HEADER    RNA                                     07-JUN-24   9C6I              
TITLE     CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: GROUP IIC INTRON;                                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS;                       
SOURCE   3 ORGANISM_TAXID: 182710;                                              
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    SPLICING, RIBOZYME, RNA                                               
EXPDTA    ELECTRON MICROSCOPY                                                   
AUTHOR    N.TOOR                                                                
REVDAT   3   05-FEB-25 9C6I    1       JRNL                                     
REVDAT   2   29-JAN-25 9C6I    1       JRNL                                     
REVDAT   1   04-DEC-24 9C6I    0                                                
JRNL        AUTH   D.B.HAACK,B.RUDOLFS,S.JIN,A.KHITUN,K.M.WEEKS,N.TOOR          
JRNL        TITL   SCAFFOLD-ENABLED HIGH-RESOLUTION CRYO-EM STRUCTURE           
JRNL        TITL 2 DETERMINATION OF RNA.                                        
JRNL        REF    NAT COMMUN                    V.  16   880 2025              
JRNL        REFN                   ESSN 2041-1723                               
JRNL        PMID   39837824                                                     
JRNL        DOI    10.1038/S41467-024-55699-5                                   
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.56 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)  : 2.560                          
REMARK   3   NUMBER OF PARTICLES               : 382753                         
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 9C6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-24.                  
REMARK 100 THE DEPOSITION ID IS D_1000284879.                                   
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                 : GROUP IIC INTRON                  
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                             : 6.50                              
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                  : FEI TITAN KRIOS                
REMARK 245   DETECTOR TYPE                     : GATAN K3 BIOQUANTUM (6K X      
REMARK 245                                       4K)                            
REMARK 245   MINIMUM DEFOCUS (NM)              : 1000.00                        
REMARK 245   MAXIMUM DEFOCUS (NM)              : 2000.00                        
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)  : 5000.00                        
REMARK 245   ILLUMINATION MODE                 : SPOT SCAN                      
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: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465       U A   389                                                      
REMARK 465       G A   390                                                      
REMARK 465       A A   391                                                      
REMARK 465       G A   392                                                      
REMARK 465       A A   393                                                      
REMARK 465       G A   394                                                      
REMARK 465       G A   395                                                      
REMARK 465       A A   396                                                      
REMARK 465       G A   397                                                      
REMARK 465       U A   398                                                      
REMARK 465       U A   399                                                      
REMARK 465       C A   400                                                      
REMARK 465       G A   401                                                      
REMARK 465       C A   402                                                      
REMARK 465       U A   403                                                      
REMARK 465       C A   404                                                      
REMARK 465       U A   405                                                      
REMARK 465       A A   406                                                      
REMARK 465       C A   407                                                      
REMARK 465       U A   408                                                      
REMARK 465       C A   409                                                      
REMARK 465       U A   410                                                      
REMARK 465       A A   411                                                      
REMARK 465       U A   412                                                      
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   N7     A A   333     O2     U A   347              2.09            
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      G A 267   O4' -  C1' -  N9  ANGL. DEV. =   5.5 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 507  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   U A  66   OP2                                                    
REMARK 620 2   A A  67   OP1  98.5                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 511  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   C A 119   OP1                                                    
REMARK 620 2   G A 239   OP1 160.1                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 518  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   A A 287   OP2                                                    
REMARK 620 2   G A 321   OP1  85.3                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 519  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   C A 289   O2                                                     
REMARK 620 2   A A 355   OP2 152.2                                              
REMARK 620 3   A A 356   OP2  76.4  76.3                                        
REMARK 620 N                    1     2                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: EMD-45247   RELATED DB: EMDB                             
REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA                          
REMARK 900 RELATED ID: 9C6I   RELATED DB: PDB                                   
REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA                          
REMARK 900 RELATED ID: EMD-45248   RELATED DB: EMDB                             
REMARK 900 GROUP IIC INTRON EMBEDDED WITH THE TPP RIBOSWITCH                    
REMARK 900 RELATED ID: 9C6J   RELATED DB: PDB                                   
REMARK 900 GROUP IIC INTRON EMBEDDED WITH THE TPP RIBOSWITCH                    
REMARK 900 RELATED ID: EMD-45249   RELATED DB: EMDB                             
REMARK 900 CRYO-EM STRUCTURE OF THE TPP RIBOSWITCH EMBEDDED IN AN RNA SCAFFOLD  
REMARK 900 BOUND TO THIAMINE PYROPHOSPHATE                                      
REMARK 900 RELATED ID: 9C6K   RELATED DB: PDB                                   
REMARK 900 CRYO-EM STRUCTURE OF THE TPP RIBOSWITCH EMBEDDED IN AN RNA SCAFFOLD  
REMARK 900 BOUND TO THIAMINE PYROPHOSPHATE                                      
REMARK 900 RELATED ID: EMD-45250   RELATED DB: EMDB                             
REMARK 900 CRYO-EM STRUCTURE OF THE APO TPP RIBOSWITCH EMBEDDED IN AN RNA       
REMARK 900 SCAFFOLD                                                             
REMARK 900 RELATED ID: EMD-45251   RELATED DB: EMDB                             
REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON EMBEDDED IN AN RNP SCAFFOLD  
DBREF  9C6I A   -5   412  PDB    9C6I     9C6I            -5    412             
SEQRES   1 A  417    G   U   U   A   U   G   U   G   U   G   C   C   C          
SEQRES   2 A  417    G   G   C   A   U   G   G   G   U   G   C   A   G          
SEQRES   3 A  417    U   C   U   A   U   A   G   G   G   U   G   A   G          
SEQRES   4 A  417    A   G   U   C   C   C   G   A   A   C   U   G   U          
SEQRES   5 A  417    G   A   A   G   G   C   A   G   A   A   G   U   A          
SEQRES   6 A  417    A   C   A   G   U   U   A   G   C   C   U   A   A          
SEQRES   7 A  417    C   G   C   A   A   G   G   G   U   G   U   C   C          
SEQRES   8 A  417    G   U   G   G   C   G   A   C   A   U   G   G   A          
SEQRES   9 A  417    A   U   C   U   G   A   A   G   G   A   A   G   C          
SEQRES  10 A  417    G   G   A   C   G   G   C   A   A   A   C   C   U          
SEQRES  11 A  417    U   C   G   G   U   C   U   G   A   G   G   A   A          
SEQRES  12 A  417    C   A   C   G   A   A   C   U   U   C   A   U   A          
SEQRES  13 A  417    U   G   A   G   G   C   U   A   G   G   U   A   U          
SEQRES  14 A  417    C   A   A   U   G   G   A   U   G   A   G   U   U          
SEQRES  15 A  417    U   G   C   A   U   A   A   C   A   A   A   A   C          
SEQRES  16 A  417    A   A   A   G   U   C   C   U   U   U   C   U   G          
SEQRES  17 A  417    C   C   A   A   A   G   U   U   G   G   U   A   C          
SEQRES  18 A  417    A   G   A   G   U   A   A   A   U   G   A   A   G          
SEQRES  19 A  417    C   A   G   A   U   U   G   A   U   G   A   A   G          
SEQRES  20 A  417    G   G   A   A   A   G   A   C   U   G   C   A   U          
SEQRES  21 A  417    U   C   U   U   A   C   C   C   G   G   G   G   A          
SEQRES  22 A  417    G   G   U   C   U   G   G   A   A   A   C   A   G          
SEQRES  23 A  417    A   A   G   U   C   A   G   C   A   G   A   A   G          
SEQRES  24 A  417    U   C   A   U   A   G   U   A   C   C   C   U   G          
SEQRES  25 A  417    U   U   C   G   C   A   G   G   G   G   A   A   G          
SEQRES  26 A  417    G   A   C   G   G   A   A   C   A   A   G   U   A          
SEQRES  27 A  417    U   G   G   C   G   U   U   C   G   C   G   C   C          
SEQRES  28 A  417    U   A   A   G   C   U   U   G   A   A   C   C   A          
SEQRES  29 A  417    C   C   G   U   A   U   A   C   C   G   A   A   C          
SEQRES  30 A  417    G   G   U   A   C   G   U   A   C   G   G   U   G          
SEQRES  31 A  417    G   U   G   U   G   A   G   A   G   G   A   G   U          
SEQRES  32 A  417    U   C   G   C   U   C   U   A   C   U   C   U   A          
SEQRES  33 A  417    U                                                          
HET     MG  A 501       1                                                       
HET     MG  A 502       1                                                       
HET     MG  A 503       1                                                       
HET     MG  A 504       1                                                       
HET     MG  A 505       1                                                       
HET     MG  A 506       1                                                       
HET     MG  A 507       1                                                       
HET     MG  A 508       1                                                       
HET     MG  A 509       1                                                       
HET     MG  A 510       1                                                       
HET     MG  A 511       1                                                       
HET     MG  A 512       1                                                       
HET     MG  A 513       1                                                       
HET     MG  A 514       1                                                       
HET     MG  A 515       1                                                       
HET     MG  A 516       1                                                       
HET     MG  A 517       1                                                       
HET     MG  A 518       1                                                       
HET     MG  A 519       1                                                       
HET     MG  A 520       1                                                       
HET     MG  A 521       1                                                       
HETNAM      MG MAGNESIUM ION                                                    
FORMUL   2   MG    21(MG 2+)                                                    
LINK         OP2   U A   4                MG    MG A 503     1555   1555  2.39  
LINK         OP2   U A  66                MG    MG A 507     1555   1555  1.93  
LINK         OP1   A A  67                MG    MG A 507     1555   1555  1.94  
LINK         OP1   G A 111                MG    MG A 505     1555   1555  2.02  
LINK         OP1   C A 119                MG    MG A 511     1555   1555  1.92  
LINK         OP1   A A 120                MG    MG A 510     1555   1555  2.11  
LINK         OP2   G A 136                MG    MG A 516     1555   1555  2.00  
LINK         OP2   C A 145                MG    MG A 515     1555   1555  2.88  
LINK         OP2   A A 186                MG    MG A 502     1555   1555  2.08  
LINK         OP1   G A 239                MG    MG A 511     1555   1555  1.89  
LINK         OP2   G A 269                MG    MG A 517     1555   1555  2.38  
LINK         OP2   A A 287                MG    MG A 518     1555   1555  2.04  
LINK         O2    C A 289                MG    MG A 519     1555   1555  2.09  
LINK         OP2   G A 320                MG    MG A 520     1555   1555  2.41  
LINK         OP1   G A 321                MG    MG A 518     1555   1555  2.01  
LINK         OP2   A A 355                MG    MG A 519     1555   1555  1.97  
LINK         OP2   A A 356                MG    MG A 519     1555   1555  2.72  
LINK         OP2   C A 372                MG    MG A 521     1555   1555  2.14  
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