HEADER TRANSFERASE, STRUCTURAL PROTEIN, SIGNALI06-APR-17 5VEY TITLE SOLUTION NMR STRUCTURE OF HISTONE H2A-H2B MONO-UBIQUITYLATED AT H2A TITLE 2 LYS15 IN COMPLEX WITH RNF169 (653-708) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H2B TYPE 1-J,HISTONE H2A TYPE 1-B/E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R,HISTONE H2A.2,HISTONE COMPND 5 H2A/A,HISTONE H2A/M; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: POLYUBIQUITIN-B; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF169; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: RING FINGER PROTEIN 169,RING-TYPE E3 UBIQUITIN TRANSFERASE COMPND 15 RNF169; COMPND 16 EC: 2.3.2.27; COMPND 17 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: HIST1H2BJ, H2BFR, HIST1H2AB, H2AFM, HIST1H2AE, H2AFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7.7; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBB; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: RNF169, KIAA1991; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS NUCLEOSOME, UBIQUITIN, UBIQUITIN LIGASE, COMPLEX, TRANSFERASE, KEYWDS 2 STRUCTURAL PROTEIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Q.HU,M.V.BOTUYAN,G.CUI,G.MER REVDAT 5 09-OCT-24 5VEY 1 REMARK REVDAT 4 23-FEB-22 5VEY 1 REMARK REVDAT 3 04-DEC-19 5VEY 1 REMARK REVDAT 2 31-MAY-17 5VEY 1 JRNL REVDAT 1 17-MAY-17 5VEY 0 JRNL AUTH Q.HU,M.V.BOTUYAN,G.CUI,D.ZHAO,G.MER JRNL TITL MECHANISMS OF UBIQUITIN-NUCLEOSOME RECOGNITION AND JRNL TITL 2 REGULATION OF 53BP1 CHROMATIN RECRUITMENT BY RNF168/169 AND JRNL TITL 3 RAD18. JRNL REF MOL. CELL V. 66 473 2017 JRNL REFN ISSN 1097-4164 JRNL PMID 28506460 JRNL DOI 10.1016/J.MOLCEL.2017.04.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227297. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 298 REMARK 210 PH : 6; 6 REMARK 210 IONIC STRENGTH : 50 MM KCL; 50 MM KCL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL; NULL; NULL; NULL; NULL; REMARK 210 NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TROSY 1H-15N HSQC; 22D TROSY REMARK 210 1H-15N HSQC; 2D 1H-15N HSQC; 2D REMARK 210 1H-13C HMQC; 2D 1H-13C HSQC; 3D REMARK 210 TROSY HNCO; 3D TROSY HNCA; 3D REMARK 210 TROSY HN(CO)CA; 3D TROSY HNCACB; REMARK 210 3D TROSY HN(COCA)CB; 3D HBHA(CO) REMARK 210 NH; 3D HCCCONH; 3D CCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY- REMARK 210 HSQC; 13C-EDITED/FILTERED NOESY; REMARK 210 15N-EDITED/FILTERED NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 NOESY-HMQC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HNCO; 3D HN(CA)CO REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRDRAW, NMRVIEW, REMARK 210 NMRPIPE, SPARKY, TALOS, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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, C 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 MET A 8 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 HIS A 25 89.70 -178.05 REMARK 500 1 PRO A 79 -175.28 -52.67 REMARK 500 1 ALA A 103 118.01 178.97 REMARK 500 1 PRO A 115 101.88 -59.85 REMARK 500 1 ALA A 192 110.96 -177.04 REMARK 500 1 GLU B 64 81.88 58.61 REMARK 500 1 ARG C 685 -18.58 84.53 REMARK 500 1 ALA C 707 -74.48 67.22 REMARK 500 2 HIS A 25 80.86 -163.62 REMARK 500 2 ALA A 101 27.05 44.96 REMARK 500 2 SER A 102 21.43 -149.66 REMARK 500 2 GLU B 64 83.65 53.76 REMARK 500 2 ARG C 685 153.27 178.07 REMARK 500 3 HIS A 25 88.17 -156.90 REMARK 500 3 PRO A 79 -179.88 -55.24 REMARK 500 3 ALA A 192 98.46 178.52 REMARK 500 3 GLU B 64 86.80 54.74 REMARK 500 3 ARG C 685 108.34 62.95 REMARK 500 3 ARG C 690 47.32 -97.96 REMARK 500 3 ASP C 695 -69.12 -121.50 REMARK 500 3 GLN C 696 -87.36 58.09 REMARK 500 3 ARG C 700 42.69 -85.21 REMARK 500 3 ALA C 705 120.14 62.03 REMARK 500 4 HIS A 25 90.13 -176.16 REMARK 500 4 SER A 102 18.45 57.21 REMARK 500 4 PRO A 115 104.26 -59.34 REMARK 500 4 GLU B 64 84.28 54.66 REMARK 500 4 ASP C 653 143.52 -177.27 REMARK 500 4 ARG C 685 74.60 65.38 REMARK 500 4 SER C 693 -66.01 -154.18 REMARK 500 5 HIS A 25 91.13 -179.33 REMARK 500 5 PRO A 79 -176.66 -63.48 REMARK 500 5 ALA A 101 -63.01 71.70 REMARK 500 5 PRO A 115 106.59 -58.95 REMARK 500 5 GLN A 193 96.77 60.85 REMARK 500 5 GLU B 64 86.57 57.14 REMARK 500 5 ASP C 653 125.37 63.52 REMARK 500 5 ARG C 685 147.96 62.42 REMARK 500 5 ALA C 705 76.31 -171.16 REMARK 500 6 HIS A 25 91.16 -178.26 REMARK 500 6 PRO A 79 179.68 -51.14 REMARK 500 6 ALA A 103 93.34 -61.63 REMARK 500 6 ASP C 653 87.22 -156.36 REMARK 500 6 ARG C 685 59.43 71.53 REMARK 500 6 ASP C 695 98.32 53.49 REMARK 500 7 HIS A 25 78.26 -151.19 REMARK 500 7 PRO A 79 179.92 -51.46 REMARK 500 7 ALA A 192 -59.38 -167.44 REMARK 500 7 GLN A 193 161.71 59.25 REMARK 500 7 GLU B 64 86.04 58.86 REMARK 500 REMARK 500 THIS ENTRY HAS 154 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30275 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HISTONE H2A-H2B MONO-UBIQUITYLATED AT H2A REMARK 900 LYS15 IN COMPLEX WITH RNF169 (653-708) DBREF 5VEY A 9 99 UNP P06899 H2B1J_HUMAN 34 124 DBREF 5VEY A 101 194 UNP P04908 H2A1B_HUMAN 13 106 DBREF 5VEY B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5VEY C 653 708 UNP Q8NCN4 RN169_HUMAN 653 708 SEQADV 5VEY MET A 1 UNP P06899 INITIATING METHIONINE SEQADV 5VEY HIS A 2 UNP P06899 EXPRESSION TAG SEQADV 5VEY HIS A 3 UNP P06899 EXPRESSION TAG SEQADV 5VEY HIS A 4 UNP P06899 EXPRESSION TAG SEQADV 5VEY HIS A 5 UNP P06899 EXPRESSION TAG SEQADV 5VEY HIS A 6 UNP P06899 EXPRESSION TAG SEQADV 5VEY HIS A 7 UNP P06899 EXPRESSION TAG SEQADV 5VEY MET A 8 UNP P06899 EXPRESSION TAG SEQADV 5VEY SER A 100 UNP P06899 LINKER SEQADV 5VEY SER A 102 UNP P04908 LYS 14 LINKER SEQADV 5VEY GLY C 650 UNP Q8NCN4 EXPRESSION TAG SEQADV 5VEY HIS C 651 UNP Q8NCN4 EXPRESSION TAG SEQADV 5VEY MET C 652 UNP Q8NCN4 EXPRESSION TAG SEQRES 1 A 194 MET HIS HIS HIS HIS HIS HIS MET ARG LYS GLU SER TYR SEQRES 2 A 194 SER ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO SEQRES 3 A 194 ASP THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SEQRES 4 A 194 SER PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU SEQRES 5 A 194 ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE SEQRES 6 A 194 THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU SEQRES 7 A 194 PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR SEQRES 8 A 194 LYS ALA VAL THR LYS TYR THR SER SER ALA SER ALA LYS SEQRES 9 A 194 THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO VAL GLY SEQRES 10 A 194 ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SER GLU SEQRES 11 A 194 ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA ALA VAL SEQRES 12 A 194 LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU ALA GLY SEQRES 13 A 194 ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE ILE PRO SEQRES 14 A 194 ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU GLU LEU SEQRES 15 A 194 ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 59 GLY HIS MET ASP PRO VAL LEU ARG GLU MET GLU GLN LYS SEQRES 2 C 59 LEU GLN GLN GLU GLU GLU ASP ARG GLN LEU ALA LEU GLN SEQRES 3 C 59 LEU GLN ARG MET PHE ASP ASN GLU ARG ARG THR VAL SER SEQRES 4 C 59 ARG ARG LYS GLY SER VAL ASP GLN TYR LEU LEU ARG SER SEQRES 5 C 59 SER ASN MET ALA GLY ALA LYS HELIX 1 AA1 TYR A 13 HIS A 25 1 13 HELIX 2 AA2 SER A 31 ASN A 60 1 30 HELIX 3 AA3 THR A 66 LEU A 78 1 13 HELIX 4 AA4 PRO A 79 SER A 100 1 22 HELIX 5 AA5 THR A 105 GLY A 111 1 7 HELIX 6 AA6 PRO A 115 GLY A 126 1 12 HELIX 7 AA7 ALA A 134 ASN A 162 1 29 HELIX 8 AA8 ILE A 168 ASP A 179 1 12 HELIX 9 AA9 ASP A 179 LEU A 186 1 8 HELIX 10 AB1 THR B 22 GLY B 35 1 14 HELIX 11 AB2 PRO B 37 ASP B 39 5 3 HELIX 12 AB3 THR B 55 ASN B 60 5 6 HELIX 13 AB4 ASP C 653 ARG C 684 1 32 SHEET 1 AA1 2 GLY A 29 ILE A 30 0 SHEET 2 AA1 2 ARG A 166 ILE A 167 1 O ILE A 167 N GLY A 29 SHEET 1 AA2 2 THR A 64 ILE A 65 0 SHEET 2 AA2 2 ARG A 131 VAL A 132 1 O ARG A 131 N ILE A 65 SHEET 1 AA3 5 THR B 12 GLU B 16 0 SHEET 2 AA3 5 GLN B 2 THR B 7 -1 N ILE B 3 O LEU B 15 SHEET 3 AA3 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA3 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA3 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK NZ LYS A 104 C GLY B 76 1555 1555 1.33 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