HEADER TRANSCRIPTION REGULATION 15-JAN-10 2KT0 TITLE SOLUTION STRUCTURE OF HUMAN STEM CELL TRANSCRIPTION FACTOR NANOG TITLE 2 HOMEODOMAIN FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN NANOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HOMEOBOX DOMAIN RESIDUES 75-157; COMPND 5 SYNONYM: NANOG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PVP68K KEYWDS NANOG, HOMEODOMAIN, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, PSI, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS, DNA- KEYWDS 3 BINDING, HOMEOBOX, STEM CELL, TRANSCRIPTION, CESG, TRANSCRIPTION KEYWDS 4 REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.C.SAHU,J.L.MARKLEY,CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 6 14-JUN-23 2KT0 1 REMARK REVDAT 5 26-FEB-20 2KT0 1 REMARK SEQADV REVDAT 4 30-JUN-10 2KT0 1 SOURCE REVDAT 3 02-MAR-10 2KT0 1 TITLE REVDAT 2 16-FEB-10 2KT0 1 COMPND REVDAT 1 02-FEB-10 2KT0 0 JRNL AUTH S.C.SAHU,J.L.MARKLEY JRNL TITL SOLUTION STRUCTURE OF HUMAN STEM CELL TRANSCRIPTION FACTOR JRNL TITL 2 NANOG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTOMATED METHODS WERE USED FOR REMARK 3 BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. REMARK 3 FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT REMARK 3 SOLVENT. STRUCTURES ARE BASED ON A TOTAL OF 1766 NOE CONSTRAINTS REMARK 3 ( 597 INTRA, 423 SEQUENTIAL, 224 MEDIUM AND 522 LONG RANGE REMARK 3 CONSTRAINTS) AND 197 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. REMARK 4 REMARK 4 2KT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000101536. 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 : 250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-95% 13C; U-90% 15N] REMARK 210 NANOG, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY (AROMATIC) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS IN EXPLICIT REMARK 210 SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING REMARK 210 A CRYOGENIC PROBE 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 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 ALA A 7 79.57 60.34 REMARK 500 1 VAL A 11 83.58 60.35 REMARK 500 1 PRO A 19 91.23 -63.66 REMARK 500 1 VAL A 20 88.00 48.26 REMARK 500 1 GLN A 23 -165.34 67.04 REMARK 500 1 THR A 25 30.39 -93.83 REMARK 500 1 ARG A 26 -74.64 67.78 REMARK 500 1 ARG A 79 -78.21 -108.86 REMARK 500 1 TRP A 80 155.88 173.90 REMARK 500 2 LYS A 2 26.12 -164.16 REMARK 500 2 ALA A 7 -83.08 -141.00 REMARK 500 2 VAL A 11 170.02 59.28 REMARK 500 2 ALA A 12 101.82 64.35 REMARK 500 2 GLU A 15 164.59 71.69 REMARK 500 2 ARG A 26 -70.61 69.55 REMARK 500 2 ARG A 79 -76.48 -137.56 REMARK 500 2 TRP A 80 -171.15 -178.63 REMARK 500 3 GLN A 3 157.63 72.46 REMARK 500 3 PRO A 4 105.67 -57.93 REMARK 500 3 SER A 10 77.77 68.28 REMARK 500 3 LYS A 17 174.67 70.13 REMARK 500 3 VAL A 18 84.64 43.04 REMARK 500 3 PRO A 19 98.55 -56.33 REMARK 500 3 ARG A 26 -70.86 71.72 REMARK 500 3 ARG A 79 -75.57 -144.42 REMARK 500 3 TRP A 80 95.69 -167.02 REMARK 500 3 GLN A 81 -172.00 58.28 REMARK 500 3 LYS A 82 66.66 -100.17 REMARK 500 4 GLN A 3 87.11 59.13 REMARK 500 4 PRO A 4 -166.47 -67.46 REMARK 500 4 THR A 5 81.28 71.84 REMARK 500 4 SER A 6 -62.25 -143.21 REMARK 500 4 ASN A 9 96.14 -66.33 REMARK 500 4 SER A 10 102.97 -166.53 REMARK 500 4 ASP A 16 -168.92 -123.44 REMARK 500 4 LYS A 21 80.22 70.44 REMARK 500 4 ARG A 79 -75.79 -142.80 REMARK 500 5 LYS A 2 90.37 66.32 REMARK 500 5 SER A 6 108.40 -53.54 REMARK 500 5 ASN A 9 -168.08 -128.91 REMARK 500 5 SER A 10 104.68 -59.37 REMARK 500 5 GLU A 15 -70.33 -56.84 REMARK 500 5 LYS A 22 39.46 -96.33 REMARK 500 6 LYS A 2 -20.10 -143.52 REMARK 500 6 GLN A 3 73.33 53.37 REMARK 500 6 THR A 5 96.07 -62.59 REMARK 500 6 VAL A 11 112.70 69.01 REMARK 500 6 LYS A 13 -58.90 -168.18 REMARK 500 6 LYS A 14 -170.72 63.18 REMARK 500 6 VAL A 18 74.28 56.02 REMARK 500 REMARK 500 THIS ENTRY HAS 185 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16680 RELATED DB: BMRB REMARK 900 RELATED ID: GO.103285 RELATED DB: TARGETDB DBREF 2KT0 A 2 84 UNP Q6NSW7 NANP8_HUMAN 75 157 SEQADV 2KT0 SER A 1 UNP Q6NSW7 EXPRESSION TAG SEQRES 1 A 84 SER LYS GLN PRO THR SER ALA GLU ASN SER VAL ALA LYS SEQRES 2 A 84 LYS GLU ASP LYS VAL PRO VAL LYS LYS GLN LYS THR ARG SEQRES 3 A 84 THR VAL PHE SER SER THR GLN LEU CYS VAL LEU ASN ASP SEQRES 4 A 84 ARG PHE GLN ARG GLN LYS TYR LEU SER LEU GLN GLN MET SEQRES 5 A 84 GLN GLU LEU SER ASN ILE LEU ASN LEU SER TYR LYS GLN SEQRES 6 A 84 VAL LYS THR TRP PHE GLN ASN GLN ARG MET LYS SER LYS SEQRES 7 A 84 ARG TRP GLN LYS ASN ASN HELIX 1 1 SER A 30 GLN A 44 1 15 HELIX 2 2 SER A 48 LEU A 59 1 12 HELIX 3 3 SER A 62 LYS A 76 1 15 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