HEADER TRANSCRIPTION REGULATION/ONCOPROTEIN 01-DEC-10 2L6Z TITLE HADDOCK MODEL OF GATA1NF:LMO2LIM2-LDB1LID WITH FOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERYTHROID TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GATA-TYPE 1 DOMAIN, RESIDUES 200-238; COMPND 5 SYNONYM: ERYF1, GATA-BINDING FACTOR 1, GATA-1, GF-1, NF-E1 DNA- COMPND 6 BINDING PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ZINC FINGER PROTEIN USH; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 202-235; COMPND 12 SYNONYM: PROTEIN U-SHAPED; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: LIM DOMAIN ONLY 2, LINKER, LIM DOMAIN-BINDING PROTEIN 1; COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: RESIDUES 84-155; LIM-BINDING DOMAIN (LID), UNP RESIDUES COMPND 18 336-348; COMPND 19 SYNONYM: LMO2, LDB1, CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2, COMPND 20 CLIM-2, LIM DOMAIN-BINDING FACTOR CLIM2, MLDB1, NUCLEAR LIM COMPND 21 INTERACTOR; COMPND 22 ENGINEERED: YES; COMPND 23 MUTATION: YES; COMPND 24 OTHER_DETAILS: INCLUDING A FLEXIBLE LINKER REGION, GGSGGSGGSGG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 11 ORGANISM_COMMON: FRUIT FLY; SOURCE 12 ORGANISM_TAXID: 7227; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PGEX; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 19 ORGANISM_COMMON: MOUSE; SOURCE 20 ORGANISM_TAXID: 10090; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 24 EXPRESSION_SYSTEM_VECTOR: PGEX KEYWDS GATA-1, LDB1, LMO2, FOG-1, TRANSCRIPTION REGULATION-ONCOPROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR L.WILKINSON-WHITE,R.GAMSJAEGER,S.DASTMALCHI,B.WIENERT,P.H.STOKES, AUTHOR 2 M.CROSSLEY,J.P.MACKAY,J.M.MATTHEWS REVDAT 3 01-MAY-24 2L6Z 1 REMARK DBREF SEQADV LINK REVDAT 2 28-SEP-11 2L6Z 1 AUTHOR JRNL REVDAT 1 31-AUG-11 2L6Z 0 JRNL AUTH L.WILKINSON-WHITE,R.GAMSJAEGER,S.DASTMALCHI,B.WIENERT, JRNL AUTH 2 P.H.STOKES,M.CROSSLEY,J.P.MACKAY,J.M.MATTHEWS JRNL TITL STRUCTURAL BASIS OF SIMULTANEOUS RECRUITMENT OF THE JRNL TITL 2 TRANSCRIPTIONAL REGULATORS LMO2 AND FOG1/ZFPM1 BY THE JRNL TITL 3 TRANSCRIPTION FACTOR GATA1 JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 14443 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21844373 JRNL DOI 10.1073/PNAS.1105898108 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK 2.1 BASED ON CNS REMARK 4 REMARK 4 2L6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000102035. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.12 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-100% 15N] GATA1NF; 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 CYS A 207 -93.14 -130.69 REMARK 500 1 ASP A 218 -165.46 -101.02 REMARK 500 1 CYS A 225 -74.61 -55.33 REMARK 500 1 ASN A 226 -31.02 178.37 REMARK 500 1 LYS A 233 -58.43 -132.35 REMARK 500 1 SER B 2 -173.52 63.53 REMARK 500 1 LEU B 3 -75.93 -74.85 REMARK 500 1 LEU B 4 -56.45 68.58 REMARK 500 1 GLN B 28 48.21 -74.58 REMARK 500 1 ALA B 29 -55.02 -158.73 REMARK 500 1 CYS B 32 70.50 -69.83 REMARK 500 1 SER B 33 -82.65 64.94 REMARK 500 1 HIS B 34 94.65 -172.25 REMARK 500 1 ARG B 35 32.75 -98.51 REMARK 500 1 ARG C 102 -165.63 -112.88 REMARK 500 1 TYR C 104 31.12 -157.29 REMARK 500 1 ASP C 112 -58.77 -162.39 REMARK 500 1 TYR C 115 -146.14 -112.82 REMARK 500 1 PHE C 120 75.11 -113.53 REMARK 500 1 ILE C 138 -156.96 -112.38 REMARK 500 1 ASP C 141 -160.84 -116.17 REMARK 500 1 CYS C 144 -160.60 -77.08 REMARK 500 1 ASN C 155 -52.71 -123.61 REMARK 500 2 CYS A 207 -91.76 -139.45 REMARK 500 2 ALA A 209 93.15 -69.39 REMARK 500 2 CYS A 225 -76.90 -60.80 REMARK 500 2 ASN A 226 -41.99 -176.95 REMARK 500 2 GLN A 237 -159.12 -92.48 REMARK 500 2 SER B 2 -174.16 64.05 REMARK 500 2 LEU B 3 -81.44 -82.89 REMARK 500 2 LEU B 4 -42.79 70.33 REMARK 500 2 ALA B 7 42.16 -90.29 REMARK 500 2 SER B 19 -33.38 -131.00 REMARK 500 2 GLN B 28 45.07 -75.81 REMARK 500 2 ALA B 29 -54.37 -147.92 REMARK 500 2 SER B 33 -96.02 63.77 REMARK 500 2 HIS B 34 85.43 -158.95 REMARK 500 2 ARG C 86 41.74 -158.76 REMARK 500 2 CYS C 97 -160.58 -100.67 REMARK 500 2 ARG C 102 -158.28 -121.79 REMARK 500 2 GLU C 105 -71.33 -65.98 REMARK 500 2 VAL C 110 -158.24 -102.60 REMARK 500 2 ASP C 112 -55.72 -150.70 REMARK 500 2 SER C 140 -84.07 -94.66 REMARK 500 2 ASP C 141 -164.76 -112.41 REMARK 500 2 CYS C 144 -167.87 -78.96 REMARK 500 3 ALA A 201 -79.73 -80.35 REMARK 500 3 CYS A 207 -88.56 -134.64 REMARK 500 3 CYS A 225 -75.03 -54.77 REMARK 500 3 ASN A 226 -40.31 -176.59 REMARK 500 REMARK 500 THIS ENTRY HAS 202 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 239 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 204 SG REMARK 620 2 CYS A 207 SG 109.6 REMARK 620 3 CYS A 225 SG 109.8 109.8 REMARK 620 4 CYS A 228 SG 111.2 111.3 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 37 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 14 SG 112.0 REMARK 620 3 HIS B 27 NE2 106.6 112.2 REMARK 620 4 CYS B 32 SG 110.4 112.6 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 180 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 94 SG REMARK 620 2 CYS C 97 SG 106.4 REMARK 620 3 HIS C 116 ND1 107.4 106.4 REMARK 620 4 CYS C 119 SG 112.1 111.8 112.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 181 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 122 SG REMARK 620 2 CYS C 125 SG 112.4 REMARK 620 3 CYS C 144 SG 119.4 117.8 REMARK 620 4 ASP C 147 OD2 101.9 99.4 101.2 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 239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 181 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L6Y RELATED DB: PDB REMARK 900 HADDOCK MODEL OF GATA1NF:LMO2LIM2-LDB1LID REMARK 900 RELATED ID: 2L3K RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LMO2(LIM2)-LDB1(LID) DBREF 2L6Z A 200 238 UNP P17679 GATA1_MOUSE 200 238 DBREF 2L6Z B 3 36 UNP Q9VPQ6 USH_DROME 202 235 DBREF 2L6Z C 84 155 UNP Q544Z2 Q544Z2_MOUSE 84 155 DBREF 2L6Z C 156 166 PDB 2L6Z 2L6Z 156 166 DBREF 2L6Z C 167 179 UNP P70662 LDB1_MOUSE 336 348 SEQADV 2L6Z GLY B 1 UNP Q9VPQ6 EXPRESSION TAG SEQADV 2L6Z SER B 2 UNP Q9VPQ6 EXPRESSION TAG SEQADV 2L6Z SER C 130 UNP Q544Z2 CYS 130 ENGINEERED MUTATION SEQRES 1 A 39 GLU ALA ARG GLU CYS VAL ASN CYS GLY ALA THR ALA THR SEQRES 2 A 39 PRO LEU TRP ARG ARG ASP ARG THR GLY HIS TYR LEU CYS SEQRES 3 A 39 ASN ALA CYS GLY LEU TYR HIS LYS MET ASN GLY GLN ASN SEQRES 1 B 36 GLY SER LEU LEU LYS PRO ALA ARG PHE MET CYS LEU PRO SEQRES 2 B 36 CYS GLY ILE ALA PHE SER SER PRO SER THR LEU GLU ALA SEQRES 3 B 36 HIS GLN ALA TYR TYR CYS SER HIS ARG ILE SEQRES 1 C 96 TYR LEU ARG LEU PHE GLY GLN ASP GLY LEU CYS ALA SER SEQRES 2 C 96 CYS ASP LYS ARG ILE ARG ALA TYR GLU MET THR MET ARG SEQRES 3 C 96 VAL LYS ASP LYS VAL TYR HIS LEU GLU CYS PHE LYS CYS SEQRES 4 C 96 ALA ALA CYS GLN LYS HIS PHE SER VAL GLY ASP ARG TYR SEQRES 5 C 96 LEU LEU ILE ASN SER ASP ILE VAL CYS GLU GLN ASP ILE SEQRES 6 C 96 TYR GLU TRP THR LYS ILE ASN GLY GLY SER GLY GLY SER SEQRES 7 C 96 GLY GLY SER GLY GLY ASP VAL MET VAL VAL GLY GLU PRO SEQRES 8 C 96 THR LEU MET GLY GLY HET ZN A 239 1 HET ZN B 37 1 HET ZN C 180 1 HET ZN C 181 1 HETNAM ZN ZINC ION FORMUL 4 ZN 4(ZN 2+) HELIX 1 1 ALA A 227 LYS A 233 5 7 HELIX 2 2 SER B 20 GLN B 28 1 9 HELIX 3 3 ASP C 147 THR C 152 1 6 SHEET 1 A 3 ILE C 142 VAL C 143 0 SHEET 2 A 3 ARG C 134 LEU C 137 -1 N LEU C 136 O VAL C 143 SHEET 3 A 3 MET C 169 VAL C 170 -1 O MET C 169 N TYR C 135 LINK SG CYS A 204 ZN ZN A 239 1555 1555 2.27 LINK SG CYS A 207 ZN ZN A 239 1555 1555 2.26 LINK SG CYS A 225 ZN ZN A 239 1555 1555 2.24 LINK SG CYS A 228 ZN ZN A 239 1555 1555 2.25 LINK SG CYS B 11 ZN ZN B 37 1555 1555 2.27 LINK SG CYS B 14 ZN ZN B 37 1555 1555 2.29 LINK NE2 HIS B 27 ZN ZN B 37 1555 1555 1.93 LINK SG CYS B 32 ZN ZN B 37 1555 1555 2.30 LINK SG CYS C 94 ZN ZN C 180 1555 1555 2.29 LINK SG CYS C 97 ZN ZN C 180 1555 1555 2.32 LINK ND1 HIS C 116 ZN ZN C 180 1555 1555 1.99 LINK SG CYS C 119 ZN ZN C 180 1555 1555 2.34 LINK SG CYS C 122 ZN ZN C 181 1555 1555 2.28 LINK SG CYS C 125 ZN ZN C 181 1555 1555 2.28 LINK SG CYS C 144 ZN ZN C 181 1555 1555 2.29 LINK OD2 ASP C 147 ZN ZN C 181 1555 1555 2.02 SITE 1 AC1 4 CYS A 204 CYS A 207 CYS A 225 CYS A 228 SITE 1 AC2 4 CYS B 11 CYS B 14 HIS B 27 CYS B 32 SITE 1 AC3 4 CYS C 94 CYS C 97 HIS C 116 CYS C 119 SITE 1 AC4 4 CYS C 122 CYS C 125 CYS C 144 ASP C 147 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