HEADER RNA 20-APR-20 6WLJ TITLE ATP-TTR-3 WITH AMP MODELS, 9.6 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (130-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS APTAMER, RNA EXPDTA ELECTRON MICROSCOPY NUMMDL 20 AUTHOR K.KAPPEL,K.ZHANG,Z.SU,A.M.WATKINS,W.KLADWANG,S.LI,G.PINTILIE, AUTHOR 2 V.V.TOPKAR,R.RANGAN,I.N.ZHELUDEV,J.D.YESSELMAN,W.CHIU,R.DAS REVDAT 3 06-MAR-24 6WLJ 1 REMARK REVDAT 2 15-JUL-20 6WLJ 1 JRNL REVDAT 1 08-JUL-20 6WLJ 0 JRNL AUTH K.KAPPEL,K.ZHANG,Z.SU,A.M.WATKINS,W.KLADWANG,S.LI, JRNL AUTH 2 G.PINTILIE,V.V.TOPKAR,R.RANGAN,I.N.ZHELUDEV,J.D.YESSELMAN, JRNL AUTH 3 W.CHIU,R.DAS JRNL TITL ACCELERATED CRYO-EM-GUIDED DETERMINATION OF JRNL TITL 2 THREE-DIMENSIONAL RNA-ONLY STRUCTURES. JRNL REF NAT.METHODS V. 17 699 2020 JRNL REFN ESSN 1548-7105 JRNL PMID 32616928 JRNL DOI 10.1038/S41592-020-0878-9 REMARK 2 REMARK 2 RESOLUTION. 9.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 9.600 REMARK 3 NUMBER OF PARTICLES : 39136 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6WLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248510. 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 : ATP-TTR-3 WITH AMP REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : UNSPECIFIED REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : RNA GENERATED BY IN VITRO REMARK 245 TRANSCRIPTION 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3000.00 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) : 200 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: A 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 1 G A 1 O5' REMARK 470 2 G A 1 O5' REMARK 470 3 G A 1 O5' REMARK 470 4 G A 1 O5' REMARK 470 5 G A 1 O5' REMARK 470 6 G A 1 O5' REMARK 470 7 G A 1 O5' REMARK 470 8 G A 1 O5' REMARK 470 9 G A 1 O5' REMARK 470 10 G A 1 O5' REMARK 470 11 G A 1 O5' REMARK 470 12 G A 1 O5' REMARK 470 13 G A 1 O5' REMARK 470 14 G A 1 O5' REMARK 470 15 G A 1 O5' REMARK 470 16 G A 1 O5' REMARK 470 17 G A 1 O5' REMARK 470 18 G A 1 O5' REMARK 470 19 G A 1 O5' REMARK 470 20 G A 1 O5' 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' A A 61 O2' U A 123 1.54 REMARK 500 N4 C A 19 O2' G A 109 2.12 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 3 A A 78 C2' - C3' - O3' ANGL. DEV. = 11.2 DEGREES REMARK 500 3 A A 80 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES REMARK 500 10 G A 33 C2' - C3' - O3' ANGL. DEV. = -16.9 DEGREES REMARK 500 11 G A 77 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-21831 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21832 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21833 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21834 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21835 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21836 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21838 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21839 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21840 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21841 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-21842 RELATED DB: EMDB DBREF 6WLJ A 1 130 PDB 6WLJ 6WLJ 1 130 SEQRES 1 A 130 G G C G A U A U G G C A U SEQRES 2 A 130 G G A A U C A G C U C A A SEQRES 3 A 130 G G A A C U G U G A A C G SEQRES 4 A 130 U A U A U C G G G C A A C SEQRES 5 A 130 G A C U A G G A A A C U A SEQRES 6 A 130 G U C G U U G G G A A G A SEQRES 7 A 130 A A C U G C C G A U A U A SEQRES 8 A 130 C G G G A G U U C C U U G SEQRES 9 A 130 A G C G G G A G A U U C C SEQRES 10 A 130 A U G C C U A A G U C G C 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 MODEL 1