HEADER LIGASE 27-OCT-03 1UR6 TITLE NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBCH5B, UBIQUITIN CARRIER PROTEIN, E2(17)KB 2; COMPND 5 EC: 6.3.2.19; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RING FINGER, RESIDUES 12-63; COMPND 10 SYNONYM: CNOT4, NOT4H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS LIGASE, UBIQUITIN CONJUGATING ENZYME, UBIQUITIN LIGASE, RING FINGER KEYWDS 2 PROTEIN, CCR4-NOT COMPLEX, TRANSCRIPTION REGULATION EXPDTA SOLUTION NMR; THEORETICAL MODEL NUMMDL 5 AUTHOR C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,F.M.A.VAN SCHAIK, AUTHOR 2 H.TH.M.TIMMERS,R.BOELENS REVDAT 3 15-MAY-24 1UR6 1 REMARK LINK REVDAT 2 24-FEB-09 1UR6 1 VERSN REVDAT 1 07-MAY-04 1UR6 0 JRNL AUTH C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,F.M.A.VAN SCHAIK, JRNL AUTH 2 H.T.M.TIMMERS,R.BOELENS JRNL TITL STRUCTURAL MODEL OF THE UBCH5B/CNOT4 COMPLEX REVEALED BY JRNL TITL 2 COMBINING NMR, MUTAGENESIS, AND DOCKING APPROACHES. JRNL REF STRUCTURE V. 12 633 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15062086 JRNL DOI 10.1016/J.STR.2004.03.004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS AS DESCIRIBED IN C. REMARK 3 DOMINGUEZ ET AL. (2003), J.AM.CHEM.SOC, 125, P1731 REMARK 4 REMARK 4 1UR6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1290013704. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NONE 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 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS THEORETICAL MODEL ENTRY WAS NOT ANNOTATED AND NOT REMARK 220 VALIDATED BY THE WWPDB STAFF AND THEREFORE MAY NOT CONFORM REMARK 220 TO THE PDB FORMAT. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 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 400 REMARK 400 COMPOUND REMARK 400 CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS REMARK 400 ATP + UBIQUITIN + PROTEIN LYSINE = AMP + DIPHOSPHATE + PROTEIN REMARK 400 N-UBIQUITYLLYSINE. 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 HA ALA A 2 HB2 CYS B 17 1.31 REMARK 500 HZ2 LYS A 63 OD2 ASP B 48 1.56 REMARK 500 OE2 GLU A 140 HZ2 LYS A 144 1.59 REMARK 500 H3 MET A 1 OE2 GLU B 19 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 PRO A 18 -157.27 -70.01 REMARK 500 1 GLN A 20 -48.54 74.95 REMARK 500 1 GLN A 34 65.53 -108.98 REMARK 500 1 VAL A 49 88.82 -162.58 REMARK 500 1 PRO A 61 32.51 -83.36 REMARK 500 1 PHE A 62 -33.81 -148.73 REMARK 500 1 GLN A 92 -164.11 66.55 REMARK 500 1 TRP A 93 -176.23 -171.66 REMARK 500 1 PRO A 95 -84.82 -15.03 REMARK 500 1 ASP A 112 93.56 61.74 REMARK 500 1 PRO A 113 178.75 -59.02 REMARK 500 1 PRO A 118 -115.73 -95.66 REMARK 500 1 PHE B 40 33.23 -77.15 REMARK 500 1 CYS B 41 -47.67 -145.32 REMARK 500 1 ALA B 55 24.86 -140.45 REMARK 500 1 CYS B 56 -28.08 -148.18 REMARK 500 1 ARG B 57 -1.38 72.47 REMARK 500 2 ALA A 2 57.57 -152.20 REMARK 500 2 ALA A 19 112.46 -171.94 REMARK 500 2 GLN A 20 -28.76 73.32 REMARK 500 2 PRO A 44 39.26 -75.55 REMARK 500 2 VAL A 49 85.07 -163.17 REMARK 500 2 PRO A 57 -154.34 -80.08 REMARK 500 2 PHE A 62 -37.39 -140.44 REMARK 500 2 SER A 91 62.99 63.47 REMARK 500 2 GLN A 92 101.17 67.05 REMARK 500 2 ASP A 112 88.49 64.15 REMARK 500 2 PRO A 113 172.93 -58.32 REMARK 500 2 PRO A 118 -135.24 -87.02 REMARK 500 2 PRO B 15 -67.09 -22.31 REMARK 500 2 ILE B 37 -157.34 -129.49 REMARK 500 2 PHE B 40 35.47 -87.36 REMARK 500 2 CYS B 41 -50.75 -149.61 REMARK 500 2 CYS B 56 -21.09 139.45 REMARK 500 3 VAL A 49 57.32 -150.38 REMARK 500 3 PRO A 57 -158.81 -75.02 REMARK 500 3 PRO A 61 36.56 -83.20 REMARK 500 3 PHE A 62 -54.61 -146.60 REMARK 500 3 GLN A 92 110.64 69.46 REMARK 500 3 LEU A 97 -151.02 -140.15 REMARK 500 3 ASP A 112 79.62 60.36 REMARK 500 3 PRO A 113 177.02 -59.40 REMARK 500 3 PRO A 118 -118.96 -86.87 REMARK 500 3 CYS B 17 -24.37 -156.26 REMARK 500 3 MET B 18 31.40 75.15 REMARK 500 3 TYR B 35 112.06 -160.24 REMARK 500 3 ARG B 46 42.14 -90.90 REMARK 500 3 THR B 47 -53.81 -156.13 REMARK 500 3 GLU B 49 -165.99 -79.30 REMARK 500 3 CYS B 56 -5.52 95.42 REMARK 500 REMARK 500 THIS ENTRY HAS 88 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 B 79 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 14 SG REMARK 620 2 CYS B 17 SG 81.2 REMARK 620 3 CYS B 38 SG 86.2 156.9 REMARK 620 4 CYS B 41 SG 84.5 79.7 79.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 80 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 31 SG REMARK 620 2 CYS B 33 SG 79.9 REMARK 620 3 CYS B 53 SG 88.9 85.8 REMARK 620 4 CYS B 56 SG 170.2 98.2 81.3 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 79 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 80 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E4U RELATED DB: PDB REMARK 900 N-TERMINAL RING FINGER DOMAIN OF HUMAN NOT-4 DBREF 1UR6 A 1 147 UNP P51669 UB5B_HUMAN 1 147 DBREF 1UR6 B 12 63 UNP O95628 O95628 12 63 SEQRES 1 A 147 MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU SEQRES 2 A 147 ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL SEQRES 3 A 147 GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY SEQRES 4 A 147 PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU SEQRES 5 A 147 THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO SEQRES 6 A 147 LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE SEQRES 7 A 147 ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SER SEQRES 8 A 147 GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SEQRES 9 A 147 SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP SEQRES 10 A 147 PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP SEQRES 11 A 147 ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN SEQRES 12 A 147 LYS TYR ALA MET SEQRES 1 B 52 VAL GLU CYS PRO LEU CYS MET GLU PRO LEU GLU ILE ASP SEQRES 2 B 52 ASP ILE ASN PHE PHE PRO CYS THR CYS GLY TYR GLN ILE SEQRES 3 B 52 CYS ARG PHE CYS TRP HIS ARG ILE ARG THR ASP GLU ASN SEQRES 4 B 52 GLY LEU CYS PRO ALA CYS ARG LYS PRO TYR PRO GLU ASP HET ZN B 79 1 HET ZN B 80 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 LEU A 3 ASP A 16 1 14 HELIX 2 2 LEU A 86 ARG A 90 5 5 HELIX 3 3 THR A 98 CYS A 111 1 14 HELIX 4 4 PRO A 121 ASP A 130 1 10 HELIX 5 5 ASP A 130 TYR A 145 1 16 HELIX 6 6 GLU B 22 ILE B 26 5 5 HELIX 7 7 CYS B 38 ARG B 46 1 9 SHEET 1 AA 3 HIS A 32 ILE A 37 0 SHEET 2 AA 3 PHE A 50 HIS A 55 -1 O PHE A 50 N ILE A 37 SHEET 3 AA 3 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 LINK SG CYS B 14 ZN ZN B 79 1555 1555 2.47 LINK SG CYS B 17 ZN ZN B 79 1555 1555 2.46 LINK SG CYS B 31 ZN ZN B 80 1555 1555 2.36 LINK SG CYS B 33 ZN ZN B 80 1555 1555 2.51 LINK SG CYS B 38 ZN ZN B 79 1555 1555 2.35 LINK SG CYS B 41 ZN ZN B 79 1555 1555 2.45 LINK SG CYS B 53 ZN ZN B 80 1555 1555 2.52 LINK SG CYS B 56 ZN ZN B 80 1555 1555 2.41 SITE 1 AC1 4 CYS B 14 CYS B 17 CYS B 38 CYS B 41 SITE 1 AC2 4 CYS B 31 CYS B 33 CYS B 53 CYS B 56 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