10 20 30 40 50 60 70 80 2N8L - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA BINDING PROTEIN/RNA 21-OCT-15 2N8L
TITLE ZIPCODE-BINDING-PROTEIN-1 KH3KH4(DD) DOMAINS IN COMPLEX WITH THE KH3 TITLE 2 RNA TARGET
COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH DOMAIN (UNP RESIDUES 387-573); COMPND 5 SYNONYM: IGF2 MRNA-BINDING PROTEIN 1, IMP-1, IGF-II MRNA-BINDING COMPND 6 PROTEIN 1, VICKZ FAMILY MEMBER 1, ZIP-CODE BINDING POLYPEPTIDE, COMPND 7 ZIPCODE-BINDING PROTEIN 1, ZBP-1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RNA (5'-R(P*GP*CP*AP*CP*AP*CP*CP*C)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: IGF2BP1, VICKZ1, ZBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630
KEYWDS KH DOMAIN, RNA BINDING PROTEIN-RNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 12
AUTHOR G.NICASTRO,A.M.CANDEL,A.RAMOS,D.HOLLINGWORTH
REVDAT 1 25-JAN-17 2N8L 0
JRNL AUTH G.NICASTRO,A.M.CANDEL,A.RAMOS,D.HOLLINGWORTH JRNL TITL ZIPCODE-BINDING-PROTEIN-1 KH3KH4(DD) DOMAINS IN COMPLEX WITH JRNL TITL 2 THE RNA TARGET GCACACCC JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.CHAO,Y.PATSKOVSKY,V.PATEL,M.LEVY,S.C.ALMO,R.H.SINGER REMARK 1 TITL ZBP1 RECOGNITION OF BETA-ACTIN ZIPCODE INDUCES RNA LOOPING. REMARK 1 REF GENES DEV. V. 24 148 2010 REMARK 1 REFN ISSN 0890-9369 REMARK 1 PMID 20080952 REMARK 1 DOI 10.1101/GAD.1862910 REMARK 1 REFERENCE 2 REMARK 1 AUTH V.L.PATEL,S.MITRA,R.HARRIS,A.R.BUXBAUM,T.LIONNET, REMARK 1 AUTH 2 M.BRENOWITZ,M.GIRVIN,M.LEVY,S.C.ALMO,R.H.SINGER,J.A.CHAO REMARK 1 TITL SPATIAL ARRANGEMENT OF AN RNA ZIPCODE IDENTIFIES MRNAS UNDER REMARK 1 TITL 2 POST-TRANSCRIPTIONAL CONTROL. REMARK 1 REF GENES DEV. V. 26 43 2012 REMARK 1 REFN ISSN 0890-9369 REMARK 1 PMID 22215810 REMARK 1 DOI 10.1101/GAD.177428.111 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.HOLLINGWORTH,A.M.CANDEL,G.NICASTRO,S.R.MARTIN,P.BRIATA, REMARK 1 AUTH 2 R.GHERZI,A.RAMOS REMARK 1 TITL KH DOMAINS WITH IMPAIRED NUCLEIC ACID BINDING AS A TOOL FOR REMARK 1 TITL 2 FUNCTIONAL ANALYSIS. REMARK 1 REF NUCLEIC ACIDS RES. V. 40 6873 2012 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 22547390 REMARK 1 DOI 10.1093/NAR/GKS368
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2N8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-15. REMARK 100 THE RCSB ID CODE IS RCSB104558.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM PHOSPHATE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ; 950 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, ARIA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HA ILE A 120 HB VAL A 127 1.12 REMARK 500 HE3 LYS A 92 HB VAL A 103 1.13 REMARK 500 HG2 GLN A 144 H ILE A 153 1.25 REMARK 500 HA2 GLY A 35 H42 C B 4 1.32 REMARK 500 O2' G B 1 H6 C B 2 1.39 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 5 107.19 -55.20 REMARK 500 1 ALA A 11 83.14 55.95 REMARK 500 1 PRO A 13 35.54 -99.29 REMARK 500 1 PHE A 14 77.35 -104.99 REMARK 500 1 SER A 16 138.94 72.00 REMARK 500 1 PRO A 20 43.58 -90.44 REMARK 500 1 LYS A 40 89.52 40.43 REMARK 500 1 PRO A 61 107.33 -37.89 REMARK 500 1 ASP A 143 -89.17 -116.93 REMARK 500 1 GLN A 144 -77.39 67.43 REMARK 500 1 GLU A 150 23.82 46.46 REMARK 500 1 LYS A 183 87.80 53.86 REMARK 500 1 SER A 186 45.18 -83.14 REMARK 500 2 MET A 3 76.60 -101.90 REMARK 500 2 SER A 7 30.47 -154.39 REMARK 500 2 VAL A 8 77.31 -157.15 REMARK 500 2 SER A 9 21.63 -147.36 REMARK 500 2 SER A 16 -69.67 70.21 REMARK 500 2 GLN A 43 -34.91 -176.19 REMARK 500 2 ASP A 122 -88.25 59.90 REMARK 500 2 ASP A 147 35.32 -78.24 REMARK 500 2 LYS A 183 83.94 60.73 REMARK 500 2 GLN A 185 96.48 -69.97 REMARK 500 3 PRO A 13 70.66 -69.84 REMARK 500 3 SER A 15 -57.18 -130.13 REMARK 500 3 LYS A 40 89.51 42.16 REMARK 500 3 LYS A 41 -0.35 66.85 REMARK 500 3 ASP A 122 -72.61 65.48 REMARK 500 3 GLN A 144 -70.26 -50.79 REMARK 500 4 MET A 3 -89.14 62.58 REMARK 500 4 MET A 18 85.31 61.00 REMARK 500 4 GLU A 21 -75.32 -62.02 REMARK 500 4 LYS A 40 -89.43 59.23 REMARK 500 4 LYS A 67 33.34 -78.39 REMARK 500 4 PRO A 112 155.82 -49.44 REMARK 500 4 ASP A 122 -73.77 -42.65 REMARK 500 4 THR A 145 70.53 -175.29 REMARK 500 4 GLU A 150 29.68 47.33 REMARK 500 4 LYS A 183 -61.87 69.72 REMARK 500 4 GLN A 188 71.75 50.96 REMARK 500 4 GLN A 190 -53.50 -121.80 REMARK 500 5 SER A 15 46.51 -78.40 REMARK 500 5 PHE A 17 -70.72 -123.71 REMARK 500 5 GLU A 21 37.86 -88.74 REMARK 500 5 PRO A 99 -4.57 -59.04 REMARK 500 5 ASP A 122 -75.16 65.21 REMARK 500 5 LYS A 125 -48.25 -173.07 REMARK 500 5 THR A 145 172.91 58.67 REMARK 500 5 ASP A 147 36.30 -78.88 REMARK 500 5 GLN A 188 152.69 69.39 REMARK 500 REMARK 500 THIS ENTRY HAS 118 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25854 RELATED DB: BMRB REMARK 900 RELATED ID: 2N8M RELATED DB: PDB
DBREF 2N8L A 5 191 UNP O42254 IF2B1_CHICK 387 573 DBREF 2N8L B 1 8 PDB 2N8L 2N8L 1 8
SEQADV 2N8L GLY A 1 UNP O42254 EXPRESSION TAG SEQADV 2N8L ALA A 2 UNP O42254 EXPRESSION TAG SEQADV 2N8L MET A 3 UNP O42254 EXPRESSION TAG SEQADV 2N8L GLY A 4 UNP O42254 EXPRESSION TAG SEQADV 2N8L PHE A 14 UNP O42254 TYR 396 ENGINEERED MUTATION SEQADV 2N8L ASP A 122 UNP O42254 LYS 504 ENGINEERED MUTATION SEQADV 2N8L ASP A 123 UNP O42254 GLY 505 ENGINEERED MUTATION
SEQRES 1 A 191 GLY ALA MET GLY PRO SER SER VAL SER GLY ALA ALA PRO SEQRES 2 A 191 PHE SER SER PHE MET PRO PRO GLU GLN GLU THR VAL HIS SEQRES 3 A 191 VAL PHE ILE PRO ALA GLN ALA VAL GLY ALA ILE ILE GLY SEQRES 4 A 191 LYS LYS GLY GLN HIS ILE LYS GLN LEU SER ARG PHE ALA SEQRES 5 A 191 SER ALA SER ILE LYS ILE ALA PRO PRO GLU THR PRO ASP SEQRES 6 A 191 SER LYS VAL ARG MET VAL VAL ILE THR GLY PRO PRO GLU SEQRES 7 A 191 ALA GLN PHE LYS ALA GLN GLY ARG ILE TYR GLY LYS LEU SEQRES 8 A 191 LYS GLU GLU ASN PHE PHE GLY PRO LYS GLU GLU VAL LYS SEQRES 9 A 191 LEU GLU THR HIS ILE ARG VAL PRO ALA SER ALA ALA GLY SEQRES 10 A 191 ARG VAL ILE GLY ASP ASP GLY LYS THR VAL ASN GLU LEU SEQRES 11 A 191 GLN ASN LEU THR ALA ALA GLU VAL VAL VAL PRO ARG ASP SEQRES 12 A 191 GLN THR PRO ASP GLU ASN GLU GLN VAL ILE VAL LYS ILE SEQRES 13 A 191 ILE GLY HIS PHE TYR ALA SER GLN MET ALA GLN ARG LYS SEQRES 14 A 191 ILE ARG ASP ILE LEU ALA GLN VAL LYS GLN GLN HIS GLN SEQRES 15 A 191 LYS GLY GLN SER GLY GLN LEU GLN ALA SEQRES 1 B 8 G C A C A C C C
HELIX 1 1 ALA A 31 GLY A 39 1 9 HELIX 2 2 LYS A 40 GLY A 42 5 3 HELIX 3 3 GLN A 43 SER A 53 1 11 HELIX 4 4 PRO A 76 ASN A 95 1 20 HELIX 5 5 ALA A 113 ILE A 120 1 8 HELIX 6 6 LYS A 125 ALA A 135 1 11 HELIX 7 7 PRO A 146 ASN A 149 5 4 HELIX 8 8 HIS A 159 GLN A 179 1 21 HELIX 9 9 GLN A 180 GLN A 182 5 3
SHEET 1 A 6 SER A 55 ILE A 58 0 SHEET 2 A 6 VAL A 68 GLY A 75 -1 O THR A 74 N SER A 55 SHEET 3 A 6 GLU A 23 PRO A 30 -1 N ILE A 29 O ARG A 69 SHEET 4 A 6 THR A 107 PRO A 112 -1 O HIS A 108 N HIS A 26 SHEET 5 A 6 GLN A 151 ILE A 157 -1 O VAL A 152 N VAL A 111 SHEET 6 A 6 GLU A 137 VAL A 139 -1 N GLU A 137 O ILE A 157
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