HEADER TRANSCRIPTION 31-MAR-22 7ZEZ TITLE TRIMOLECULAR COMPLEX CYP33-RRMDELTA ALPHA : MLL1-PHD3 : H3K4ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 3 OF PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM (UNP RESIDUES 1-90); COMPND 5 SYNONYM: PPIASE E,CYCLOPHILIN E,CYCLOPHILIN-33,ROTAMASE E; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MLL CLEAVAGE PRODUCT N320; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: PHD ZINC FINGER (UNP RESIDUES 1564-1627); COMPND 12 SYNONYM: N-TERMINAL CLEAVAGE PRODUCT OF 320 KDA,P320; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: HISTONE H3; COMPND 16 CHAIN: D; COMPND 17 FRAGMENT: N-TERMINAL TAIL (UNP RESIDUES 2-14); COMPND 18 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PTYB11; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 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 2 03-MAY-23 7ZEZ 1 TITLE JRNL REVDAT 1 13-APR-22 7ZEZ 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 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 7ZEZ 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_1292113921. 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 REMARK 210 MM [U-100% 15N] HISTONE-LYSINE N- REMARK 210 METHYLTRANSFERASE 2A, 1 MM REMARK 210 HISTONE H3, 40 MM SODIUM REMARK 210 CHLORIDE, 40 MM SODIUM PHOSPHATE, REMARK 210 50 UM ZINC CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] PEPTIDYL-PROLYL CIS-TRANS REMARK 210 ISOMERASE E, 1 MM [U-100% 13C; U- REMARK 210 100% 15N] HISTONE-LYSINE N- REMARK 210 METHYLTRANSFERASE 2A, 1 MM REMARK 210 HISTONE H3, 40 MM SODIUM REMARK 210 CHLORIDE, 40 MM SODIUM PHOSPHATE, REMARK 210 10 UM ZINC CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] PEPTIDYL-PROLYL CIS-TRANS REMARK 210 ISOMERASE E, 1 MM HISTONE-LYSINE REMARK 210 N-METHYLTRANSFERASE 2A, 1 MM REMARK 210 HISTONE H3, 40 MM SODIUM REMARK 210 CHLORIDE, 40 MM SODIUM PHOSPHATE, REMARK 210 10 UM ZINC CHLORIDE, 100% D2O; REMARK 210 1 MM PEPTIDYL-PROLYL CIS-TRANS REMARK 210 ISOMERASE E, 1 MM [U-100% 13C; U- REMARK 210 100% 15N] HISTONE-LYSINE N- REMARK 210 METHYLTRANSFERASE 2A, 1 MM REMARK 210 HISTONE H3, 40 MM SODIUM REMARK 210 CHLORIDE, 40 MM SODIUM PHOSPHATE, REMARK 210 10 UM ZINC CHLORIDE, 100% 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 REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 LEU A 72 -60.16 -120.22 REMARK 500 1 ALA A 82 32.67 -84.29 REMARK 500 1 ASP B1592 19.96 54.06 REMARK 500 1 ALA D 7 12.81 -151.55 REMARK 500 2 MET A 1 14.97 -141.74 REMARK 500 2 LEU A 13 -82.28 -54.67 REMARK 500 2 LEU A 72 -59.94 -120.30 REMARK 500 2 ASP B1580 28.63 -72.15 REMARK 500 2 ASP B1592 19.87 55.05 REMARK 500 2 ASN B1601 21.30 -143.70 REMARK 500 3 MET A 1 12.16 -154.69 REMARK 500 3 LEU A 13 -81.32 -53.00 REMARK 500 3 LEU A 72 -60.10 -120.23 REMARK 500 3 LYS A 88 13.56 -66.35 REMARK 500 3 ASP B1578 -21.24 62.82 REMARK 500 3 ASP B1580 30.76 -84.85 REMARK 500 3 ASP B1592 19.95 56.41 REMARK 500 3 LYS D 9 -167.12 46.91 REMARK 500 4 LEU A 72 -60.31 -120.12 REMARK 500 4 ASP B1580 27.63 -73.48 REMARK 500 4 ASP B1592 19.90 56.26 REMARK 500 4 LYS B1598 -59.46 -130.11 REMARK 500 4 CYS B1599 -130.09 45.58 REMARK 500 4 ASN B1601 14.49 -146.70 REMARK 500 4 ALA D 7 22.54 -141.66 REMARK 500 5 MET A 1 11.28 -144.00 REMARK 500 5 LEU A 72 -60.11 -120.18 REMARK 500 5 ASP B1580 32.21 -76.34 REMARK 500 5 ASP B1592 19.99 56.92 REMARK 500 5 ASN B1601 10.38 -66.32 REMARK 500 6 LEU A 72 -60.14 -120.16 REMARK 500 6 LYS A 88 9.48 -65.65 REMARK 500 6 CYS B1591 10.59 -140.30 REMARK 500 6 ASP B1592 19.87 56.01 REMARK 500 6 LYS D 9 139.41 60.04 REMARK 500 6 SER D 10 16.35 55.59 REMARK 500 7 THR A 43 10.47 -144.39 REMARK 500 7 LEU A 72 -59.97 -120.29 REMARK 500 7 ASP B1578 10.21 -67.52 REMARK 500 7 TYR B1581 12.47 -141.11 REMARK 500 7 ASP B1592 19.82 54.35 REMARK 500 8 LEU A 72 -60.03 -120.24 REMARK 500 8 ASP B1579 -11.46 63.39 REMARK 500 8 ASP B1592 19.84 53.65 REMARK 500 8 GLU B1600 -60.22 -120.06 REMARK 500 8 ASN B1601 115.49 -169.00 REMARK 500 8 ARG D 2 41.62 -78.73 REMARK 500 9 LEU A 72 -60.17 -120.28 REMARK 500 9 ASP B1579 -42.04 65.63 REMARK 500 9 ASP B1592 19.87 55.12 REMARK 500 REMARK 500 THIS ENTRY HAS 139 RAMACHANDRAN OUTLIERS. 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 ZN B1701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1569 SG REMARK 620 2 CYS B1572 SG 104.3 REMARK 620 3 HIS B1596 ND1 106.9 107.1 REMARK 620 4 CYS B1599 SG 112.6 112.2 113.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1588 SG REMARK 620 2 CYS B1591 SG 108.1 REMARK 620 3 CYS B1621 SG 108.0 109.0 REMARK 620 4 CYS B1624 SG 111.0 112.2 108.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34728 RELATED DB: BMRB REMARK 900 RNA BINDING INDUCES AN ALLOSTERIC SWITCH IN CYP33 TO REPRESS MLL1 REMARK 900 MEDIATED TRANSCRIPTION REGULATION REMARK 900 RELATED ID: 7ZEV RELATED DB: PDB REMARK 900 CYP33-RRM REMARK 900 RELATED ID: 34724 RELATED DB: BMRB REMARK 900 CYP33-RRM REMARK 900 RELATED ID: 7ZEW RELATED DB: PDB REMARK 900 CYP33RRM_AAUAAA REMARK 900 RELATED ID: 34725 RELATED DB: BMRB REMARK 900 CYP33RRM_AAUAAA REMARK 900 RELATED ID: 7ZEX RELATED DB: PDB REMARK 900 CYP33RRM90_UAAUGUCG REMARK 900 RELATED ID: 34726 RELATED DB: BMRB REMARK 900 CYP33RRM90_UAAUGUCG REMARK 900 RELATED ID: 7ZEY RELATED DB: PDB REMARK 900 CYP33_MLL REMARK 900 RELATED ID: 34727 RELATED DB: BMRB REMARK 900 CYP33_MLL DBREF 7ZEZ A 1 90 UNP Q9UNP9 PPIE_HUMAN 1 90 DBREF 7ZEZ B 1564 1627 UNP Q03164 KMT2A_HUMAN 1564 1627 DBREF 7ZEZ D 1 13 UNP B4E380 B4E380_HUMAN 2 14 SEQADV 7ZEZ ALA A -3 UNP Q9UNP9 EXPRESSION TAG SEQADV 7ZEZ GLY A -2 UNP Q9UNP9 EXPRESSION TAG SEQADV 7ZEZ 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 64 ALA LYS GLY ASN PHE CYS PRO LEU CYS ASP LYS CYS TYR SEQRES 2 B 64 ASP ASP ASP ASP TYR GLU SER LYS MET MET GLN CYS GLY SEQRES 3 B 64 LYS CYS ASP ARG TRP VAL HIS SER LYS CYS GLU ASN LEU SEQRES 4 B 64 SER ASP GLU MET TYR GLU ILE LEU SER ASN LEU PRO GLU SEQRES 5 B 64 SER VAL ALA TYR THR CYS VAL ASN CYS THR GLU ARG SEQRES 1 D 13 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY GLY MODRES 7ZEZ M3L D 4 LYS MODIFIED RESIDUE HET M3L D 4 31 HET ZN B1701 1 HET ZN B1702 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 3 M3L C9 H21 N2 O2 1+ FORMUL 4 ZN 2(ZN 2+) 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 HELIX 4 AA4 SER B 1603 LEU B 1613 1 11 SHEET 1 AA1 5 ILE A 32 GLN A 36 0 SHEET 2 AA1 5 PHE A 49 PHE A 54 -1 O PHE A 51 N GLN A 36 SHEET 3 AA1 5 VAL A 7 GLY A 11 -1 N VAL A 10 O ALA A 50 SHEET 4 AA1 5 THR A 76 LEU A 81 -1 O ARG A 78 N GLY A 11 SHEET 5 AA1 5 SER A 70 GLU A 71 -1 N SER A 70 O ILE A 77 SHEET 1 AA2 3 LYS A 45 HIS A 46 0 SHEET 2 AA2 3 LEU A 39 ASP A 40 -1 N ASP A 40 O LYS A 45 SHEET 3 AA2 3 VAL B1617 ALA B1618 -1 O ALA B1618 N LEU A 39 SHEET 1 AA3 2 MET B1585 GLN B1587 0 SHEET 2 AA3 2 TRP B1594 HIS B1596 -1 O VAL B1595 N MET B1586 LINK C THR D 3 N M3L D 4 1555 1555 1.34 LINK C M3L D 4 N GLN D 5 1555 1555 1.34 LINK SG CYS B1569 ZN ZN B1701 1555 1555 2.31 LINK SG CYS B1572 ZN ZN B1701 1555 1555 2.32 LINK SG CYS B1588 ZN ZN B1702 1555 1555 2.30 LINK SG CYS B1591 ZN ZN B1702 1555 1555 2.31 LINK ND1 HIS B1596 ZN ZN B1701 1555 1555 2.01 LINK SG CYS B1599 ZN ZN B1701 1555 1555 2.31 LINK SG CYS B1621 ZN ZN B1702 1555 1555 2.31 LINK SG CYS B1624 ZN ZN B1702 1555 1555 2.31 SITE 1 AC1 4 CYS B1569 CYS B1572 HIS B1596 CYS B1599 SITE 1 AC2 4 CYS B1588 CYS B1591 CYS B1621 CYS B1624 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