PDB Short entry for 1D7G HEADER TRANSCRIPTION FACTOR/DNA 18-OCT-99 1D7G TITLE A MODEL FOR THE COMPLEX BETWEEN THE HYPOXIA-INDUCIBLE TITLE 2 FACTOR-1 (HIF-1) AND ITS CONSENSUS DNA SEQUENCE CAVEAT 1D7G CHIRALITY ERROR AT THE CA CENTER OF RESIDUES 29 AND 45 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 SYNONYM: ARNT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA; COMPND 8 CHAIN: D; COMPND 9 FRAGMENT: DNA BINDING DOMAIN; COMPND 10 SYNONYM: HIF-1; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: HYPOXIA RESPONSIVE ELEMENT (HRE); COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA; COMPND 18 CHAIN: B; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED; SOURCE 10 MOL_ID: 4; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED KEYWDS TRANSCRIPTION FACTOR, BASIC HELIX LOOP HELIX, COMPLEX KEYWDS 2 (TRANSCRIPTION FACTOR/DNA) EXPDTA THEORETICAL MODEL AUTHOR G.MICHEL,E.MINET,F.DURANT,J.REMACLE,C.MICHIELS REVDAT 3 04-APR-01 1D7G 1 JRNL REMARK REVDAT 2 08-NOV-99 1D7G 3 ATOM REMARK JRNL REVDAT 1 22-OCT-99 1D7G 0 JRNL AUTH G.MICHEL,E.MINET,I.ERNEST,I.ROLAND,F.DURANT, JRNL AUTH 2 J.REMACLE,C.MICHIELS JRNL TITL A MODEL FOR THE COMPLEX BETWEEN THE JRNL TITL 2 HYPOXIA-INDUCIBLE FACTOR-1 (HIF-1) AND ITS JRNL TITL 3 CONSENSUS DNA SEQUENCE. JRNL REF J.BIOMOL.STRUCT.DYN. V. 18 169 2000 JRNL REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D7G COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-1999. REMARK 100 THE RCSB ID CODE IS RCSB009858. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: HYPOXIA-INDUCIBLE FACTOR-1 (HIF-1) IS A HETERODIMERIC REMARK 220 TRANSCRIPTION FACTOR ACTIVATED BY HYPOXIA. IT IS REMARK 220 COMPOSED OF TWO DIFFERENT SUBUNITS, HIF-1A AND ARNT REMARK 220 (ARYL RECEPTOR NUCLEAR TRANSLOCATOR). THESE TWO SUBUNITS REMARK 220 BELONG TO THE BHLH (BASIC HELIX-LOOP-HELIX) PAS (PER, REMARK 220 AHR/ARNT, SIM) FAMILY. THE BHLH DOMAIN OF THESE FACTORS REMARK 220 IS RESPONSIBLE FOR DIMERIZATION THROUGH THE TWO HELICES REMARK 220 AND FOR DNA BINDING THOUGH THEIR BASIC DOMAIN. WE HAVE REMARK 220 GENERATED A STRUCTURAL MODEL FOR THE INTERACTION OF HIF- REMARK 220 1 DNA BINDING DOMAIN (DBD) WITH HRE USING A MONTE CARLO REMARK 220 PROGRAM CALLED MONTY. PROTEIN-DNA COMPLEXES WERE REMARK 220 GENERATED BY DOCKING THE MODEL OF HIF-1 (DBD) (REF 1) REMARK 220 ONTO THE HRE SEQUENCE. THE COMPLEX WHICH CONTAINED MOST REMARK 220 OF THE CONTACTS OBSERVED IN THE WHOLE SET OF COMPLEXES REMARK 220 WAS CHOSEN AND WAS MINIMIZED USING THE AMBER FORCEFIELD. REMARK 220 THE TWO PROTEINS SUBUNITS HAVE BEEN ASSIGNED CHAIN D AND REMARK 220 C. DNA CHAINS HAVE BEEN ASSIGNED CHAIN INDICATORS A AND REMARK 220 B. THE DNA CHAINS ARE ALIGNED AS FOLLOWS : CHAIN A : 5 REMARK 220 PRIME : GCCCTACGTGCTGC CHAIN B : 3 PRIME : CGGGATGCACGACG 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 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU C 1 CD GLU C 1 OE2 0.116 REMARK 500 GLU C 6 CD GLU C 6 OE2 0.115 REMARK 500 GLU C 10 CD GLU C 10 OE2 0.115 REMARK 500 GLU C 12 CD GLU C 12 OE2 0.115 REMARK 500 GLU C 25 CD GLU C 25 OE2 0.115 REMARK 500 ASP C 28 CG ASP C 28 OD2 0.115 REMARK 500 ASP C 41 CG ASP C 41 OD2 0.117 REMARK 500 GLU D 2 CD GLU D 2 OE2 0.116 REMARK 500 GLU D 6 CD GLU D 6 OE2 0.117 REMARK 500 ASP D 10 CG ASP D 10 OD2 0.116 REMARK 500 GLU D 19 CD GLU D 19 OE2 0.115 REMARK 500 GLU D 21 CD GLU D 21 OE2 0.115 REMARK 500 GLU D 25 CD GLU D 25 OE2 0.115 REMARK 500 ASP D 41 CG ASP D 41 OD2 0.115 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE C 45 C - N - CA ANGL. DEV. = 12.1 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LEU C 36 -94.84 59.19 REMARK 500 ARG C 38 163.81 68.37 REMARK 500 LEU C 43 157.85 62.91 REMARK 500 ASP D 41 -59.80 76.20 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU C 43 THR C 44 -146.05 DBREF 1D7G C 1 59 UNP P27540 ARNT_HUMAN 87 145 DBREF 1D7G D 1 59 UNP Q16665 HIFA_HUMAN 15 73 SEQRES 1 C 59 GLU ARG LEU ALA ARG GLU ASN HIS SER GLU ILE GLU ARG SEQRES 2 C 59 ARG ARG ARG ASN LYS MET THR ALA TYR ILE THR GLU LEU SEQRES 3 C 59 SER ASP MET VAL PRO THR CYS SER ALA LEU ALA ARG LYS SEQRES 4 C 59 PRO ASP LYS LEU THR ILE LEU ARG MET ALA VAL SER HIS SEQRES 5 C 59 MET LYS SER LEU ARG GLY THR SEQRES 1 D 59 SER GLU ARG ARG LYS GLU LYS SER ARG ASP ALA ALA ARG SEQRES 2 D 59 SER ARG ARG SER LYS GLU SER GLU VAL PHE TYR GLU LEU SEQRES 3 D 59 ALA HIS GLN LEU PRO LEU PRO HIS ASN VAL SER SER HIS SEQRES 4 D 59 LEU ASP LYS ALA SER VAL MET ARG LEU THR ILE SER TYR SEQRES 5 D 59 LEU ARG VAL ARG LYS LEU LEU SEQRES 1 A 14 G C C C T A C G T G C T G SEQRES 2 A 14 C SEQRES 1 B 14 G C A G C A C G T A G G G SEQRES 2 B 14 C HELIX 1 1 GLU C 1 ASP C 28 1 28 HELIX 2 2 ILE C 45 THR C 59 1 15 HELIX 3 3 SER D 1 HIS D 28 1 28 HELIX 4 4 SER D 44 LEU D 59 1 16 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