HEADER TRANSCRIPTION 27-MAR-25 9QPF TITLE SOLUTION STRUCTURE OF SOX2 DBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SOX-2; COMPND 3 CHAIN: A; COMPND 4 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: SOX2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HMG, DNA-BINDING, PIONEER TRANSCRIPTION FACTOR, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.ORSETTI,H.VAN INGEN REVDAT 2 10-DEC-25 9QPF 1 JRNL REVDAT 1 19-NOV-25 9QPF 0 JRNL AUTH A.ORSETTI,J.SLEJFER,S.HA,D.I.KEVELAM,J.TEKKELENBURG, JRNL AUTH 2 T.VAN DUIJN,A.LEPPAKOSKI,A.SEDRAKYAN,A.SZILAGYI, JRNL AUTH 3 R.D.SCHELLEVIS,A.SOUFI,V.COJOCARU,H.VAN INGEN JRNL TITL SOLUTION STRUCTURE OF THE SOX2 DNA-BINDING DOMAIN REVEALS JRNL TITL 2 CONFORMATIONAL SELECTION IN DNA BINDING. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 41189057 JRNL DOI 10.1093/NAR/GKAF1121 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9QPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146698. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.30 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 0.25 MM [U-13C; U-15N] SOX2-DBD, REMARK 210 135 MM POTASSIUM CHLORIDE, 20 MM REMARK 210 TRIS, 15 MM SODIUM CHLORIDE, REMARK 210 0.01 % V/V SODIUM AZIDE, 90% H2O/ REMARK 210 10% D2O; 0.25 MM [U-13C; U-15N] REMARK 210 SOX2-DBD, 135 MM POTASSIUM REMARK 210 CHLORIDE, 20 MM TRIS, 15 MM REMARK 210 SODIUM CHLORIDE, 0.01 % V/V REMARK 210 SODIUM AZIDE, 5 % V/V REMARK 210 PENTAETHYLENE GLYCOL MONODECYL/N- REMARK 210 HEXANOL, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 2D 1H-15N HSQC; REMARK 210 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 1200 MHZ; 900 MHZ; 600 MHZ; 850 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98.15, POKY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 35 -62.53 -96.48 REMARK 500 1 ASP A 39 163.15 63.25 REMARK 500 1 LYS A 42 -168.35 -168.58 REMARK 500 1 ARG A 43 160.55 65.72 REMARK 500 1 GLU A 104 46.57 38.78 REMARK 500 1 ASP A 107 48.67 -91.01 REMARK 500 1 LYS A 115 -48.66 -141.92 REMARK 500 1 THR A 118 -50.65 -167.83 REMARK 500 1 LEU A 119 79.93 61.50 REMARK 500 1 ASP A 123 49.57 -147.25 REMARK 500 2 PRO A 38 -177.80 -69.72 REMARK 500 2 ASP A 39 -176.21 61.15 REMARK 500 2 PRO A 44 -171.34 -69.77 REMARK 500 2 ASP A 107 164.27 63.79 REMARK 500 2 TYR A 108 58.56 -109.73 REMARK 500 2 ARG A 114 161.11 63.24 REMARK 500 2 THR A 116 78.62 59.82 REMARK 500 3 ASN A 33 -177.52 57.23 REMARK 500 3 SER A 37 72.89 -169.71 REMARK 500 3 LYS A 42 37.79 -173.61 REMARK 500 3 GLU A 104 50.82 38.18 REMARK 500 3 TYR A 108 96.81 62.01 REMARK 500 3 LYS A 109 108.05 -178.05 REMARK 500 3 LYS A 117 70.28 -159.96 REMARK 500 4 ASN A 33 -75.70 69.18 REMARK 500 4 GLN A 34 172.16 61.70 REMARK 500 4 ASN A 36 -174.17 59.79 REMARK 500 4 SER A 37 72.02 53.03 REMARK 500 4 PRO A 38 -175.90 -69.79 REMARK 500 4 ARG A 40 148.78 -170.41 REMARK 500 4 PRO A 44 -172.03 -69.76 REMARK 500 4 TYR A 108 122.30 -178.97 REMARK 500 4 LYS A 109 39.29 -176.42 REMARK 500 4 ARG A 113 149.48 65.57 REMARK 500 4 LYS A 115 172.65 -58.01 REMARK 500 4 LEU A 119 -43.04 -147.37 REMARK 500 5 GLN A 34 104.04 -163.31 REMARK 500 5 PRO A 38 97.80 -69.82 REMARK 500 5 LYS A 42 41.83 -151.92 REMARK 500 5 PRO A 44 -172.87 -69.71 REMARK 500 5 ASP A 107 -177.74 -179.05 REMARK 500 5 TYR A 108 -165.82 -128.00 REMARK 500 5 LYS A 109 39.98 -163.13 REMARK 500 6 SER A 32 67.43 -118.32 REMARK 500 6 ASN A 33 140.03 -172.94 REMARK 500 6 LYS A 35 -45.03 -179.19 REMARK 500 6 ASN A 36 93.42 -173.55 REMARK 500 6 PRO A 38 -170.83 -69.76 REMARK 500 6 ASP A 39 99.67 60.55 REMARK 500 6 ARG A 40 -168.30 -102.66 REMARK 500 REMARK 500 THIS ENTRY HAS 231 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34988 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF SOX2 DBD DBREF 9QPF A 33 127 UNP P48431 SOX2_HUMAN 33 127 SEQADV 9QPF GLY A 31 UNP P48431 EXPRESSION TAG SEQADV 9QPF SER A 32 UNP P48431 EXPRESSION TAG SEQRES 1 A 97 GLY SER ASN GLN LYS ASN SER PRO ASP ARG VAL LYS ARG SEQRES 2 A 97 PRO MET ASN ALA PHE MET VAL TRP SER ARG GLY GLN ARG SEQRES 3 A 97 ARG LYS MET ALA GLN GLU ASN PRO LYS MET HIS ASN SER SEQRES 4 A 97 GLU ILE SER LYS ARG LEU GLY ALA GLU TRP LYS LEU LEU SEQRES 5 A 97 SER GLU THR GLU LYS ARG PRO PHE ILE ASP GLU ALA LYS SEQRES 6 A 97 ARG LEU ARG ALA LEU HIS MET LYS GLU HIS PRO ASP TYR SEQRES 7 A 97 LYS TYR ARG PRO ARG ARG LYS THR LYS THR LEU MET LYS SEQRES 8 A 97 LYS ASP LYS TYR THR LEU HELIX 1 AA1 ASN A 46 ASN A 63 1 18 HELIX 2 AA2 HIS A 67 LEU A 82 1 16 HELIX 3 AA3 SER A 83 GLU A 104 1 22 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 152 0 0 3 0 0 0 6 822 1 0 8 END