HEADER DNA BINDING PROTEIN/GENE REGULATION 21-SEP-10 2L3R TITLE NMR STRUCTURE OF UHRF1 TANDEM TUDOR DOMAINS IN A COMPLEX WITH HISTONE TITLE 2 H3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 126-285; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3; COMPND 8 CHAIN: B; COMPND 9 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: UHRF1, ICBP90, NP95, RNF106; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_COMMON: SYNTHETIC; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS TUDOR DOMAIN, HETEROCHROMATIN, TRANSCRIPTIONAL REPRESSION, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA BINDING PROTEIN, KEYWDS 3 DNA BINDING PROTEIN-GENE REGULATION COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR N.NADY,A.LEMAK,C.FARES,A.GUTMANAS,G.AVVAKUMOV,S.XUE,C.ARROWSMITH, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 05-FEB-20 2L3R 1 REMARK SEQADV LINK REVDAT 3 24-AUG-11 2L3R 1 JRNL VERSN REVDAT 2 27-APR-11 2L3R 1 JRNL REVDAT 1 13-APR-11 2L3R 0 JRNL AUTH N.NADY,A.LEMAK,J.R.WALKER,G.V.AVVAKUMOV,M.S.KARETA,M.ACHOUR, JRNL AUTH 2 S.XUE,S.DUAN,A.ALLALI-HASSANI,X.ZUO,Y.X.WANG,C.BRONNER, JRNL AUTH 3 F.CHEDIN,C.H.ARROWSMITH,S.DHE-PAGANON JRNL TITL RECOGNITION OF MULTIVALENT HISTONE STATES ASSOCIATED WITH JRNL TITL 2 HETEROCHROMATIN BY UHRF1 PROTEIN. JRNL REF J.BIOL.CHEM. V. 286 24300 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21489993 JRNL DOI 10.1074/JBC.M111.234104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ABACUS, CNS REMARK 3 AUTHORS : LEMAK (ABACUS), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000101919. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 250 REMARK 210 PRESSURE : 1 AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 15N] PROTEIN, 0.6 REMARK 210 MM [U-100% 13C] PROTEIN, 3 MM REMARK 210 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 ARO-NOESY; ARO-2D-1H-13C HSQC; REMARK 210 ARO-3D-TOCSY; 2D-TOCSY; 3D- REMARK 210 EDITED-15N/13C NOESY; IPAP-15N- REMARK 210 1H HSQC; J-EVOLUTION-13CO-13CA; REMARK 210 J-EVOLUTION-15N-13CO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, NMRPIPE, SPARKY, REMARK 210 FUDA, TALOS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLY A 124 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 LEU A 225 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 4 LEU A 225 N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 5 LEU A 225 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 6 LEU A 225 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 7 LEU A 225 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 8 LEU A 225 N - CA - C ANGL. DEV. = 17.3 DEGREES REMARK 500 9 LEU A 225 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 11 LEU A 225 N - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 12 LEU A 225 N - CA - C ANGL. DEV. = 16.5 DEGREES REMARK 500 13 LEU A 225 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 14 LEU A 225 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 15 LEU A 225 N - CA - C ANGL. DEV. = -17.4 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 MET A 126 -114.41 -111.95 REMARK 500 1 GLU A 129 62.50 64.65 REMARK 500 1 GLU A 131 75.05 56.77 REMARK 500 1 LEU A 132 -136.12 -116.79 REMARK 500 1 VAL A 137 103.99 -45.86 REMARK 500 1 ASN A 138 5.08 81.55 REMARK 500 1 SER A 165 -62.37 -158.99 REMARK 500 1 ARG A 166 -40.55 -144.02 REMARK 500 1 ASP A 167 45.53 -146.63 REMARK 500 1 GLU A 168 72.28 58.92 REMARK 500 1 SER A 171 -44.33 -144.81 REMARK 500 1 VAL A 182 -155.66 -96.38 REMARK 500 1 TYR A 191 73.80 -116.11 REMARK 500 1 ALA A 208 90.85 -67.66 REMARK 500 1 LEU A 217 85.09 -68.19 REMARK 500 1 ASP A 263 -61.85 -143.28 REMARK 500 1 GLU A 276 42.93 -156.50 REMARK 500 1 ARG B 8 161.45 73.88 REMARK 500 2 MET A 126 -116.34 -98.39 REMARK 500 2 GLU A 129 65.86 65.94 REMARK 500 2 GLU A 131 72.79 55.11 REMARK 500 2 LEU A 132 -140.35 -113.49 REMARK 500 2 ASN A 138 0.32 80.72 REMARK 500 2 ARG A 158 143.76 179.97 REMARK 500 2 LYS A 162 75.46 -69.77 REMARK 500 2 SER A 165 -59.07 -152.56 REMARK 500 2 ARG A 166 -36.76 -145.23 REMARK 500 2 CYS A 170 79.51 -65.60 REMARK 500 2 SER A 171 -68.76 -142.56 REMARK 500 2 SER A 172 19.40 56.55 REMARK 500 2 VAL A 182 -156.90 -100.08 REMARK 500 2 TYR A 191 72.20 -119.25 REMARK 500 2 ALA A 208 80.83 -68.70 REMARK 500 2 LEU A 217 96.57 -66.92 REMARK 500 2 ASP A 263 -56.53 -143.90 REMARK 500 2 ASP A 268 63.01 39.07 REMARK 500 2 GLU A 276 34.83 -141.76 REMARK 500 2 ALA B 7 -163.74 -160.02 REMARK 500 2 SER B 10 81.17 -62.63 REMARK 500 3 MET A 126 -152.35 -127.10 REMARK 500 3 TRP A 127 171.54 -40.87 REMARK 500 3 GLU A 129 68.01 67.40 REMARK 500 3 GLU A 131 79.70 53.15 REMARK 500 3 LEU A 132 -136.61 -121.03 REMARK 500 3 ASN A 138 1.91 83.70 REMARK 500 3 ARG A 158 102.28 -174.25 REMARK 500 3 LYS A 162 72.15 -68.87 REMARK 500 3 SER A 165 -56.92 -153.31 REMARK 500 3 ARG A 166 -37.76 -144.90 REMARK 500 3 SER A 171 -55.36 -143.89 REMARK 500 REMARK 500 THIS ENTRY HAS 331 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 164 SER A 165 1 144.84 REMARK 500 GLU A 168 PRO A 169 1 146.65 REMARK 500 PRO A 164 SER A 165 2 144.03 REMARK 500 PRO A 164 SER A 165 3 143.92 REMARK 500 PRO A 164 SER A 165 5 138.25 REMARK 500 PRO A 164 SER A 165 6 146.65 REMARK 500 PRO A 164 SER A 165 7 146.56 REMARK 500 GLU A 168 PRO A 169 7 119.29 REMARK 500 PRO A 164 SER A 165 8 147.48 REMARK 500 PRO A 164 SER A 165 9 149.52 REMARK 500 PRO A 164 SER A 165 11 147.02 REMARK 500 GLU A 168 PRO A 169 12 117.81 REMARK 500 PRO A 164 SER A 165 13 146.57 REMARK 500 GLU A 168 PRO A 169 13 145.21 REMARK 500 PRO A 164 SER A 165 14 149.35 REMARK 500 PRO A 164 SER A 165 15 136.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17200 RELATED DB: BMRB DBREF 2L3R A 126 285 UNP Q96T88 UHRF1_HUMAN 126 285 DBREF 2L3R B 1 11 UNP Q3BDD9 Q3BDD9_9INSE 2 12 SEQADV 2L3R GLY A 124 UNP Q96T88 EXPRESSION TAG SEQADV 2L3R GLY A 125 UNP Q96T88 EXPRESSION TAG SEQRES 1 A 162 GLY GLY MET TRP ASP GLU THR GLU LEU GLY LEU TYR LYS SEQRES 2 A 162 VAL ASN GLU TYR VAL ASP ALA ARG ASP THR ASN MET GLY SEQRES 3 A 162 ALA TRP PHE GLU ALA GLN VAL VAL ARG VAL THR ARG LYS SEQRES 4 A 162 ALA PRO SER ARG ASP GLU PRO CYS SER SER THR SER ARG SEQRES 5 A 162 PRO ALA LEU GLU GLU ASP VAL ILE TYR HIS VAL LYS TYR SEQRES 6 A 162 ASP ASP TYR PRO GLU ASN GLY VAL VAL GLN MET ASN SER SEQRES 7 A 162 ARG ASP VAL ARG ALA ARG ALA ARG THR ILE ILE LYS TRP SEQRES 8 A 162 GLN ASP LEU GLU VAL GLY GLN VAL VAL MET LEU ASN TYR SEQRES 9 A 162 ASN PRO ASP ASN PRO LYS GLU ARG GLY PHE TRP TYR ASP SEQRES 10 A 162 ALA GLU ILE SER ARG LYS ARG GLU THR ARG THR ALA ARG SEQRES 11 A 162 GLU LEU TYR ALA ASN VAL VAL LEU GLY ASP ASP SER LEU SEQRES 12 A 162 ASN ASP CYS ARG ILE ILE PHE VAL ASP GLU VAL PHE LYS SEQRES 13 A 162 ILE GLU ARG PRO GLY GLU SEQRES 1 B 11 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR MODRES 2L3R M3L B 9 LYS N-TRIMETHYLLYSINE HET M3L B 9 31 HETNAM M3L N-TRIMETHYLLYSINE FORMUL 2 M3L C9 H21 N2 O2 1+ HELIX 1 1 TYR A 191 ASN A 194 5 4 HELIX 2 2 LYS A 213 LEU A 217 5 5 HELIX 3 3 PHE A 273 GLU A 276 5 4 SHEET 1 A 7 VAL A 196 ASN A 200 0 SHEET 2 A 7 ILE A 183 LYS A 187 -1 N VAL A 186 O VAL A 197 SHEET 3 A 7 ALA A 150 THR A 160 -1 N GLN A 155 O LYS A 187 SHEET 4 A 7 PHE A 237 GLU A 248 -1 O TRP A 238 N TRP A 151 SHEET 5 A 7 VAL A 222 TYR A 227 -1 N LEU A 225 O TYR A 239 SHEET 6 A 7 VAL A 277 LYS A 279 -1 O PHE A 278 N MET A 224 SHEET 7 A 7 ILE A 211 ILE A 212 -1 N ILE A 212 O VAL A 277 SHEET 1 B 6 VAL A 204 ALA A 206 0 SHEET 2 B 6 TYR A 140 ARG A 144 -1 N ASP A 142 O ARG A 205 SHEET 3 B 6 ALA A 150 THR A 160 -1 O ALA A 154 N VAL A 141 SHEET 4 B 6 PHE A 237 GLU A 248 -1 O TRP A 238 N TRP A 151 SHEET 5 B 6 ARG A 253 VAL A 260 -1 O VAL A 260 N ASP A 240 SHEET 6 B 6 SER A 265 ILE A 271 -1 O CYS A 269 N ALA A 257 LINK C ARG B 8 N M3L B 9 1555 1555 1.35 LINK C M3L B 9 N SER B 10 1555 1555 1.35 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