HEADER RNA 01-DEC-22 8FCS TITLE STRUCTURE OF PRE-MIR-31 REVEALS AN ACTIVE ROLE IN DICER PROCESSING COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICRORNA 31; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MIR31; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS RNA, PRE-MIRNA, DICER, DICER PROCESSING, BIOGENESIS, PRE-MIR-31, MIR- KEYWDS 2 31, APICAL LOOP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.KOTAR,S.MA,S.KEANE REVDAT 2 15-MAY-24 8FCS 1 REMARK REVDAT 1 22-FEB-23 8FCS 0 JRNL AUTH S.MA,A.KOTAR,S.GROTE,S.ROUSKIN,S.C.KEANE JRNL TITL STRUCTURE OF PRE-MIR-31 REVEALS AN ACTIVE ROLE IN DICER JRNL TITL 2 PROCESSING. JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL PMID 36711709 JRNL DOI 10.1101/2023.01.03.519659 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8FCS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270397. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 0.0025; 0.0025 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM NON REMARK 210 MGCL2, 100% D2O; 0.45 MM A2RGR- REMARK 210 LABELED RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 100% D2O; 0.45 MM A2RGRUR- REMARK 210 LABELED RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 100% D2O; 0.45 MM AHCH-LABELED REMARK 210 RNA (71-MER), 50 MM KPHOSPHATE REMARK 210 BUFFER, 1 MM MGCL2, 100% D2O; REMARK 210 0.45 MM GHU6R-LABELED RNA (71- REMARK 210 MER), 50 MM KPHOSPHATE BUFFER, 1 REMARK 210 MM MGCL2, 100% D2O; 0.48 MM 15N/ REMARK 210 13C AG-LABELED RNA (71-MER), 50 REMARK 210 MM KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 100% D2O; 0.56 MM 15N AU- REMARK 210 LABELED RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 90% H2O/10% D2O; 0.48 MM 15N/13C REMARK 210 AG-LABELED_2 RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 100% D2O; 0.40 MM 15N/13C AG- REMARK 210 LABELED_3 RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM MGCL2, REMARK 210 90% H2O/10% D2O; 0.60 MM 15N/13C REMARK 210 AG-LABELED_4 RNA (71-MER), 50 MM REMARK 210 KPHOSPHATE BUFFER, 1 MM NON REMARK 210 MGCL2, 10 MG/ML NON PF1 PHAGE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 2D 1H-15N BESTSELLR HNN COSY; 2D REMARK 210 1H-13C IPAP-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFX, NMRVIEWJ 9.2.0 REMARK 210 -B24, CYANA, AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 640 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 8 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 8 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 12 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 13 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 15 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 18 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 23 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 23 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 25 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 25 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 25 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 33 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 33 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 33 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 34 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 34 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 35 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 40 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 41 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 41 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 41 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 42 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 46 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 48 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 48 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 51 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 52 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 53 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 53 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 53 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 54 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 54 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 54 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1306 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 19 A A 53 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31061 RELATED DB: BMRB REMARK 900 STRUCTURE OF PRE-MIR-31 REVEALS AN ACTIVE ROLE IN DICER PROCESSING DBREF1 8FCS A 1 71 GB NR_029505.1 DBREF2 8FCS A NR_029505.1 1 71 SEQRES 1 A 71 G G A G A G G A G G C A A SEQRES 2 A 71 G A U G C U G G C A U A G SEQRES 3 A 71 C U G U U G A A C U G G G SEQRES 4 A 71 A A C C U G C U A U G C C SEQRES 5 A 71 A A C A U A U U G C C A U SEQRES 6 A 71 C U U U C 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