10 20 30 40 50 60 70 80 1HRY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER DNA BINDING PROTEIN/DNA 09-MAY-95 1HRY
TITLE THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY TITLE 2 MULTID-DIMENSIONAL HETERONUCLEAR-EDITED AND-FILTERED NMR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*AP*CP*AP*AP*AP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*TP*TP*TP*GP*TP*GP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HUMAN SRY; COMPND 11 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606
KEYWDS DNA, NMR, SRY, DNA-BINDING PROTEIN, DNA BINDING PROTEIN/DNA KEYWDS 2 COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,M.H.WERNER,J.R.HUTH,A.M.GRONENBORN
REVDAT 3 24-FEB-09 1HRY 1 VERSN REVDAT 2 01-APR-03 1HRY 1 JRNL REVDAT 1 15-SEP-95 1HRY 0
JRNL AUTH M.H.WERNER,J.R.HUTH,A.M.GRONENBORN,G.M.CLORE JRNL TITL MOLECULAR BASIS OF HUMAN 46X,Y SEX REVERSAL JRNL TITL 2 REVEALED FROM THE THREE-DIMENSIONAL SOLUTION JRNL TITL 3 STRUCTURE OF THE HUMAN SRY-DNA COMPLEX. JRNL REF CELL(CAMBRIDGE,MASS.) V. 81 704 1995 JRNL REFN ISSN 0092-8674 JRNL PMID 7774012 JRNL DOI 10.1016/0092-8674(95)90532-4
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 NUMBER OF ATOMS USED IN REFINEMENT. REMARK 3 NUMBER OF PROTEIN ATOMS 644 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 322 REMARK 3 NUMBER OF HETEROGEN ATOMS 0 REMARK 3 NUMBER OF SOLVENT ATOMS 0 REMARK 3 REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, REMARK 3 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED REMARK 3 TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. REMARK 3 MAGN. RESON. SERIES B 104, 99 - 103) AND CARBON CHEMICAL REMARK 3 SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) MAGN. RESON. REMARK 3 SERIES B 106, 92 - 96). REMARK 3 REMARK 3 THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY REMARK 3 MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR REMARK 3 IS BASED ON 1805 EXPERIMENTAL RESTRAINTS: REMARK 3 (A) INTRA-PROTEIN: REMARK 3 290 SEQUENTIAL (|I-J|=1), REMARK 3 221 MEDIUM RANGE (1 < |I-J| >=5) AND REMARK 3 107 LONG RANGE (|I-J| >5) INTERRESIDUES. REMARK 3 238 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE REMARK 3 RESTRAINTS; REMARK 3 70 DISTANCE RESTRAINTS FOR 35 HYDROGEN BONDS; REMARK 3 153 TORSION ANGLE (71 PHI, 10 PSI, 56 CHI1 AND 16 CHI2) REMARK 3 RESTRAINTS; REMARK 3 56 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; REMARK 3 145 (73 CALPHA AND 72 CBETA) 13C SHIFT RESTRAINTS. REMARK 3 (B) INTRA-DNA: REMARK 3 206 INTRARESIDUE, REMARK 3 96 SEQUENTIAL INTRASTRAND, REMARK 3 36 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; REMARK 3 40 H-BOND RESTRAINTS; REMARK 3 72 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA, GAMMA, REMARK 3 EPSILON AND ZETA BACKBONE TORSION ANGLES. REMARK 3 (C) INTERMOLECULAR: REMARK 3 75 INTERPROTON DISTANCE RESTRAINTS REMARK 3 REMARK 3 THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED REMARK 3 MEAN STRUCTURE. THE LAST COLUMN REPRESENTS THE RMS OF THE REMARK 3 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN REMARK 3 COORDINATE POSITIONS. THE 35 INDIVIDUAL STRUCTURES CAN BE REMARK 3 FOUND IN PDB ENTRY 1HRZ. THE LAST COLUMN IN THE INDIVIDUAL REMARK 3 SA STRUCTURES HAS NO MEANING.
REMARK 4 REMARK 4 1HRY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY REMARK 210 MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS REMARK 210 BASED ON 1805 EXPERIMENTAL RESTRAINTS: (A) INTRA-PROTEIN: 290 REMARK 210 SEQUENTIAL (|I-J|=1), 221 MEDIUM RANGE (1 < |I-J| >=5) AND 107 REMARK 210 LONG RANGE (|I-J| >5) INTERRESIDUES. 238 INTRARESIDUE REMARK 210 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 70 DISTANCE REMARK 210 RESTRAINTS FOR 35 HYDROGEN BONDS; 153 TORSION ANGLE (71 PHI, REMARK 210 10 PSI, 56 CHI1 AND 16 CHI2) RESTRAINTS; 56 THREE-BOND HN-HA REMARK 210 COUPLING CONSTANT RESTRAINTS; 145 (73 CALPHA AND 72 CBETA) 13C REMARK 210 SHIFT RESTRAINTS. (B) INTRA-DNA: 206 INTRARESIDUE, 96 REMARK 210 SEQUENTIAL INTRASTRAND, 36 INTERSTRAND INTERPROTON DISTANCE REMARK 210 RESTRAINTS; 40 H-BOND RESTRAINTS; 72 TORSION ANGLE RESTRAINTS REMARK 210 (FOR ALPHA, BETA, GAMMA, EPSILON AND ZETA BACKBONE TORSION REMARK 210 ANGLES. (C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS
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 RES C SSSEQI REMARK 465 VAL A 1 REMARK 465 GLN A 2 REMARK 465 PRO A 76
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 DT C 2 C5 DT C 2 C7 0.037 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 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 1 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG B 1 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 3 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 3 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DA B 3 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 5 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 5 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 5 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DA B 5 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 6 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 6 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DA B 6 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 7 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 7 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DA B 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG C 1 N7 - C8 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 DG C 1 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT C 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG C 5 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG C 5 N7 - C8 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG C 5 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 7 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG C 7 N7 - C8 - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG C 7 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.3 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 PRO A 8 -173.11 -66.76 REMARK 500 ARG A 17 -77.01 -41.07 REMARK 500 ARG A 31 -74.71 -64.61 REMARK 500 ILE A 35 -15.60 -48.78 REMARK 500 LYS A 51 -78.70 -69.30 REMARK 500 PRO A 53 -76.64 -42.15 REMARK 500 PRO A 70 -70.10 -50.34 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 ARG A 31 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HRZ RELATED DB: PDB REMARK 900 ENSEMBLE OF 35 STRUCTURES
DBREF 1HRY A 1 76 UNP Q05066 SRY_HUMAN 56 131 DBREF 1HRY B 1 8 PDB 1HRY 1HRY 1 8 DBREF 1HRY C 1 8 PDB 1HRY 1HRY 1 8
SEQRES 1 B 8 DG DC DA DC DA DA DA DC SEQRES 1 C 8 DG DT DT DT DG DT DG DC SEQRES 1 A 76 VAL GLN ASP ARG VAL LYS ARG PRO MET ASN ALA PHE ILE SEQRES 2 A 76 VAL TRP SER ARG ASP GLN ARG ARG LYS MET ALA LEU GLU SEQRES 3 A 76 ASN PRO ARG MET ARG ASN SER GLU ILE SER LYS GLN LEU SEQRES 4 A 76 GLY TYR GLN TRP LYS MET LEU THR GLU ALA GLU LYS TRP SEQRES 5 A 76 PRO PHE PHE GLN GLU ALA GLN LYS LEU GLN ALA MET HIS SEQRES 6 A 76 ARG GLU LYS TYR PRO ASN TYR LYS TYR ARG PRO
HELIX 1 1 ALA A 11 GLU A 26 1 16 HELIX 2 2 GLU A 34 MET A 45 1 12 HELIX 3 3 GLU A 48 LYS A 68 1 21
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