10 20 30 40 50 60 70 80 2HV1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION, PROTEIN BINDING 27-JUL-06 2HV1
TITLE HADDOCK STRUCTURE OF ARNT PAS-B HOMODIMER
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL PAS DOMAIN (PAS-B), RESIDUES 356-470; COMPND 5 SYNONYM: ARNT PROTEIN, DIOXIN RECEPTOR, NUCLEAR COMPND 6 TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1 BETA, HIF-1 BETA; COMPND 7 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: ARNT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PHIS-PARALLEL
KEYWDS ARNT TRANSCRIPTION PAS HADDOCK, TRANSCRIPTION, PROTEIN KEYWDS 2 BINDING
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR P.B.CARD,K.H.GARDNER
REVDAT 2 24-FEB-09 2HV1 1 VERSN REVDAT 1 07-AUG-07 2HV1 0
JRNL AUTH P.B.CARD,K.H.GARDNER JRNL TITL PRACTICAL ASPECTS OF USING PARAMAGNETIC RELAXATION JRNL TITL 2 ENHANCEMENTS FOR PROTEIN DOCKING: APPLICATION TO JRNL TITL 3 THE ARNT PAS-B HOMODIMER JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2HV1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB038795.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 50MM TRIS, 17MM NACL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1MM DOWN TO 125 MICRO M (15N) REMARK 210 ARNT PAS-B, 50MM TRIS, 17MM REMARK 210 NACL, 5MM DTT; 75 MICRO M REMARK 210 (15N) ARNT PAS-B, 400 MICRO M REMARK 210 ARNT PAS-B WITH CMSTL SPIN REMARK 210 LABEL ATTACHED (TO C358 OR REMARK 210 C451), 50MM TRIS, 17MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N/1H HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK 1.2, NMRPIPE 2.3, CNS REMARK 210 1.1, NMRVIEW 5.0.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 15N/1H HSQC WAS USED TO MONITOR (A) CHEMICAL SHIFT REMARK 210 PERTURBATION UPON COMPLEX FORMATION TO IDENTIFY INTERACTION REMARK 210 INTERFACE, AND (B) TO IDENTIFY BACKBONE AMIDE RESONANCES THAT REMARK 210 ARE SIGNIFICANTLY BROADENED DUE TO THEIR PROXIMITY TO A REMARK 210 PARAMAGNETIC SPIN LABEL ATTACHED TO ITS NATURAL ABUNDANCE REMARK 210 HOMODIMERIC INTERACTION PARTNER.
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 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 1-8 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 ALA A 2 REMARK 465 MET A 3 REMARK 465 ASP A 4 REMARK 465 ASN A 5 REMARK 465 VAL A 6 REMARK 465 ASN A 115 REMARK 465 SER A 116 REMARK 465 SER A 117 REMARK 465 GLN A 118 REMARK 465 GLU A 119 REMARK 465 GLY B 1 REMARK 465 ALA B 2 REMARK 465 MET B 3 REMARK 465 ASP B 4 REMARK 465 ASN B 5 REMARK 465 VAL B 6 REMARK 465 ASN B 115 REMARK 465 SER B 116 REMARK 465 SER B 117 REMARK 465 GLN B 118 REMARK 465 GLU B 119
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 6 GLU A 11 CG GLU A 11 CD 0.150 REMARK 500 6 GLU B 11 CG GLU B 11 CD 0.152 REMARK 500 REMARK 500 REMARK: NULL 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 6 GLU A 11 CG - CD - OE1 ANGL. DEV. = -43.7 DEGREES REMARK 500 6 GLU A 11 CG - CD - OE2 ANGL. DEV. = -61.3 DEGREES REMARK 500 6 GLU B 11 CG - CD - OE1 ANGL. DEV. = -32.8 DEGREES REMARK 500 6 GLU B 11 CG - CD - OE2 ANGL. DEV. = -76.0 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 LYS A 68 99.47 59.61 REMARK 500 1 TYR A 99 -74.70 -62.98 REMARK 500 1 LYS B 68 108.99 65.52 REMARK 500 1 PRO B 98 21.67 -69.68 REMARK 500 1 TYR B 99 -68.72 -94.69 REMARK 500 2 LYS A 68 99.37 66.01 REMARK 500 2 TYR A 99 -55.25 -125.95 REMARK 500 2 THR B 10 57.89 -90.97 REMARK 500 2 LYS B 68 88.46 56.60 REMARK 500 2 PRO B 98 73.27 -62.32 REMARK 500 2 TYR B 99 -137.58 -147.40 REMARK 500 2 SER B 100 49.30 -80.54 REMARK 500 2 ASP B 101 77.00 50.53 REMARK 500 3 LYS A 68 91.46 60.33 REMARK 500 3 PRO A 98 28.61 -75.15 REMARK 500 3 TYR A 99 -64.69 -98.70 REMARK 500 3 LYS B 68 90.57 47.29 REMARK 500 3 TYR B 99 -70.56 -86.34 REMARK 500 4 LYS A 68 83.47 62.97 REMARK 500 4 ARG A 89 77.40 -100.66 REMARK 500 4 TYR A 99 -66.57 -97.71 REMARK 500 4 ARG B 28 -21.57 -169.53 REMARK 500 4 LYS B 68 111.22 66.18 REMARK 500 4 TYR B 99 -77.82 -138.02 REMARK 500 5 ASP A 26 -179.55 -68.80 REMARK 500 5 LYS A 68 103.65 62.21 REMARK 500 5 PRO A 98 36.59 -73.60 REMARK 500 5 TYR A 99 -68.61 -109.77 REMARK 500 5 HIS B 27 37.03 -80.26 REMARK 500 5 LYS B 68 112.23 63.85 REMARK 500 5 ARG B 89 72.69 -100.38 REMARK 500 5 PRO B 98 20.02 -74.71 REMARK 500 6 THR A 10 43.25 -77.35 REMARK 500 6 LYS A 68 104.96 62.47 REMARK 500 6 ARG A 89 76.84 -101.52 REMARK 500 6 SER A 100 19.91 -142.38 REMARK 500 6 THR B 10 46.57 -82.33 REMARK 500 6 LYS B 68 102.31 59.44 REMARK 500 6 PRO B 98 49.83 -78.61 REMARK 500 6 TYR B 99 -58.14 -128.71 REMARK 500 7 LYS A 68 94.98 61.40 REMARK 500 7 ARG A 89 73.97 -101.87 REMARK 500 7 SER A 100 27.95 -145.31 REMARK 500 7 THR B 10 47.04 -99.32 REMARK 500 7 LYS B 68 98.41 60.75 REMARK 500 7 PRO B 98 45.39 -70.37 REMARK 500 7 TYR B 99 -54.22 -126.53 REMARK 500 8 LYS A 68 97.59 59.67 REMARK 500 8 ARG A 89 70.14 -100.87 REMARK 500 8 PRO A 98 28.87 -75.69 REMARK 500 8 ASP A 101 76.18 51.01 REMARK 500 8 LYS B 68 113.37 63.26 REMARK 500 8 PRO B 98 42.72 -71.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 6 GLU A 11 0.14 SIDE_CHAIN REMARK 500 6 GLU B 11 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HV3 RELATED DB: PDB REMARK 900 HADDOCK STRUCTURE OF ARNT PAS-B HOMODIMER
DBREF 2HV1 A 5 119 UNP P27540 ARNT_HUMAN 356 470 DBREF 2HV1 B 5 119 UNP P27540 ARNT_HUMAN 356 470
SEQADV 2HV1 GLY A 1 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 ALA A 2 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 MET A 3 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 ASP A 4 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 GLY B 1 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 ALA B 2 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 MET B 3 UNP P27540 CLONING ARTIFACT SEQADV 2HV1 ASP B 4 UNP P27540 CLONING ARTIFACT
SEQRES 1 A 119 GLY ALA MET ASP ASN VAL CYS GLN PRO THR GLU PHE ILE SEQRES 2 A 119 SER ARG HIS ASN ILE GLU GLY ILE PHE THR PHE VAL ASP SEQRES 3 A 119 HIS ARG CYS VAL ALA THR VAL GLY TYR GLN PRO GLN GLU SEQRES 4 A 119 LEU LEU GLY LYS ASN ILE VAL GLU PHE CYS HIS PRO GLU SEQRES 5 A 119 ASP GLN GLN LEU LEU ARG ASP SER PHE GLN GLN VAL VAL SEQRES 6 A 119 LYS LEU LYS GLY GLN VAL LEU SER VAL MET PHE ARG PHE SEQRES 7 A 119 ARG SER LYS ASN GLN GLU TRP LEU TRP MET ARG THR SER SEQRES 8 A 119 SER PHE THR PHE GLN ASN PRO TYR SER ASP GLU ILE GLU SEQRES 9 A 119 TYR ILE ILE CYS THR ASN THR ASN VAL LYS ASN SER SER SEQRES 10 A 119 GLN GLU SEQRES 1 B 119 GLY ALA MET ASP ASN VAL CYS GLN PRO THR GLU PHE ILE SEQRES 2 B 119 SER ARG HIS ASN ILE GLU GLY ILE PHE THR PHE VAL ASP SEQRES 3 B 119 HIS ARG CYS VAL ALA THR VAL GLY TYR GLN PRO GLN GLU SEQRES 4 B 119 LEU LEU GLY LYS ASN ILE VAL GLU PHE CYS HIS PRO GLU SEQRES 5 B 119 ASP GLN GLN LEU LEU ARG ASP SER PHE GLN GLN VAL VAL SEQRES 6 B 119 LYS LEU LYS GLY GLN VAL LEU SER VAL MET PHE ARG PHE SEQRES 7 B 119 ARG SER LYS ASN GLN GLU TRP LEU TRP MET ARG THR SER SEQRES 8 B 119 SER PHE THR PHE GLN ASN PRO TYR SER ASP GLU ILE GLU SEQRES 9 B 119 TYR ILE ILE CYS THR ASN THR ASN VAL LYS ASN SER SER SEQRES 10 B 119 GLN GLU
HELIX 1 1 ARG A 28 VAL A 33 1 6 HELIX 2 2 GLN A 36 LEU A 41 1 6 HELIX 3 3 ASN A 44 CYS A 49 5 6 HELIX 4 4 HIS A 50 GLU A 52 5 3 HELIX 5 5 ASP A 53 LYS A 68 1 16 HELIX 6 6 ARG B 28 VAL B 33 1 6 HELIX 7 7 GLN B 36 LEU B 41 1 6 HELIX 8 8 HIS B 50 GLU B 52 5 3 HELIX 9 9 ASP B 53 LYS B 68 1 16
SHEET 1 A 5 PHE A 22 VAL A 25 0 SHEET 2 A 5 GLU A 11 HIS A 16 -1 N ARG A 15 O THR A 23 SHEET 3 A 5 ILE A 103 ASN A 112 -1 O ILE A 106 N HIS A 16 SHEET 4 A 5 TRP A 85 GLN A 96 -1 N ARG A 89 O THR A 111 SHEET 5 A 5 LEU A 72 ARG A 79 -1 N VAL A 74 O THR A 90 SHEET 1 B 5 PHE B 22 VAL B 25 0 SHEET 2 B 5 GLU B 11 HIS B 16 -1 N ARG B 15 O PHE B 24 SHEET 3 B 5 GLU B 102 ASN B 112 -1 O ILE B 106 N HIS B 16 SHEET 4 B 5 TRP B 85 ASN B 97 -1 N ARG B 89 O THR B 111 SHEET 5 B 5 VAL B 71 ARG B 79 -1 N PHE B 76 O MET B 88
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