HEADER PROTEIN BINDING/TRANSCRIPTION 03-AUG-07 2JTN TITLE NMR SOLUTION STRUCTURE OF A LDB1-LID:LHX3-LIM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIM DOMAIN-BINDING PROTEIN 1, LIM/HOMEOBOX PROTEIN LHX3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FUSION OF LDB1 RESIDUES 295-340 AND LHX3 LIM ZINC-BINDING COMPND 5 DOMAINS 1 AND 2; COMPND 6 SYNONYM: NUCLEAR LIM INTERACTOR, LIM HOMEOBOX PROTEIN 3, HOMEOBOX COMPND 7 PROTEIN LIM-3, HOMEOBOX PROTEIN P-LIM; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 GENE: LDB1, NLI, LHX3, LIM-3, LIM3, PLIM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-2T KEYWDS INTRAMOLECULAR (FUSION) PROTEIN-PROTEIN COMPLEX, PROTEIN BINDING- KEYWDS 2 TRANSCRIPTION COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.LEE,A.L.NANCARROW,J.P.MACKAY,J.M.MATTHEWS REVDAT 4 16-MAR-22 2JTN 1 REMARK REVDAT 3 24-FEB-09 2JTN 1 VERSN REVDAT 2 05-AUG-08 2JTN 1 JRNL REVDAT 1 17-JUN-08 2JTN 0 JRNL AUTH M.BHATI,C.LEE,A.L.NANCARROW,M.LEE,V.J.CRAIG,I.BACH,J.M.GUSS, JRNL AUTH 2 J.P.MACKAY,J.M.MATTHEWS JRNL TITL IMPLEMENTING THE LIM CODE: THE STRUCTURAL BASIS FOR CELL JRNL TITL 2 TYPE-SPECIFIC ASSEMBLY OF LIM-HOMEODOMAIN COMPLEXES JRNL REF EMBO J. V. 27 2018 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18583962 JRNL DOI 10.1038/EMBOJ.2008.123 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, ARIA 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TOTAL OF 2679 NOE DISTANCE RESTRAINTS REMARK 3 (9 AMBIGUOUS) AND 204 TALOS DIHEDRAL RESTRAINTS REMARK 4 REMARK 4 2JTN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000100275. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 MM PHOSPHATE, 40 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM [U-99% 13C; U-99% 15N] REMARK 210 FLIX3 - FUSION OF LDB1-LID AND REMARK 210 LHX3 LIM DOMAINS, 3 MM ZINC ION, REMARK 210 15-30 UM DSS, 1 MM DTT, 20 MM REMARK 210 SODIUM PHOSPHATE, 40 MM SODIUM REMARK 210 CHLORIDE, 10 % [U-99% 2H] D2O, REMARK 210 90 % H2O; 1.2 MM FLIX3 - FUSION REMARK 210 OF LDB1-LID AND LHX3 LIM DOMAINS, REMARK 210 4.8 MM ZINC ION, 15-30 UM DSS, REMARK 210 1 MM DTT, 20 MM SODIUM PHOSPHATE, REMARK 210 40 MM SODIUM CHLORIDE, 90 % H2O, REMARK 210 10 % [U-99% 2H] D2O; 0.6 MM [U- REMARK 210 10% 13C; U-99% 15N] FLIX3 - REMARK 210 FUSION OF LDB1-LID AND LHX3 LIM REMARK 210 DOMAINS, 2.4 MM ZINC ION, 15-30 REMARK 210 UM DSS, 1 MM DTT, 20 MM SODIUM REMARK 210 PHOSPHATE, 40 MM SODIUM CHLORIDE, REMARK 210 90 % [U-99% 2H] D2O, 10 % H2O; REMARK 210 0.3 MM [U-99% 15N] FLIX3 - REMARK 210 FUSION OF LDB1-LID AND LHX3 LIM REMARK 210 DOMAINS, 1.2 MM ZINC ION, 15-30 REMARK 210 UM DSS, 1 MM DTT, 20 MM SODIUM REMARK 210 PHOSPHATE, 40 MM SODIUM CHLORIDE, REMARK 210 90 % [U-99% 2H] D2O, 10 % H2O; REMARK 210 0.6 MM [U-99% 13C; U-99% 15N] REMARK 210 FLIX3 - FUSION OF LDB1-LID AND REMARK 210 LHX3 LIM DOMAINS, 2.4 MM ZINC REMARK 210 ION, 15-30 UM DSS, 1 MM DTT, 20 REMARK 210 MM SODIUM PHOSPHATE, 40 MM REMARK 210 SODIUM CHLORIDE, 99 % [U-99% 2H] REMARK 210 D2O, 1 % H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCO; HNCA; HNCACO; HNCOCA; HCCH REMARK 210 -TOCSY; HCCH-COSY; HNHA; 15N- REMARK 210 HSQC; 13C-CT-HSQC; 2D- REMARK 210 HOMONUCLEAR TOCSY; 2D- REMARK 210 HOMONUCLEAR NOESY; HNCACB; REMARK 210 CBCACONH; 3D 15N-SEPARATED NOESY; REMARK 210 3D 13C-SEPARATED NOESY; 15N- REMARK 210 HSQC (OPTIMISED FOR HISTIDINE REMARK 210 SIDECHAIN J-COUPLING); 13C-CT- REMARK 210 HSQC (10% 13C SAMPLE) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 1.2, SPARKY, TOPSPIN 1.2, REMARK 210 CNS REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, CARTESIAN REMARK 210 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 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 PRO A 5 -167.77 -70.18 REMARK 500 1 ASP A 6 80.15 -64.80 REMARK 500 1 PHE A 20 -168.93 58.93 REMARK 500 1 ASP A 24 -74.98 -59.46 REMARK 500 1 PHE A 36 31.49 -98.69 REMARK 500 1 ASP A 37 33.39 -167.31 REMARK 500 1 ALA A 39 -179.11 59.95 REMARK 500 1 ASP A 44 158.33 60.55 REMARK 500 1 SER A 48 110.61 60.59 REMARK 500 1 GLN A 68 -166.54 -107.31 REMARK 500 1 LEU A 71 30.84 -163.46 REMARK 500 1 ARG A 73 -74.33 -84.46 REMARK 500 1 HIS A 84 175.32 -51.57 REMARK 500 1 ASP A 92 -63.08 -99.69 REMARK 500 1 LEU A 97 63.05 -111.04 REMARK 500 1 ALA A 98 39.49 -96.78 REMARK 500 1 GLU A 99 -49.18 -148.25 REMARK 500 1 ARG A 104 139.46 -176.64 REMARK 500 1 ALA A 124 -58.08 -125.24 REMARK 500 1 PRO A 130 175.39 -47.52 REMARK 500 1 GLN A 133 -168.73 -57.00 REMARK 500 1 GLN A 139 -86.33 55.75 REMARK 500 1 ALA A 149 -177.01 -172.24 REMARK 500 1 SER A 169 83.66 57.14 REMARK 500 1 CYS A 173 -169.37 -58.38 REMARK 500 1 LYS A 181 -66.57 -146.74 REMARK 500 2 ASP A 6 90.69 -170.07 REMARK 500 2 PHE A 20 -179.01 -59.17 REMARK 500 2 ASP A 24 -70.73 -57.89 REMARK 500 2 THR A 34 86.92 -60.18 REMARK 500 2 GLN A 35 -76.64 -150.32 REMARK 500 2 ASP A 37 78.49 -176.67 REMARK 500 2 ALA A 39 124.65 63.19 REMARK 500 2 SER A 48 -41.85 -174.59 REMARK 500 2 HIS A 51 35.53 -170.35 REMARK 500 2 SER A 54 -74.59 -69.02 REMARK 500 2 GLN A 68 134.44 -179.47 REMARK 500 2 LEU A 71 35.32 -172.55 REMARK 500 2 HIS A 84 171.55 -57.08 REMARK 500 2 LEU A 97 71.03 -103.24 REMARK 500 2 GLU A 99 -49.28 -148.55 REMARK 500 2 GLU A 106 35.86 -152.02 REMARK 500 2 ALA A 123 34.21 -97.66 REMARK 500 2 ALA A 124 -58.14 -125.12 REMARK 500 2 PRO A 130 171.69 -44.83 REMARK 500 2 GLN A 133 -176.04 -61.42 REMARK 500 2 ALA A 138 96.65 -57.43 REMARK 500 2 GLN A 139 -87.34 52.98 REMARK 500 2 CYS A 173 -169.27 -76.07 REMARK 500 2 LYS A 181 175.35 61.79 REMARK 500 REMARK 500 THIS ENTRY HAS 515 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 183 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 CYS A 66 SG 111.5 REMARK 620 3 HIS A 84 ND1 85.1 125.1 REMARK 620 4 CYS A 87 SG 122.9 104.8 108.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 184 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 CYS A 93 SG 115.4 REMARK 620 3 CYS A 110 SG 118.5 116.3 REMARK 620 4 ASP A 113 OD2 102.5 98.8 100.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 185 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 122 SG REMARK 620 2 CYS A 125 SG 120.4 REMARK 620 3 HIS A 144 ND1 95.5 90.8 REMARK 620 4 CYS A 147 SG 122.7 115.2 96.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 186 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 153 SG 116.2 REMARK 620 3 CYS A 173 SG 107.1 123.8 REMARK 620 4 ASP A 176 OD2 109.1 98.2 99.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 183 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 184 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 186 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS COMPOSED OF LIM DOMAIN-BINDING REMARK 999 PROTEIN 1 AND LIM/HOMEOBOX PROTEIN LHX3 WITH A REMARK 999 LINKER, GGSGGHMGSGG. DBREF 2JTN A 1 45 UNP P70662 LDB1_MOUSE 295 339 DBREF 2JTN A 57 182 UNP P50481 LHX3_MOUSE 28 153 SEQADV 2JTN GLY A 46 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 47 UNP P50481 SEE REMARK 999 SEQADV 2JTN SER A 48 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 49 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 50 UNP P50481 SEE REMARK 999 SEQADV 2JTN HIS A 51 UNP P50481 SEE REMARK 999 SEQADV 2JTN MET A 52 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 53 UNP P50481 SEE REMARK 999 SEQADV 2JTN SER A 54 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 55 UNP P50481 SEE REMARK 999 SEQADV 2JTN GLY A 56 UNP P50481 SEE REMARK 999 SEQRES 1 A 182 SER SER GLN VAL PRO ASP VAL MET VAL VAL GLY GLU PRO SEQRES 2 A 182 THR LEU MET GLY GLY GLU PHE GLY ASP GLU ASP GLU ARG SEQRES 3 A 182 LEU ILE THR ARG LEU GLU ASN THR GLN PHE ASP ALA ALA SEQRES 4 A 182 ASN GLY ILE ASP ASP GLU GLY GLY SER GLY GLY HIS MET SEQRES 5 A 182 GLY SER GLY GLY THR PRO GLU ILE PRO MET CYS ALA GLY SEQRES 6 A 182 CYS ASP GLN HIS ILE LEU ASP ARG PHE ILE LEU LYS ALA SEQRES 7 A 182 LEU ASP ARG HIS TRP HIS SER LYS CYS LEU LYS CYS SER SEQRES 8 A 182 ASP CYS HIS VAL PRO LEU ALA GLU ARG CYS PHE SER ARG SEQRES 9 A 182 GLY GLU SER VAL TYR CYS LYS ASP ASP PHE PHE LYS ARG SEQRES 10 A 182 PHE GLY THR LYS CYS ALA ALA CYS GLN LEU GLY ILE PRO SEQRES 11 A 182 PRO THR GLN VAL VAL ARG ARG ALA GLN ASP PHE VAL TYR SEQRES 12 A 182 HIS LEU HIS CYS PHE ALA CYS VAL VAL CYS LYS ARG GLN SEQRES 13 A 182 LEU ALA THR GLY ASP GLU PHE TYR LEU MET GLU ASP SER SEQRES 14 A 182 ARG LEU VAL CYS LYS ALA ASP TYR GLU THR ALA LYS GLN HET ZN A 183 1 HET ZN A 184 1 HET ZN A 185 1 HET ZN A 186 1 HETNAM ZN ZINC ION FORMUL 2 ZN 4(ZN 2+) HELIX 1 1 CYS A 110 ARG A 117 1 8 HELIX 2 2 CYS A 173 LYS A 181 1 9 SHEET 1 A 3 MET A 8 VAL A 9 0 SHEET 2 A 3 GLU A 162 LEU A 165 -1 O PHE A 163 N MET A 8 SHEET 3 A 3 LEU A 171 VAL A 172 -1 O VAL A 172 N TYR A 164 SHEET 1 B 3 THR A 29 GLU A 32 0 SHEET 2 B 3 PHE A 74 ALA A 78 -1 O LYS A 77 N THR A 29 SHEET 3 B 3 ARG A 81 TRP A 83 -1 O TRP A 83 N LEU A 76 SHEET 1 C 2 PHE A 102 ARG A 104 0 SHEET 2 C 2 SER A 107 TYR A 109 -1 O SER A 107 N ARG A 104 SHEET 1 D 2 ARG A 137 ALA A 138 0 SHEET 2 D 2 PHE A 141 VAL A 142 -1 N PHE A 141 O ALA A 138 LINK SG CYS A 63 ZN ZN A 183 1555 1555 2.31 LINK SG CYS A 66 ZN ZN A 183 1555 1555 2.30 LINK ND1 HIS A 84 ZN ZN A 183 1555 1555 2.00 LINK SG CYS A 87 ZN ZN A 183 1555 1555 2.31 LINK SG CYS A 90 ZN ZN A 184 1555 1555 2.30 LINK SG CYS A 93 ZN ZN A 184 1555 1555 2.30 LINK SG CYS A 110 ZN ZN A 184 1555 1555 2.30 LINK OD2 ASP A 113 ZN ZN A 184 1555 1555 2.03 LINK SG CYS A 122 ZN ZN A 185 1555 1555 2.30 LINK SG CYS A 125 ZN ZN A 185 1555 1555 2.30 LINK ND1 HIS A 144 ZN ZN A 185 1555 1555 1.99 LINK SG CYS A 147 ZN ZN A 185 1555 1555 2.31 LINK SG CYS A 150 ZN ZN A 186 1555 1555 2.30 LINK SG CYS A 153 ZN ZN A 186 1555 1555 2.30 LINK SG CYS A 173 ZN ZN A 186 1555 1555 2.30 LINK OD2 ASP A 176 ZN ZN A 186 1555 1555 2.03 SITE 1 AC1 5 CYS A 63 GLY A 65 CYS A 66 ILE A 70 SITE 2 AC1 5 HIS A 84 SITE 1 AC2 5 CYS A 90 ASP A 92 TYR A 109 CYS A 110 SITE 2 AC2 5 ASP A 113 SITE 1 AC3 6 CYS A 122 ALA A 124 CYS A 125 LEU A 127 SITE 2 AC3 6 TYR A 143 HIS A 144 SITE 1 AC4 4 ALA A 149 CYS A 150 CYS A 153 ARG A 155 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