANOTECHNOL V. 18 808 2023 JRNL REFN ESSN 1748-3395 JRNL PMID 36849548 JRNL DOI 10.1038/S41565-023-01321-6 REMARK 2 REMARK 2 RESOLUTION. 5.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, ISOLDE, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 5.140 REMARK 3 NUMBER OF PARTICLES : 166751 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 7QDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119464. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : TWIST-CORRECTED 5-HELIX TILE A. REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : 15MA CURRENT ON A GLOCUBE. REMARK 245 SAMPLE VITRIFICATION DETAILS : 3 MICROLITRE DROPLET, 4 SECOND REMARK 245 DELAY BEFORE BLOTTING, 6 SECOND REMARK 245 BLOT, 0 SECOND DELAY BEFORE REMARK 245 PLUNGING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : IN VITRO TRANSCRIBED RNA REMARK 245 PURIFIED BY SEC. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 6122 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Q 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 HO2' G Q 334 OP1 A Q 335 1.56 REMARK 500 HO2' A Q 304 OP1 G Q 305 1.57 REMARK 500 HO2' U Q 171 OP1 A Q 172 1.58 REMARK 500 HO2' A Q 173 OP1 C Q 174 1.58 REMARK 500 HO2' G Q 168 O5' G Q 169 1.59 REMARK 500 HO2' U Q 65 O6 G Q 68 1.59 REMARK 500 HO2' G Q 136 OP1 A Q 137 1.59 REMARK 500 HO2' U Q 385 OP1 C Q 386 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 C Q 4 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A Q 5 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 A Q 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A Q 5 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 C Q 6 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C Q 6 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 U Q 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U Q 8 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 A Q 9 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 C Q 10 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 C Q 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 C Q 11 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 C Q 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 C Q 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 U Q 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 U Q 15 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 A Q 16 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 A Q 16 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A Q 16 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 G Q 19 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 C Q 20 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 C Q 20 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 C Q 20 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 G Q 21 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 A Q 22 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 A Q 22 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A Q 22 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 A Q 23 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 A Q 23 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 A Q 23 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 A Q 23 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 G Q 24 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G Q 25 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G Q 25 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 U Q 26 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U Q 27 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 U Q 28 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C Q 29 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 G Q 30 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 A Q 31 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 C Q 32 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 C Q 32 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C Q 33 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C Q 33 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 U Q 35 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES REMARK 500 U Q 35 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 C Q 36 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 C Q 36 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 G Q 37 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 G Q 37 C4' - C3' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 675 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G Q 1 0.07 SIDE CHAIN REMARK 500 U Q 13 0.09 SIDE CHAIN REMARK 500 G Q 17 0.07 SIDE CHAIN REMARK 500 G Q 21 0.10 SIDE CHAIN REMARK 500 G Q 24 0.10 SIDE CHAIN REMARK 500 G Q 25 0.07 SIDE CHAIN REMARK 500 G Q 30 0.09 SIDE CHAIN REMARK 500 C Q 33 0.17 SIDE CHAIN REMARK 500 U Q 34 0.11 SIDE CHAIN REMARK 500 G Q 37 0.05 SIDE CHAIN REMARK 500 A Q 42 0.12 SIDE CHAIN REMARK 500 U Q 43 0.10 SIDE CHAIN REMARK 500 U Q 45 0.07 SIDE CHAIN REMARK 500 G Q 46 0.10 SIDE CHAIN REMARK 500 U Q 48 0.11 SIDE CHAIN REMARK 500 C Q 49 0.09 SIDE CHAIN REMARK 500 A Q 52 0.12 SIDE CHAIN REMARK 500 A Q 53 0.10 SIDE CHAIN REMARK 500 G Q 56 0.10 SIDE CHAIN REMARK 500 G Q 58 0.23 SIDE CHAIN REMARK 500 A Q 59 0.08 SIDE CHAIN REMARK 500 G Q 61 0.07 SIDE CHAIN REMARK 500 A Q 73 0.08 SIDE CHAIN REMARK 500 G Q 77 0.08 SIDE CHAIN REMARK 500 G Q 79 0.09 SIDE CHAIN REMARK 500 G Q 82 0.09 SIDE CHAIN REMARK 500 C Q 84 0.07 SIDE CHAIN REMARK 500 U Q 88 0.13 SIDE CHAIN REMARK 500 C Q 89 0.10 SIDE CHAIN REMARK 500 A Q 90 0.10 SIDE CHAIN REMARK 500 G Q 91 0.06 SIDE CHAIN REMARK 500 U Q 97 0.07 SIDE CHAIN REMARK 500 G Q 99 0.09 SIDE CHAIN REMARK 500 U Q 105 0.07 SIDE CHAIN REMARK 500 C Q 108 0.08 SIDE CHAIN REMARK 500 C Q 110 0.09 SIDE CHAIN REMARK 500 C Q 111 0.12 SIDE CHAIN REMARK 500 A Q 112 0.10 SIDE CHAIN REMARK 500 C Q 113 0.06 SIDE CHAIN REMARK 500 C Q 125 0.08 SIDE CHAIN REMARK 500 A Q 126 0.07 SIDE CHAIN REMARK 500 G Q 129 0.07 SIDE CHAIN REMARK 500 A Q 131 0.06 SIDE CHAIN REMARK 500 U Q 133 0.07 SIDE CHAIN REMARK 500 G Q 141 0.07 SIDE CHAIN REMARK 500 U Q 147 0.10 SIDE CHAIN REMARK 500 U Q 153 0.07 SIDE CHAIN REMARK 500 C Q 154 0.10 SIDE CHAIN REMARK 500 G Q 155 0.13 SIDE CHAIN REMARK 500 U Q 156 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 216 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13926 RELATED DB: EMDB REMARK 900 TWIST-CORRECTED RNA ORIGAMI 5-HELIX TILE A DBREF 7QDU Q 1 552 PDB 7QDU 7QDU 1 552 SEQRES 1 Q 552 G G G C A C U U A C C C U SEQRES 2 Q 552 U U A G U G C G A A G G U SEQRES 3 Q 552 U U C G A C C U U C G A U SEQRES 4 Q 552 C C A U U U G U U C G C A SEQRES 5 Q 552 A A U G G G A U G A U C U SEQRES 6 Q 552 U C G G A U C A U C C G C SEQRES 7 Q 552 G U A G U C U G U U C A G SEQRES 8 Q 552 U C G U U U C G A C G A C SEQRES 9 Q 552 U G G C C C C A C U U C G SEQRES 10 Q 552 G U G G G G C C A C G G U SEQRES 11 Q 552 A C U U A G A A G U G A A SEQRES 12 Q 552 C A C U A A G U G U C G U SEQRES 13 Q 552 G A A C A C C A U U U G G SEQRES 14 Q 552 U U A A C U G C U C A A A SEQRES 15 Q 552 C U A A A U G G U G A U G SEQRES 16 Q 552 A G G G A A G G A A U G A SEQRES 17 Q 552 C C C U C A U C G G A C U SEQRES 18 Q 552 A C G C G A U C C G A G U SEQRES 19 Q 552 G A U G G G A A U G G C U SEQRES 20 Q 552 G A C C C A U C G C U C G SEQRES 21 Q 552 G C A C U G G A G G G U G SEQRES 22 Q 552 A G U G C C C C U C A U U SEQRES 23 Q 552 C G C A U A A G G G C C G SEQRES 24 Q 552 A C C C A G A C A A C A G SEQRES 25 Q 552 C C A A G U U U G G G U C SEQRES 26 Q 552 G G A G A U G C G A A C A SEQRES 27 Q 552 U U C C A C G C A U C U G SEQRES 28 Q 552 A A C G G U U G A G A A C SEQRES 29 Q 552 U U A C A A G G G C A A G SEQRES 30 Q 552 A G C A G A G U C C U U G SEQRES 31 Q 552 U A A G G G C U U U A C A SEQRES 32 Q 552 C G U C A A G U U C A C A SEQRES 33 Q 552 G A C G U G U A A G G C C SEQRES 34 Q 552 C G U C G C C C U U C G G SEQRES 35 Q 552 G G C G A C G U U C A C G SEQRES 36 Q 552 G C A U U U C G A U G C C SEQRES 37 Q 552 G U G C A G C C U G U U C SEQRES 38 Q 552 G C A G G C U G C U U G A SEQRES 39 Q 552 C C G U U C C C C U G C C SEQRES 40 Q 552 C U U U C G A G G G C A G SEQRES 41 Q 552 A C U A C U C U U C G G A SEQRES 42 Q 552 G U A G U C U U A U G U G SEQRES 43 Q 552 A A U G A G 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 TER 17694 G Q 552 MASTER 258 0 0 0 0 0 0 611752 1 0 43 END