PDB Short entry for 2HV1 HEADER 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 TRANSLOCATOR, COMPND 6 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 BINDING EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR P.B.CARD,K.H.GARDNER REVDAT 3 09-MAR-22 2HV1 1 REMARK SEQADV 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 THE ARNT JRNL TITL 3 PAS-B HOMODIMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.2, CNS 1.1 REMARK 3 AUTHORS : BONVIN (HADDOCK), BRUNGER (CNS) 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 DEPOSITION ID IS D_1000038795. 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 NACL, REMARK 210 5MM DTT; 75 MICRO M (15N) ARNT REMARK 210 PAS-B, 400 MICRO M ARNT PAS-B REMARK 210 WITH CMSTL SPIN LABEL ATTACHED REMARK 210 (TO C358 OR C451), 50MM TRIS, REMARK 210 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 : NMRPIPE 2.3, CNS 1.1, NMRVIEW REMARK 210 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 REMARK 210 INTERACTION INTERFACE, AND (B) TO IDENTIFY BACKBONE AMIDE REMARK 210 RESONANCES THAT ARE SIGNIFICANTLY BROADENED DUE TO THEIR REMARK 210 PROXIMITY TO A PARAMAGNETIC SPIN LABEL ATTACHED TO ITS REMARK 210 NATURAL ABUNDANCE 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 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 1-8 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: 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 HB3 SER A 14 HE2 PHE A 22 1.27 REMARK 500 HH12 ARG A 15 OE2 GLU B 104 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. 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