HEADER TRANSCRIPTION 28-AUG-20 7CWH TITLE STRUCTURAL BASIS OF RACK7 PHD TO READ A PEDIATRIC GLIOBLASTOMA- TITLE 2 ASSOCIATED HISTONE MUTATION H3.3G34R COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE FROM HISTONE H3.3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN KINASE C-BINDING PROTEIN 1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: PHD-TYPE; COMPND 10 SYNONYM: RACK7; COMPND 11 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: ZMYND8; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RACK7, PHD, H3.3G34R, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.X.LAN,Z.LI,F.F.JIAO,C.X.WANG,R.GUO,C.Y.CAO REVDAT 2 01-MAY-24 7CWH 1 REMARK REVDAT 1 26-MAY-21 7CWH 0 JRNL AUTH W.X.LAN,Z.LI,F.F.JIAO,C.X.WANG,R.GUO,C.Y.CAO JRNL TITL STRUCTURAL BASIS OF RACK7 PHD DOMAIN TO READ A PEDIATRIC JRNL TITL 2 GLIOBLASTOMA‐ASSOCIATED HISTONE MUTATION H3.3G34R JRNL REF CHIN.J.CHEM. 2021 JRNL REFN ISSN 1001-604X JRNL DOI 10.1002/CJOC.202100277 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018265. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 500 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-13C; U-15N] RACK7 PHD, REMARK 210 1.4 MM H3.3G34R, 100 MM SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 50 MM SODIUM PHOSPHATE, 2 REMARK 210 MM [U-2H] DDT, 90% H2O/10% D2O; REMARK 210 0.7 MM [U-13C; U-15N] RACK7 PHD, REMARK 210 1.4 MM H3.3G34R, 100 MM SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 50 MM SODIUM PHOSPHATE, 2 REMARK 210 MM [U-2H] DTT, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N] G34R, 1.2 MM RACK7 REMARK 210 PHD, 100 MM SODIUM CHLORIDE, REMARK 210 0.02 % W/V SODIUM AZIDE, 50 MM REMARK 210 SODIUM PHOSPHATE, 2 MM [U-2H] REMARK 210 DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N TOCSY; 3D REMARK 210 1H-15N NOESY; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC; 2D FILTER REMARK 210 TOCSY; 2D FILTER NOESY; 3D 15N- REMARK 210 FILTER-EDIT NOESY; 3D 13C-FILTER- REMARK 210 EDIT NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DD2 REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY, NMRDRAW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 O CYS B 111 H HIS B 115 1.59 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 THR A 32 -176.37 49.72 REMARK 500 1 HIS A 39 85.38 55.67 REMARK 500 1 ARG B 106 79.54 29.68 REMARK 500 1 PHE B 109 -94.13 -165.64 REMARK 500 1 GLN B 119 70.53 52.07 REMARK 500 1 PRO B 127 123.93 -17.73 REMARK 500 1 PRO B 148 -31.45 -37.64 REMARK 500 1 GLU B 157 -171.43 51.29 REMARK 500 1 CYS B 158 101.19 -49.16 REMARK 500 2 LYS A 37 -62.22 -153.38 REMARK 500 2 HIS A 39 -37.98 -169.57 REMARK 500 2 ARG B 106 80.78 28.64 REMARK 500 2 PHE B 109 -79.03 -138.97 REMARK 500 2 CYS B 123 -167.82 -104.36 REMARK 500 2 PRO B 127 126.62 -15.52 REMARK 500 2 GLU B 157 -158.68 51.54 REMARK 500 2 GLU B 160 76.85 -171.70 REMARK 500 3 THR A 32 -0.40 -145.35 REMARK 500 3 ARG A 34 -85.63 -170.18 REMARK 500 3 LYS A 36 37.90 -82.62 REMARK 500 3 ARG B 106 79.44 29.84 REMARK 500 3 PHE B 109 -113.84 -159.12 REMARK 500 3 GLN B 119 73.98 55.48 REMARK 500 3 PRO B 127 124.90 -16.63 REMARK 500 3 ARG B 136 44.31 70.42 REMARK 500 3 PRO B 148 -31.56 -37.67 REMARK 500 4 ARG A 34 -70.71 -158.86 REMARK 500 4 LYS A 37 54.06 -171.03 REMARK 500 4 ARG B 106 81.30 29.87 REMARK 500 4 PHE B 109 -113.76 -162.73 REMARK 500 4 PRO B 127 128.26 -17.15 REMARK 500 5 LYS A 37 54.13 -153.47 REMARK 500 5 ARG B 106 84.78 29.27 REMARK 500 5 PHE B 109 -91.83 -150.06 REMARK 500 5 GLN B 119 90.01 47.48 REMARK 500 5 LEU B 125 14.90 -143.90 REMARK 500 5 PRO B 127 117.94 -16.22 REMARK 500 5 PRO B 148 -29.58 -37.06 REMARK 500 5 GLU B 157 155.59 57.87 REMARK 500 6 LYS A 37 -61.93 -155.66 REMARK 500 6 HIS A 39 -61.75 -170.96 REMARK 500 6 ARG B 106 79.28 29.61 REMARK 500 6 ASN B 107 63.37 -103.80 REMARK 500 6 PHE B 109 -121.58 -171.21 REMARK 500 6 PRO B 127 118.00 -17.25 REMARK 500 6 PRO B 148 -30.79 -38.07 REMARK 500 6 GLU B 157 -146.91 33.22 REMARK 500 6 CYS B 158 95.76 -49.81 REMARK 500 7 PHE B 109 -124.51 -171.02 REMARK 500 7 GLN B 119 75.75 51.72 REMARK 500 REMARK 500 THIS ENTRY HAS 157 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 2 HIS B 131 0.11 SIDE CHAIN REMARK 500 3 HIS B 131 0.09 SIDE CHAIN REMARK 500 4 HIS B 131 0.10 SIDE CHAIN REMARK 500 5 HIS B 131 0.09 SIDE CHAIN REMARK 500 6 HIS B 131 0.10 SIDE CHAIN REMARK 500 8 HIS B 131 0.09 SIDE CHAIN REMARK 500 9 HIS B 131 0.10 SIDE CHAIN REMARK 500 10 HIS B 131 0.10 SIDE CHAIN REMARK 500 11 HIS B 131 0.09 SIDE CHAIN REMARK 500 12 HIS B 131 0.09 SIDE CHAIN REMARK 500 13 HIS B 131 0.10 SIDE CHAIN REMARK 500 15 HIS B 131 0.09 SIDE CHAIN REMARK 500 16 HIS B 131 0.09 SIDE CHAIN REMARK 500 17 HIS B 131 0.09 SIDE CHAIN REMARK 500 18 HIS B 131 0.10 SIDE CHAIN REMARK 500 19 HIS B 131 0.10 SIDE CHAIN REMARK 500 20 HIS B 131 0.10 SIDE CHAIN 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 B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 111 SG REMARK 620 2 CYS B 114 SG 113.2 REMARK 620 3 HIS B 131 NE2 116.2 110.0 REMARK 620 4 CYS B 134 SG 114.9 88.0 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 123 SG REMARK 620 2 CYS B 126 SG 109.0 REMARK 620 3 CYS B 147 SG 109.2 123.9 REMARK 620 4 CYS B 150 SG 124.5 100.8 89.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36376 RELATED DB: BMRB REMARK 900 STRUCTURAL BASIS OF RACK7 PHD TO READ A PEDIATRIC GLIOBLASTOMA- REMARK 900 ASSOCIATED HISTONE MUTATION H3.3G34R DBREF 7CWH A 31 41 UNP P84243 H33_HUMAN 32 42 DBREF 7CWH B 103 163 UNP Q5TH12 Q5TH12_HUMAN 58 118 SEQADV 7CWH ARG A 34 UNP P84243 GLY 35 ENGINEERED MUTATION SEQRES 1 A 11 SER THR GLY ARG VAL LYS LYS PRO HIS ARG TYR SEQRES 1 B 61 GLN ASP GLY ARG ASN ASP PHE TYR CYS TRP VAL CYS HIS SEQRES 2 B 61 ARG GLU GLY GLN VAL LEU CYS CYS GLU LEU CYS PRO ARG SEQRES 3 B 61 VAL TYR HIS ALA LYS CYS LEU ARG LEU THR SER GLU PRO SEQRES 4 B 61 GLU GLY ASP TRP PHE CYS PRO GLU CYS GLU LYS ILE THR SEQRES 5 B 61 VAL ALA GLU CYS ILE GLU THR GLN SER HET ZN B 201 1 HET ZN B 202 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 CYS B 147 GLU B 157 1 11 SHEET 1 AA1 2 VAL B 120 LEU B 121 0 SHEET 2 AA1 2 TYR B 130 HIS B 131 -1 O TYR B 130 N LEU B 121 LINK SG CYS B 111 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 114 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 123 ZN ZN B 202 1555 1555 2.31 LINK SG CYS B 126 ZN ZN B 202 1555 1555 2.31 LINK NE2 HIS B 131 ZN ZN B 201 1555 1555 2.10 LINK SG CYS B 134 ZN ZN B 201 1555 1555 2.39 LINK SG CYS B 147 ZN ZN B 202 1555 1555 2.29 LINK SG CYS B 150 ZN ZN B 202 1555 1555 2.29 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