HEADER PEPTIDE BINDING PROTEIN 06-JAN-20 6VFO TITLE SOLUTION STRUCTURE OF THE PHD OF MOUSE UHRF1 (NP95) COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR PROTEIN 95,NUCLEAR ZINC FINGER PROTEIN NP95,RING- COMPND 5 TYPE E3 UBIQUITIN TRANSFERASE UHRF1,UBIQUITIN-LIKE PHD AND RING COMPND 6 FINGER DOMAIN-CONTAINING PROTEIN 1,MUHRF1,UBIQUITIN-LIKE-CONTAINING COMPND 7 PHD AND RING FINGER DOMAINS PROTEIN 1; COMPND 8 EC: 2.3.2.27; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: UHRF1, NP95; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE, PLANT HOMEODOMAIN, NP95, H3K9ME3, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.LEMAK,S.HOULISTON,S.DUAN,C.H.ARROWSMITH REVDAT 5 15-MAY-24 6VFO 1 REMARK REVDAT 4 14-JUN-23 6VFO 1 REMARK REVDAT 3 02-SEP-20 6VFO 1 JRNL REVDAT 2 15-JUL-20 6VFO 1 JRNL REVDAT 1 17-JUN-20 6VFO 0 JRNL AUTH M.TAUBER,S.KREUZ,A.LEMAK,P.MANDAL,Z.YERKESH,A.VELUCHAMY, JRNL AUTH 2 B.AL-GASHGARI,A.ALJAHANI,L.V.CORTES-MEDINA,D.AZHIBEK,L.FAN, JRNL AUTH 3 M.S.ONG,S.DUAN,S.HOULISTON,C.H.ARROWSMITH,W.FISCHLE JRNL TITL ALTERNATIVE SPLICING AND ALLOSTERIC REGULATION MODULATE THE JRNL TITL 2 CHROMATIN BINDING OF UHRF1. JRNL REF NUCLEIC ACIDS RES. V. 48 7728 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32609811 JRNL DOI 10.1093/NAR/GKAA520 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246279. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 200 UM [U-99% 13C; U-99% 15N] REMARK 210 PHD, 5 MM DTT, 2 MM BETA- REMARK 210 MERCAPTOETHANOL, 5 MM TCEP, 150 REMARK 210 MM SODIUM CHLORIDE, 50 MM SODIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D CBCA(CO)NH; 3D HNCA; REMARK 210 3D HBHA(CO)NH; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, ABACUS, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: MONOMERIC 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 380 O 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 PRO A 305 83.52 -67.55 REMARK 500 1 ASP A 312 -29.07 74.76 REMARK 500 1 ALA A 331 65.75 63.42 REMARK 500 2 ASP A 312 90.29 53.01 REMARK 500 2 ALA A 331 80.02 52.05 REMARK 500 3 LYS A 311 -69.16 66.96 REMARK 500 3 ASP A 312 73.54 132.01 REMARK 500 3 ALA A 331 84.17 77.44 REMARK 500 3 SER A 372 54.84 -90.96 REMARK 500 4 SER A 306 102.18 -57.57 REMARK 500 4 LYS A 311 -31.77 72.28 REMARK 500 4 ASP A 312 75.75 61.66 REMARK 500 4 PRO A 317 -156.89 -79.12 REMARK 500 4 ARG A 329 34.50 -98.68 REMARK 500 4 ALA A 331 93.35 66.02 REMARK 500 5 ALA A 331 76.08 52.57 REMARK 500 5 ASP A 342 17.32 58.75 REMARK 500 6 ALA A 331 93.04 59.72 REMARK 500 6 SER A 373 93.22 -64.19 REMARK 500 6 VAL A 375 96.88 -58.84 REMARK 500 7 ALA A 331 83.25 68.23 REMARK 500 8 SER A 306 109.51 -58.79 REMARK 500 8 ARG A 308 -35.92 -132.59 REMARK 500 8 CYS A 310 76.60 -110.11 REMARK 500 8 LYS A 311 92.85 -33.28 REMARK 500 8 ASP A 312 39.08 35.20 REMARK 500 8 ALA A 331 77.12 48.84 REMARK 500 8 ASP A 342 17.26 55.37 REMARK 500 8 PRO A 353 108.34 -58.30 REMARK 500 9 SER A 306 95.53 -67.30 REMARK 500 9 ALA A 331 82.88 35.34 REMARK 500 9 ASP A 342 16.49 57.60 REMARK 500 9 ASP A 371 0.47 -62.82 REMARK 500 9 SER A 372 -26.66 82.32 REMARK 500 9 SER A 373 98.11 -68.82 REMARK 500 10 PRO A 305 44.14 -79.04 REMARK 500 10 LYS A 311 -71.65 66.39 REMARK 500 10 ASP A 312 49.30 133.48 REMARK 500 10 ALA A 331 87.31 67.00 REMARK 500 10 SER A 372 86.60 71.67 REMARK 500 11 LYS A 311 -38.45 73.51 REMARK 500 11 ASP A 312 90.36 61.20 REMARK 500 11 PRO A 317 -163.95 -72.10 REMARK 500 11 ARG A 319 -63.58 -126.84 REMARK 500 11 ALA A 331 70.83 68.73 REMARK 500 11 ASP A 371 -6.29 71.08 REMARK 500 11 SER A 372 34.17 -90.67 REMARK 500 11 SER A 373 -173.73 -66.61 REMARK 500 12 ASP A 312 86.73 45.71 REMARK 500 12 PRO A 366 -54.98 -29.81 REMARK 500 REMARK 500 THIS ENTRY HAS 89 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 307 SG REMARK 620 2 CYS A 310 SG 110.4 REMARK 620 3 CYS A 318 SG 111.0 106.4 REMARK 620 4 CYS A 321 SG 110.4 109.4 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 323 SG REMARK 620 2 CYS A 326 SG 109.8 REMARK 620 3 HIS A 346 ND1 104.8 109.1 REMARK 620 4 CYS A 349 SG 112.6 111.6 108.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 338 SG REMARK 620 2 GLU A 340 OE2 69.5 REMARK 620 3 CYS A 341 SG 110.9 72.8 REMARK 620 4 CYS A 365 SG 106.7 175.9 110.5 REMARK 620 5 CYS A 368 SG 112.4 72.6 108.3 108.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30705 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE PHD OF MOUSE UHRF1 (NP95) DBREF 6VFO A 303 380 UNP Q8VDF2 UHRF1_MOUSE 303 380 SEQRES 1 A 78 SER GLY PRO SER CYS ARG PHE CYS LYS ASP ASP GLU ASN SEQRES 2 A 78 LYS PRO CYS ARG LYS CYS ALA CYS HIS VAL CYS GLY GLY SEQRES 3 A 78 ARG GLU ALA PRO GLU LYS GLN LEU LEU CYS ASP GLU CYS SEQRES 4 A 78 ASP MET ALA PHE HIS LEU TYR CYS LEU LYS PRO PRO LEU SEQRES 5 A 78 THR SER VAL PRO PRO GLU PRO GLU TRP TYR CYS PRO SER SEQRES 6 A 78 CYS ARG THR ASP SER SER GLU VAL VAL GLN ALA GLY GLU HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 AA1 CYS A 318 ALA A 322 5 5 HELIX 2 AA2 ALA A 331 GLU A 333 5 3 HELIX 3 AA3 TYR A 348 LEU A 350 5 3 HELIX 4 AA4 CYS A 365 ARG A 369 5 5 SHEET 1 AA1 2 GLN A 335 CYS A 338 0 SHEET 2 AA1 2 MET A 343 HIS A 346 -1 O MET A 343 N CYS A 338 LINK SG CYS A 307 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 318 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 321 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 323 ZN ZN A 402 1555 1555 2.32 LINK SG CYS A 326 ZN ZN A 402 1555 1555 2.35 LINK SG CYS A 338 ZN ZN A 403 1555 1555 2.39 LINK OE2 GLU A 340 ZN ZN A 403 1555 1555 2.29 LINK SG CYS A 341 ZN ZN A 403 1555 1555 2.38 LINK ND1 HIS A 346 ZN ZN A 402 1555 1555 2.08 LINK SG CYS A 349 ZN ZN A 402 1555 1555 2.35 LINK SG CYS A 365 ZN ZN A 403 1555 1555 2.33 LINK SG CYS A 368 ZN ZN A 403 1555 1555 2.40 CISPEP 1 LYS A 351 PRO A 352 1 5.54 CISPEP 2 LYS A 351 PRO A 352 2 2.37 CISPEP 3 LYS A 351 PRO A 352 3 -0.55 CISPEP 4 LYS A 351 PRO A 352 4 1.97 CISPEP 5 LYS A 351 PRO A 352 5 3.67 CISPEP 6 LYS A 351 PRO A 352 6 1.37 CISPEP 7 LYS A 351 PRO A 352 7 4.27 CISPEP 8 LYS A 351 PRO A 352 8 -3.14 CISPEP 9 LYS A 351 PRO A 352 9 2.28 CISPEP 10 LYS A 351 PRO A 352 10 -3.42 CISPEP 11 LYS A 351 PRO A 352 11 -3.98 CISPEP 12 LYS A 351 PRO A 352 12 2.84 CISPEP 13 LYS A 351 PRO A 352 13 -0.25 CISPEP 14 LYS A 351 PRO A 352 14 4.64 CISPEP 15 LYS A 351 PRO A 352 15 3.64 CISPEP 16 LYS A 351 PRO A 352 16 1.63 CISPEP 17 LYS A 351 PRO A 352 17 1.34 CISPEP 18 LYS A 351 PRO A 352 18 7.27 CISPEP 19 LYS A 351 PRO A 352 19 -1.51 CISPEP 20 LYS A 351 PRO A 352 20 1.43 SITE 1 AC1 4 CYS A 307 CYS A 310 CYS A 318 CYS A 321 SITE 1 AC2 4 CYS A 323 CYS A 326 HIS A 346 CYS A 349 SITE 1 AC3 5 CYS A 338 GLU A 340 CYS A 341 CYS A 365 SITE 2 AC3 5 CYS A 368 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