HEADER TRANSCRIPTION 31-MAR-22 7ZEX TITLE COMPLEX CYP33-RRMDELTA ALPHA : UAAUGUCG RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 3 OF PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE E,CYCLOPHILIN E,CYCLOPHILIN-33,ROTAMASE E; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*UP*AP*AP*UP*GP*UP*CP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIE, CYP33; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTYB12; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS RRM, RNA BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX, HISTONE 3, KEYWDS 2 H3K4ME3, EPIGENETIC, MLL1 TRANSCRIPTION REGULATION, INFANT LEUKEMIA, KEYWDS 3 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.BLATTER,F.ALLAIN,C.MEYLAN REVDAT 3 19-JUN-24 7ZEX 1 REMARK REVDAT 2 03-MAY-23 7ZEX 1 TITLE JRNL REVDAT 1 04-MAY-22 7ZEX 0 JRNL AUTH M.BLATTER,C.MEYLAN,A.CLERY,R.GIAMBRUNO,Y.NIKOLAEV, JRNL AUTH 2 M.HEIDECKER,J.A.SOLANKI,M.O.DIAZ,D.GABELLINI,F.H.ALLAIN JRNL TITL RNA BINDING INDUCES AN ALLOSTERIC SWITCH IN CYP33 TO REPRESS JRNL TITL 2 MLL1-MEDIATED TRANSCRIPTION. JRNL REF SCI ADV V. 9 F5330 2023 JRNL REFN ESSN 2375-2548 JRNL PMID 37075125 JRNL DOI 10.1126/SCIADV.ADF5330 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 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 7ZEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292113916. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.15 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 80 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] PEPTIDYL REMARK 210 -PROLYL CIS-TRANS ISOMERASE E, 1 MM RNA (5'-R(*UP*AP*AP*UP*GP*UP* REMARK 210 CP*G)-3'), 40 MM SODIUM CHLORIDE, 40 MM SODIUM PHOSPHATE, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS- REMARK 210 TRANS ISOMERASE E, 1 MM RNA (5'-R(*UP*AP*AP*UP*GP*UP*CP*G)-3'), REMARK 210 40 MM SODIUM CHLORIDE, 40 MM SODIUM PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D F3-FILTERED- REMARK 210 F2-EDITED 13C NOESY; 2D F2- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 250 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 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 1 C B 7 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 13 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 14 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 16 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 17 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 ALA A 2 -165.38 -163.05 REMARK 500 1 GLU A 42 -30.98 -148.60 REMARK 500 1 GLU A 69 14.69 56.41 REMARK 500 2 GLU A 42 -12.71 -165.80 REMARK 500 2 GLU A 69 16.32 56.54 REMARK 500 2 LYS A 88 29.12 -77.20 REMARK 500 3 ALA A 2 -161.31 -163.22 REMARK 500 3 GLU A 42 -18.33 -163.49 REMARK 500 3 GLU A 69 15.64 56.51 REMARK 500 3 LYS A 88 22.02 -72.96 REMARK 500 4 ALA A 2 -169.86 -161.45 REMARK 500 4 GLU A 42 -33.30 -148.74 REMARK 500 4 GLU A 69 14.44 56.14 REMARK 500 4 PHE A 73 19.26 54.55 REMARK 500 5 ALA A 2 -169.71 -161.51 REMARK 500 5 GLU A 42 -15.11 -165.60 REMARK 500 5 GLU A 69 15.03 56.15 REMARK 500 5 PHE A 73 19.47 54.24 REMARK 500 6 THR A 3 0.98 -64.70 REMARK 500 6 GLU A 42 -31.79 -148.77 REMARK 500 6 GLU A 69 15.44 56.00 REMARK 500 6 PHE A 73 19.62 54.10 REMARK 500 6 LYS A 88 10.71 -65.75 REMARK 500 7 GLU A 42 -35.30 -147.83 REMARK 500 7 GLU A 69 15.99 56.25 REMARK 500 8 ALA A 2 -52.45 -163.51 REMARK 500 8 THR A 3 -6.88 -163.64 REMARK 500 8 GLU A 42 -31.53 -147.61 REMARK 500 8 GLU A 69 15.57 55.94 REMARK 500 8 SER A 70 -168.49 -76.98 REMARK 500 9 GLU A 42 -27.54 -151.36 REMARK 500 9 GLU A 69 13.32 56.76 REMARK 500 9 PHE A 73 17.58 55.79 REMARK 500 9 LYS A 88 36.00 -86.97 REMARK 500 10 MET A 1 -15.88 59.99 REMARK 500 10 THR A 3 4.14 -68.53 REMARK 500 10 GLU A 42 -34.88 -149.09 REMARK 500 10 GLU A 69 16.58 56.30 REMARK 500 10 PHE A 73 19.45 53.65 REMARK 500 11 ALA A 2 -166.29 53.31 REMARK 500 11 GLU A 42 -14.18 -166.68 REMARK 500 11 MET A 67 -14.68 -140.26 REMARK 500 11 GLU A 69 15.95 56.25 REMARK 500 11 SER A 70 -169.80 -76.17 REMARK 500 11 LYS A 88 48.86 -80.54 REMARK 500 12 GLU A 42 -27.24 -151.44 REMARK 500 12 GLU A 69 14.32 56.34 REMARK 500 12 SER A 70 -167.28 -75.68 REMARK 500 13 THR A 3 -35.54 -167.54 REMARK 500 13 LEU A 39 -169.65 -113.63 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. 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 13 A B 2 0.06 SIDE CHAIN REMARK 500 15 A B 2 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34726 RELATED DB: BMRB REMARK 900 RNA BINDING INDUCES AN ALLOSTERIC SWITCH IN CYP33 TO REPRESS MLL1 REMARK 900 MEDIATED TRANSCRIPTION REGULATION DBREF 7ZEX A 1 90 UNP Q9UNP9 PPIE_HUMAN 1 90 DBREF 7ZEX B 1 8 PDB 7ZEX 7ZEX 1 8 SEQADV 7ZEX ALA A -3 UNP Q9UNP9 EXPRESSION TAG SEQADV 7ZEX GLY A -2 UNP Q9UNP9 EXPRESSION TAG SEQADV 7ZEX HIS A -1 UNP Q9UNP9 EXPRESSION TAG SEQRES 1 A 93 ALA GLY HIS MET ALA THR THR LYS ARG VAL LEU TYR VAL SEQRES 2 A 93 GLY GLY LEU ALA GLU GLU VAL ASP ASP LYS VAL LEU HIS SEQRES 3 A 93 ALA ALA PHE ILE PRO PHE GLY ASP ILE THR ASP ILE GLN SEQRES 4 A 93 ILE PRO LEU ASP TYR GLU THR GLU LYS HIS ARG GLY PHE SEQRES 5 A 93 ALA PHE VAL GLU PHE GLU LEU ALA GLU ASP ALA ALA ALA SEQRES 6 A 93 ALA ILE ASP ASN MET ASN GLU SER GLU LEU PHE GLY ARG SEQRES 7 A 93 THR ILE ARG VAL ASN LEU ALA LYS PRO MET ARG ILE LYS SEQRES 8 A 93 GLU GLY SEQRES 1 B 8 U A A U G U C G HELIX 1 AA1 ASP A 18 ILE A 27 1 10 HELIX 2 AA2 PRO A 28 GLY A 30 5 3 HELIX 3 AA3 LEU A 56 ASN A 68 1 13 SHEET 1 AA1 4 ILE A 32 GLN A 36 0 SHEET 2 AA1 4 PHE A 49 PHE A 54 -1 O GLU A 53 N THR A 33 SHEET 3 AA1 4 VAL A 7 GLY A 11 -1 N LEU A 8 O VAL A 52 SHEET 4 AA1 4 ARG A 78 ASN A 80 -1 O ASN A 80 N TYR A 9 SHEET 1 AA2 2 GLU A 71 LEU A 72 0 SHEET 2 AA2 2 ARG A 75 THR A 76 -1 O ARG A 75 N LEU A 72 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 MODEL 1