HEADER RNA BINDING PROTEIN/RNA 09-AUG-22 7YR7 TITLE CRYO-EM STRUCTURE OF PSEUDOMONAS AERUGINOSA RSMZ RNA IN COMPLEX WITH TITLE 2 THREE RSMA PROTEIN DIMERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATIONAL REGULATOR CSRA; COMPND 3 CHAIN: F, E, G, B, C, D; COMPND 4 SYNONYM: CARBON STORAGE REGULATOR; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RSMZ RNA (118-MER); COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: CSRA, PAMH27_4484; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 9 ORGANISM_TAXID: 287; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA-PROTEIN COMPLEX, RNA, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.JIA,Z.PAN,Y.YUAN,B.LUO,Y.LUO,S.MUKHERJEE,G.JIA,L.LIU,X.LING,X.YANG, AUTHOR 2 Y.WU,T.LIU,Z.MIAO,X.WEI,J.M.BUJNICKI,K.ZHAO,Z.SU REVDAT 1 17-MAY-23 7YR7 0 JRNL AUTH X.JIA,Z.PAN,Y.YUAN,B.LUO,Y.LUO,S.MUKHERJEE,G.JIA,L.LIU, JRNL AUTH 2 X.LING,X.YANG,Z.MIAO,X.WEI,J.M.BUJNICKI,K.ZHAO,Z.SU JRNL TITL STRUCTURAL BASIS OF SRNA RSMZ REGULATION OF PSEUDOMONAS JRNL TITL 2 AERUGINOSA VIRULENCE. JRNL REF CELL RES. V. 33 328 2023 JRNL REFN ISSN 1001-0602 JRNL PMID 36828938 JRNL DOI 10.1038/S41422-023-00786-3 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, PHENIX, COOT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2MF0 REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 483925 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 7YR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031291. 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 : RNP1-6 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 : 7.40 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1700.00 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) : 5970.00 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 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: HEPTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E, G, B, A, C, D 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 LYS F 26 CG CD CE NZ REMARK 470 LYS F 53 CE NZ REMARK 470 LEU E 23 CB CG CD1 CD2 REMARK 470 LYS E 26 CE NZ REMARK 470 LYS E 53 CE NZ REMARK 470 LYS G 26 CG CD CE NZ REMARK 470 LYS G 53 CE NZ REMARK 470 LYS B 26 CE NZ REMARK 470 LYS B 53 CE NZ REMARK 470 ASP C 17 CG OD1 OD2 REMARK 470 LYS C 26 CE NZ REMARK 470 LYS C 53 CE NZ REMARK 470 LYS D 26 CG CD CE NZ REMARK 470 LYS D 53 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR F 5 70.97 55.83 REMARK 500 THR F 19 65.60 60.16 REMARK 500 ARG F 44 -157.74 -83.44 REMARK 500 GLU F 45 -166.91 -76.43 REMARK 500 GLU F 46 0.36 -68.98 REMARK 500 ASP E 16 -166.50 -126.91 REMARK 500 LEU E 23 126.72 -176.99 REMARK 500 LYS G 26 53.61 -93.64 REMARK 500 GLU G 46 -159.68 -146.91 REMARK 500 LEU B 4 -72.15 -64.36 REMARK 500 ARG B 7 -169.72 -100.45 REMARK 500 GLU B 10 -156.56 -140.69 REMARK 500 THR B 11 73.31 64.95 REMARK 500 THR B 19 65.11 37.51 REMARK 500 GLU B 45 -169.93 -78.42 REMARK 500 LEU C 12 -31.48 -130.42 REMARK 500 THR C 19 63.50 60.51 REMARK 500 LEU C 23 -32.55 -130.66 REMARK 500 GLU C 46 -23.46 -159.92 REMARK 500 THR D 5 65.34 63.96 REMARK 500 GLU D 10 -162.79 -122.08 REMARK 500 THR D 11 63.90 64.25 REMARK 500 THR D 19 70.56 47.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VPZ RELATED DB: PDB REMARK 900 RELATED ID: 2MF0 RELATED DB: PDB REMARK 900 RELATED ID: EMD-34048 RELATED DB: EMDB REMARK 900 RNP1-6 DBREF 7YR7 F 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 DBREF 7YR7 E 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 DBREF 7YR7 G 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 DBREF 7YR7 B 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 DBREF 7YR7 A 1 118 PDB 7YR7 7YR7 1 118 DBREF 7YR7 C 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 DBREF 7YR7 D 1 55 UNP V6AK05 V6AK05_PSEAI 1 55 SEQRES 1 F 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 F 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 F 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 F 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 F 55 LYS GLU LYS SEQRES 1 E 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 E 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 E 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 E 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 E 55 LYS GLU LYS SEQRES 1 G 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 G 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 G 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 G 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 G 55 LYS GLU LYS SEQRES 1 B 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 B 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 B 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 B 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 B 55 LYS GLU LYS SEQRES 1 A 118 G C G U A C A G G G A A C SEQRES 2 A 118 A C G C A A C C C C G A A SEQRES 3 A 118 G G A U C G G G G A A G G SEQRES 4 A 118 G A C G U C G C C A G G G SEQRES 5 A 118 A G G C G A U U C C A U C SEQRES 6 A 118 A G G A U G A U G A C G A SEQRES 7 A 118 G G G A C U G A A G A G U SEQRES 8 A 118 G G G C G G G G U A A U A SEQRES 9 A 118 C C C C G C C C C U U U U SEQRES 10 A 118 U SEQRES 1 C 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 C 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 C 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 C 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 C 55 LYS GLU LYS SEQRES 1 D 55 MET LEU ILE LEU THR ARG ARG VAL GLY GLU THR LEU MET SEQRES 2 D 55 VAL GLY ASP ASP VAL THR VAL THR VAL LEU GLY VAL LYS SEQRES 3 D 55 GLY ASN GLN VAL ARG ILE GLY VAL ASN ALA PRO LYS GLU SEQRES 4 D 55 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 D 55 LYS GLU LYS HELIX 1 AA1 GLU F 46 LYS F 55 1 10 HELIX 2 AA2 GLU E 46 LYS E 55 1 10 HELIX 3 AA3 GLU G 46 LYS G 55 1 10 HELIX 4 AA4 GLU B 46 LYS B 53 1 8 HELIX 5 AA5 GLU C 46 LYS C 55 1 10 HELIX 6 AA6 GLU D 45 LYS D 55 1 11 SHEET 1 AA1 2 VAL F 20 LYS F 26 0 SHEET 2 AA1 2 GLN F 29 VAL F 34 -1 O ARG F 31 N LEU F 23 SHEET 1 AA2 3 LEU E 4 ARG E 6 0 SHEET 2 AA2 3 GLN G 29 ILE G 32 -1 O VAL G 30 N ARG E 6 SHEET 3 AA2 3 VAL G 25 LYS G 26 -1 N LYS G 26 O GLN G 29 SHEET 1 AA3 3 VAL E 20 LYS E 26 0 SHEET 2 AA3 3 GLN E 29 VAL E 34 -1 O GLY E 33 N THR E 21 SHEET 3 AA3 3 LEU G 4 ARG G 6 -1 O ARG G 6 N VAL E 30 SHEET 1 AA4 3 VAL B 20 LYS B 26 0 SHEET 2 AA4 3 GLN B 29 VAL B 34 -1 O GLY B 33 N THR B 21 SHEET 3 AA4 3 ILE D 3 LEU D 4 -1 O ILE D 3 N ILE B 32 SHEET 1 AA5 2 VAL C 25 LYS C 26 0 SHEET 2 AA5 2 GLN C 29 VAL C 30 -1 O GLN C 29 N LYS C 26 SHEET 1 AA6 2 THR D 21 LYS D 26 0 SHEET 2 AA6 2 GLN D 29 GLY D 33 -1 O ARG D 31 N GLY D 24 CISPEP 1 ARG C 44 GLU C 45 0 -22.64 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