HEADER RNA BINDING PROTEIN 28-FEB-23 8COO TITLE SOLUTION STRUCTURE OF ZIPCODE BINDING PROTEIN 1 (ZBP1) KH3(DD)KH4 TITLE 2 DOMAINS IN COMPLEX WITH N6-METHYLADENOSINE CONTAINING RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGF2 MRNA-BINDING PROTEIN 1,IMP-1,IGF-II MRNA-BINDING COMPND 5 PROTEIN 1,VICKZ FAMILY MEMBER 1,ZIP-CODE BINDING POLYPEPTIDE,ZIPCODE- COMPND 6 BINDING PROTEIN 1,ZBP-1; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: GLY A 1 EXPRESSION TAG ALA A 2 EXPRESSION TAG MET A 3 COMPND 9 EXPRESSION TAG GLY A 4 EXPRESSION TAG PHE A 14 ENGINEERED MUTATION COMPND 10 ASP A 40 ENGINEERED MUTATION ASP A 41 ENGINEERED MUTATION; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: RNA_(5'-R(*(UP*CP*GP*GP*(6MZ)P*CP*U)-3'); COMPND 13 CHAIN: B; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; 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 PROTEIN-RNA INTERACTIONS; NMR; BINDING MECHANISM; NEURONAL MRNA KEYWDS 2 GRANULES; NEURONAL DEVELOPMENT; MRNA LOCAL TRANSLATION; ZBP1; IMP1; KEYWDS 3 M6A-N6-METHYLADENOSINE RNA;, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.NICASTRO,G.ABIS,I.A.TAYLOR,A.RAMOS REVDAT 1 07-FEB-24 8COO 0 JRNL AUTH G.NICASTRO,G.ABIS,P.KLEIN,S.ESTEBAN-SERNA,C.GALLAGHER, JRNL AUTH 2 B.CHAVES-ARQUERO,Y.CAI,A.M.FIGUEIREDO,S.R.MARTIN,R.PATANI, JRNL AUTH 3 I.A.TAYLOR,A.RAMOS JRNL TITL DIRECT M6A RECOGNITION BY IMP1 UNDERLAYS AN ALTERNATIVE JRNL TITL 2 MODEL OF TARGET SELECTION FOR NON-CANONICAL METHYL-READERS. JRNL REF NUCLEIC ACIDS RES. V. 51 8774 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37377445 JRNL DOI 10.1093/NAR/GKAD534 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.NICASTRO,A.M.CANDEL,M.UHL,A.OREGIONI,D.HOLLINGWORTH, REMARK 1 AUTH 2 R.BACKOFEN,S.R.MARTIN,A.RAMOS REMARK 1 TITL MECHANISM OF B-ACTIN MRNA RECOGNITION BY ZBP1. REMARK 1 REF CELL REP V. 18 1187 2017 REMARK 1 REFN ESSN 2211-1247 REMARK 1 DOI 10.1016/J.CELREP.2016.12.091 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 8COO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128941. 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 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-100% 13C; U-100% 15N] REMARK 210 SAMPLE 1, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 15N NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : 950 AVANCE; 800 AVANCE; 700 REMARK 210 AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, XEASY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13550 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 2 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.7 DEGREES REMARK 500 3 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 4 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 5 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.5 DEGREES REMARK 500 6 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 7 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 8 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 9 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.5 DEGREES REMARK 500 10 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.7 DEGREES REMARK 500 11 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 12 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 13 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 14 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 15 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 16 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 17 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.7 DEGREES REMARK 500 18 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 19 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES REMARK 500 20 6MZ B 5 C3' - O3' - P ANGL. DEV. = -8.6 DEGREES 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 MET A 3 -47.49 -131.25 REMARK 500 1 SER A 7 115.65 56.64 REMARK 500 1 VAL A 8 -59.84 -123.09 REMARK 500 1 SER A 9 117.50 54.43 REMARK 500 1 ASP A 40 79.92 -66.22 REMARK 500 1 ASP A 41 16.28 53.10 REMARK 500 1 PRO A 76 -176.99 -54.91 REMARK 500 1 GLU A 101 -168.16 -108.27 REMARK 500 1 LYS A 122 85.15 -60.54 REMARK 500 1 ALA A 135 -11.05 66.89 REMARK 500 1 PRO A 141 156.44 -39.94 REMARK 500 1 ASP A 147 -159.03 -92.62 REMARK 500 1 LEU A 189 113.21 52.47 REMARK 500 2 ALA A 2 -45.22 -137.74 REMARK 500 2 SER A 15 -46.05 -136.93 REMARK 500 2 ASP A 40 81.89 -63.88 REMARK 500 2 ASP A 41 9.67 59.29 REMARK 500 2 PRO A 76 -176.68 -56.67 REMARK 500 2 GLU A 101 -150.53 -108.17 REMARK 500 2 ALA A 135 -11.00 70.91 REMARK 500 2 PRO A 141 160.80 -46.74 REMARK 500 2 LYS A 183 111.68 53.55 REMARK 500 2 GLN A 188 127.10 57.49 REMARK 500 2 GLN A 190 -46.14 -138.74 REMARK 500 3 SER A 6 -35.99 -130.57 REMARK 500 3 SER A 7 -54.13 65.65 REMARK 500 3 SER A 9 112.33 57.07 REMARK 500 3 SER A 16 -40.19 -144.02 REMARK 500 3 ASP A 40 76.97 -67.70 REMARK 500 3 ASP A 41 18.12 53.05 REMARK 500 3 PRO A 76 -178.70 -54.85 REMARK 500 3 ALA A 135 -9.03 73.77 REMARK 500 3 ASP A 147 -158.61 -91.54 REMARK 500 3 HIS A 159 -176.39 74.67 REMARK 500 3 GLN A 185 -47.30 -136.28 REMARK 500 3 GLN A 190 127.91 57.11 REMARK 500 4 SER A 7 -51.35 -139.99 REMARK 500 4 VAL A 8 98.35 66.45 REMARK 500 4 SER A 9 118.64 55.45 REMARK 500 4 PHE A 17 153.30 58.55 REMARK 500 4 ASP A 40 79.17 -67.39 REMARK 500 4 ASP A 41 15.20 54.21 REMARK 500 4 SER A 53 -0.15 64.21 REMARK 500 4 PRO A 76 -179.68 -55.12 REMARK 500 4 LYS A 122 82.00 -63.14 REMARK 500 4 ALA A 135 -9.76 69.33 REMARK 500 4 ASP A 143 -0.32 57.57 REMARK 500 4 HIS A 159 -154.45 -134.45 REMARK 500 4 LEU A 189 140.82 58.81 REMARK 500 5 ALA A 11 -55.69 64.15 REMARK 500 REMARK 500 THIS ENTRY HAS 290 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 38 GLY A 39 2 -149.70 REMARK 500 ILE A 38 GLY A 39 5 -147.67 REMARK 500 ILE A 38 GLY A 39 6 -149.44 REMARK 500 ILE A 38 GLY A 39 7 -148.79 REMARK 500 ILE A 38 GLY A 39 8 -147.85 REMARK 500 ILE A 38 GLY A 39 9 -149.67 REMARK 500 ILE A 38 GLY A 39 10 -148.52 REMARK 500 GLY A 98 PRO A 99 10 -148.28 REMARK 500 ILE A 38 GLY A 39 15 -147.79 REMARK 500 ILE A 38 GLY A 39 20 -149.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2N8M RELATED DB: PDB REMARK 900 RELATED ID: 34660 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF ZIPCODE BINDING PROTEIN 1 (ZBP1) KH3(DD)KH4 REMARK 900 DOMAINS IN COMPLEX WITH N6-METHYLADENOSINE CONTAINING RNA DBREF 8COO A 5 191 UNP O42254 IF2B1_CHICK 387 573 DBREF 8COO B 1 7 PDB 8COO 8COO 1 7 SEQADV 8COO GLY A 1 UNP O42254 EXPRESSION TAG SEQADV 8COO ALA A 2 UNP O42254 EXPRESSION TAG SEQADV 8COO MET A 3 UNP O42254 EXPRESSION TAG SEQADV 8COO GLY A 4 UNP O42254 EXPRESSION TAG SEQADV 8COO PHE A 14 UNP O42254 TYR 396 ENGINEERED MUTATION SEQADV 8COO ASP A 40 UNP O42254 LYS 422 ENGINEERED MUTATION SEQADV 8COO ASP A 41 UNP O42254 LYS 423 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 ASP ASP 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 LYS GLY 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 7 U C G G 6MZ C U HET 6MZ B 5 36 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE FORMUL 2 6MZ C11 H16 N5 O7 P HELIX 1 AA1 ALA A 33 ILE A 38 1 6 HELIX 2 AA2 HIS A 44 ALA A 52 1 9 HELIX 3 AA3 PRO A 76 ASN A 95 1 20 HELIX 4 AA4 ALA A 115 GLY A 121 1 7 HELIX 5 AA5 GLY A 124 THR A 134 1 11 HELIX 6 AA6 HIS A 159 LYS A 183 1 25 SHEET 1 AA1 5 SER A 55 ILE A 58 0 SHEET 2 AA1 5 VAL A 68 THR A 74 -1 O VAL A 72 N LYS A 57 SHEET 3 AA1 5 THR A 24 PRO A 30 -1 N VAL A 25 O ILE A 73 SHEET 4 AA1 5 LEU A 105 PRO A 112 -1 O GLU A 106 N PHE A 28 SHEET 5 AA1 5 GLN A 151 GLY A 158 -1 O VAL A 152 N VAL A 111 LINK O3' G B 4 P 6MZ B 5 1555 1555 1.63 LINK O3' 6MZ B 5 P C B 6 1555 1555 1.61 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