HEADER VIRAL PROTEIN/PROTEIN BINDING 01-JUL-13 2MA9 TITLE HIV-1 VIF SOCS-BOX AND ELONGIN BC SOLUTION STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRION INFECTIVITY FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 139-174; COMPND 5 SYNONYM: VIF, SOR PROTEIN, VIRION INFECTIVITY FACTOR P17, VIRION COMPND 6 INFECTIVITY FACTOR P7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: ELONGIN 18 KDA SUBUNIT, ELONGIN-B, ELOB, RNA POLYMERASE II COMPND 12 TRANSCRIPTION FACTOR SIII SUBUNIT B, SIII P18; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1; COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: UNP RESIDUES 19-109; COMPND 18 SYNONYM: ELONGIN 15 KDA SUBUNIT, ELONGIN-C, ELOC, RNA POLYMERASE II COMPND 19 TRANSCRIPTION FACTOR SIII SUBUNIT C, SIII P15; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11698; SOURCE 5 GENE: VIF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: TCEB2; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PETDUET; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: TCEB1; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PETDUET KEYWDS HIV-1 VIF SOCS-BOX, ELONGIN BC, VIRAL PROTEIN-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.LU,J.R.BERGERON,R.A.ATKINSON,T.SCHALLER,D.A.VESELKOV,A.OREGIONI, AUTHOR 2 Y.YANG,S.J.MATTHEWS,M.H.MALIM,M.R.SANDERSON REVDAT 2 27-APR-16 2MA9 1 DBREF REMARK SEQADV SEQRES REVDAT 1 11-DEC-13 2MA9 0 JRNL AUTH Z.LU,J.R.BERGERON,R.A.ATKINSON,T.SCHALLER,D.A.VESELKOV, JRNL AUTH 2 A.OREGIONI,Y.YANG,S.J.MATTHEWS,M.H.MALIM,M.R.SANDERSON JRNL TITL INSIGHT INTO THE HIV-1 VIF SOCS-BOX-ELONGINBC INTERACTION. JRNL REF OPEN BIOLOGY V. 3 30100 2013 JRNL REFN ESSN 2046-2441 JRNL PMID 24225024 JRNL DOI 10.1098/RSOB.130100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA, HADDOCK REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX (CS-ROSETTA), REMARK 3 ALEXANDRE BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STARTING STRUCTURE OF HADDOCK REMARK 3 DOCKING IS PDB ENTRY 3DCG. REMARK 4 REMARK 4 2MA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB103405. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-99% 13C; U-99% 15N] REMARK 210 VIF SOCS, 0.2 MM ELONGIN B, 0.2 REMARK 210 MM ELONGIN C, 90% H2O/10% D2O; REMARK 210 0.2 MM VIF SOCS, 0.2 MM [U-99% REMARK 210 13C; U-99% 15N] ELONGIN B, 0.2 MM REMARK 210 [U-99% 13C; U-99% 15N] ELONGIN C, REMARK 210 90% H2O/10% D2O; 0.2 MM VIF SOCS, REMARK 210 0.2 MM [U-99% 13C; U-99% 15N] REMARK 210 ELONGIN B, 0.2 MM [U-99% 13C; U- REMARK 210 99% 15N] ELONGIN C, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-13C NOESY; 3D 1H-15N NOESY; REMARK 210 3D HCCH-TOCSY; 3D HNCO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCACO; REMARK 210 3D HNHA; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 5.5, TOPSPIN 3.0, CCPN REMARK 210 2.2, CS-ROSETTA, HADDOCK 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 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 HIS A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 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 OE2 GLU B 114 HZ1 LYS C 54 1.51 REMARK 500 OD1 ASP B 2 HZ1 LYS B 19 1.56 REMARK 500 HZ1 LYS A 31 OE2 GLU C 84 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 19 45.11 -97.96 REMARK 500 1 PRO A 24 136.04 -38.50 REMARK 500 1 VAL A 29 -118.69 -126.82 REMARK 500 1 ARG A 30 63.09 -163.91 REMARK 500 1 ASP A 35 -82.34 -150.67 REMARK 500 1 ARG A 36 -54.78 -175.36 REMARK 500 1 ARG B 9 59.49 -96.18 REMARK 500 1 HIS B 10 -83.47 66.30 REMARK 500 1 ALA B 18 -167.82 -122.36 REMARK 500 1 PHE B 62 55.09 -94.93 REMARK 500 1 ALA B 71 93.70 -161.41 REMARK 500 1 ASP B 83 -32.84 75.31 REMARK 500 1 SER B 94 -45.71 -142.72 REMARK 500 1 ASN B 113 -30.48 73.14 REMARK 500 1 MET C 27 26.33 -78.22 REMARK 500 1 PHE C 34 75.70 -109.75 REMARK 500 1 ASN C 67 -75.86 -119.09 REMARK 500 1 ILE C 77 45.70 -78.71 REMARK 500 1 ALA C 89 -56.99 67.74 REMARK 500 2 PRO A 19 35.77 -94.70 REMARK 500 2 PRO A 24 144.77 -38.91 REMARK 500 2 VAL A 29 -128.75 -130.18 REMARK 500 2 ARG A 30 59.76 -156.10 REMARK 500 2 ASP A 35 -77.57 -164.14 REMARK 500 2 ARG A 36 -53.56 174.97 REMARK 500 2 HIS B 10 -82.09 67.29 REMARK 500 2 ALA B 18 -168.57 -118.44 REMARK 500 2 ALA B 71 75.53 -150.99 REMARK 500 2 ASP B 83 -7.38 73.10 REMARK 500 2 LYS C 25 93.24 -64.67 REMARK 500 2 MET C 27 28.01 -77.58 REMARK 500 2 PHE C 34 72.48 -118.45 REMARK 500 2 THR C 66 43.21 -86.20 REMARK 500 2 ASN C 67 -54.79 -155.39 REMARK 500 2 SER C 68 -40.12 -132.91 REMARK 500 2 ALA C 89 -65.31 66.17 REMARK 500 3 LYS A 23 142.00 179.92 REMARK 500 3 VAL A 29 -138.63 -133.10 REMARK 500 3 ARG A 30 49.23 -154.66 REMARK 500 3 ASP A 35 -65.46 -162.55 REMARK 500 3 ARG A 36 -57.61 175.07 REMARK 500 3 HIS B 10 -81.38 68.02 REMARK 500 3 ALA B 18 -167.75 -122.77 REMARK 500 3 ALA B 71 84.51 -153.14 REMARK 500 3 MET B 103 59.19 -113.88 REMARK 500 3 LYS B 104 -50.88 -138.33 REMARK 500 3 MET C 27 36.97 -80.07 REMARK 500 3 SER C 68 -31.24 -145.72 REMARK 500 3 SER C 69 31.70 -81.44 REMARK 500 3 ILE C 77 47.19 -79.58 REMARK 500 REMARK 500 THIS ENTRY HAS 347 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19333 RELATED DB: BMRB REMARK 900 RELATED ID: 3DCG RELATED DB: PDB REMARK 900 THE STARTING STRUCTURE OF HADDOCK DOCKING DBREF 2MA9 A 2 37 UNP P12504 VIF_HV1N5 139 174 DBREF 2MA9 B 1 118 UNP Q15370 ELOB_HUMAN 1 118 DBREF 2MA9 C 1 91 UNP Q15369 ELOC_HUMAN 19 109 SEQRES 1 A 36 HIS ASN LYS VAL GLY SER LEU GLN TYR LEU ALA LEU ALA SEQRES 2 A 36 ALA LEU ILE LYS PRO LYS GLN ILE LYS PRO PRO LEU PRO SEQRES 3 A 36 SER VAL ARG LYS LEU THR GLU ASP ARG TRP SEQRES 1 B 118 MET ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR SEQRES 2 B 118 ILE PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU SEQRES 3 B 118 LEU LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO SEQRES 4 B 118 ASP GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP SEQRES 5 B 118 ASP GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN SEQRES 6 B 118 THR ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA SEQRES 7 B 118 PHE ARG ALA ASP ASP THR PHE GLU ALA LEU CYS ILE GLU SEQRES 8 B 118 PRO PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS SEQRES 9 B 118 PRO GLN ASP SER GLY SER SER ALA ASN GLU GLN ALA VAL SEQRES 10 B 118 GLN SEQRES 1 C 91 VAL LYS LEU ILE SER SER ASP GLY HIS GLU PHE ILE VAL SEQRES 2 C 91 LYS ARG GLU HIS ALA LEU THR SER GLY THR ILE LYS ALA SEQRES 3 C 91 MET LEU SER GLY PRO GLY GLN PHE ALA GLU ASN GLU THR SEQRES 4 C 91 ASN GLU VAL ASN PHE ARG GLU ILE PRO SER HIS VAL LEU SEQRES 5 C 91 SER LYS VAL CYS MET TYR PHE THR TYR LYS VAL ARG TYR SEQRES 6 C 91 THR ASN SER SER THR GLU ILE PRO GLU PHE PRO ILE ALA SEQRES 7 C 91 PRO GLU ILE ALA LEU GLU LEU LEU MET ALA ALA ASN PHE HELIX 1 1 GLY A 6 ALA A 12 1 7 HELIX 2 2 THR B 23 LYS B 36 1 14 HELIX 3 3 PRO B 38 ASP B 40 5 3 HELIX 4 4 THR B 56 GLY B 61 5 6 HELIX 5 5 PHE B 85 ILE B 90 1 6 HELIX 6 6 PRO B 100 LYS B 104 5 5 HELIX 7 7 LYS C 14 ILE C 24 1 11 HELIX 8 8 ALA C 35 ASN C 40 1 6 HELIX 9 9 PRO C 48 THR C 66 1 19 HELIX 10 10 ILE C 81 MET C 87 1 7 SHEET 1 A 2 PRO A 25 LEU A 26 0 SHEET 2 A 2 LYS A 31 LEU A 32 -1 O LYS A 31 N LEU A 26 SHEET 1 B 8 GLN B 49 LEU B 50 0 SHEET 2 B 8 GLN B 42 LYS B 46 -1 N LYS B 46 O GLN B 49 SHEET 3 B 8 ALA B 73 PHE B 79 -1 O GLY B 76 N TYR B 45 SHEET 4 B 8 ASP B 2 ARG B 9 1 N ARG B 8 O VAL B 75 SHEET 5 B 8 THR B 12 LYS B 19 -1 O THR B 12 N ARG B 9 SHEET 6 B 8 GLU C 10 ILE C 12 1 O ILE C 12 N THR B 13 SHEET 7 B 8 LYS C 2 ILE C 4 -1 N LEU C 3 O PHE C 11 SHEET 8 B 8 GLU C 41 ASN C 43 1 O VAL C 42 N ILE C 4 SHEET 1 C 2 ASP B 107 SER B 108 0 SHEET 2 C 2 GLN B 115 ALA B 116 -1 O ALA B 116 N ASP B 107 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