HEADER TRANSPORT PROTEIN 10-AUG-10 2L21 TITLE CHICKEN IGF2R DOMAIN 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 11, RESIDUES 1485-1630; COMPND 5 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: IGF2R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26A KEYWDS GENOMIC IMPRINTING, INSULIN-LIKE GROWTH FACTOR 2, MANNOSE 6 PHOSPHATE KEYWDS 2 RECEPTOR, PROTEIN EVOLUTION, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.WILLIAMS,H.HOPPE,M.STRICKLAND,S.FRAGO,R.Z.ELLIS,P.WATTANA-AMORN, AUTHOR 2 S.N.PRINCE,O.J.ZACCHEO,B.FORBES,E.Y.JONES,D.Z.REZGUI,M.P.CRUMP, AUTHOR 3 A.B.HASSAN REVDAT 3 14-JUN-23 2L21 1 REMARK REVDAT 2 05-FEB-20 2L21 1 REMARK SEQADV REVDAT 1 15-FEB-12 2L21 0 JRNL AUTH C.WILLIAMS,H.HOPPE,D.REZGUI,M.STRICKLAND,S.FRAGO,R.Z.ELLIS, JRNL AUTH 2 P.WATTANA-AMORN,S.N.PRINCE,O.J.ZACCHEO,E.Y.JONES,B.FORBES, JRNL AUTH 3 M.P.CRUMP,A.B.HASSAN JRNL TITL CD LOOP DEPENDENCY OF THE IGF2: M6P/IGF2 RECEPTOR BINDING JRNL TITL 2 INTERACTION PREDATES IMPRINTING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, CNS 1.2, ARIA 1.2, ICING R765 REMARK 3 AUTHORS : VARIAN (VNMRJ), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA), VUISTER, DORELEIJERS, SOUSA DA REMARK 3 SILVA (ICING) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARIA1.2 PROTOCOL. COOL_1 AND COOL_2 REMARK 3 STEPS INCREASED TO 40K AND COOL_2, ARIA1.2 WATER REFINEMENT REMARK 3 MODIFIED WITH RECOORD WATER REFINEMENT PARAMATERS REMARK 4 REMARK 4 2L21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101857. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5% D2O, 20 MM SODIUM ACETATE, REMARK 210 0.1 MM EDTA, 100 UM SODIUM AZIDE, REMARK 210 0.5-1 MM [U-98% 15N] IGF2R, 95% REMARK 210 H2O/5% D2O; 5% D2O, 20 MM SODIUM REMARK 210 PHOSPHATE, 0.1 MM EDTA, 100 UM REMARK 210 SODIUM AZIDE, 0.5-1 MM [U-98% REMARK 210 13C; U-98% 15N] IGF2R, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 C(CO)NH; 3D CBCA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CNS 1.2, TALOS, ARIA REMARK 210 1.2, CCPNMR ANALYSIS 2.13 REMARK 210 METHOD USED : SIMULATED ANNEALING, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: SOME BACKBONE DATASETS ACQUIRED USING ASCOM WITH A REDUCED REMARK 210 NUMBER OF POINTS IN THE NITROGEN DIMENSION 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 2033 REMARK 465 HIS A 2034 REMARK 465 HIS A 2035 REMARK 465 HIS A 2036 REMARK 465 HIS A 2037 REMARK 465 HIS A 2038 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 OE1 GLU A 1973 HZ3 LYS A 1987 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 6 TYR A1915 CE1 TYR A1915 CZ -0.091 REMARK 500 6 TYR A1915 CZ TYR A1915 CE2 0.087 REMARK 500 7 PHE A1904 CE1 PHE A1904 CZ 0.170 REMARK 500 7 PHE A1904 CZ PHE A1904 CE2 -0.128 REMARK 500 8 TYR A1972 CE1 TYR A1972 CZ -0.089 REMARK 500 8 TYR A1972 CZ TYR A1972 CE2 0.078 REMARK 500 9 TYR A1972 CE1 TYR A1972 CZ -0.129 REMARK 500 9 TYR A1972 CZ TYR A1972 CE2 0.102 REMARK 500 12 PHE A1904 CE1 PHE A1904 CZ 0.116 REMARK 500 12 TYR A1915 CE1 TYR A1915 CZ 0.107 REMARK 500 12 TYR A1915 CZ TYR A1915 CE2 -0.118 REMARK 500 14 TYR A1915 CZ TYR A1915 CE2 -0.087 REMARK 500 17 TYR A1989 CE1 TYR A1989 CZ 0.100 REMARK 500 17 TYR A1989 CZ TYR A1989 CE2 -0.086 REMARK 500 18 PHE A1904 CE1 PHE A1904 CZ 0.177 REMARK 500 18 PHE A1904 CZ PHE A1904 CE2 -0.138 REMARK 500 18 TYR A1972 CE1 TYR A1972 CZ -0.160 REMARK 500 18 TYR A1972 CZ TYR A1972 CE2 0.139 REMARK 500 19 TYR A1915 CE1 TYR A1915 CZ -0.103 REMARK 500 19 TYR A1915 CZ TYR A1915 CE2 0.099 REMARK 500 20 PHE A1904 CE1 PHE A1904 CZ 0.177 REMARK 500 20 PHE A1904 CZ PHE A1904 CE2 -0.123 REMARK 500 20 TYR A1915 CE1 TYR A1915 CZ 0.090 REMARK 500 20 TYR A1915 CZ TYR A1915 CE2 -0.105 REMARK 500 20 TYR A1972 CZ TYR A1972 CE2 -0.079 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 SER A1887 -67.14 -100.96 REMARK 500 1 ASN A1891 -69.12 70.26 REMARK 500 1 ASP A1892 -90.24 -148.94 REMARK 500 1 CYS A1893 63.32 63.24 REMARK 500 1 ASN A1922 -58.21 74.98 REMARK 500 1 ARG A1923 156.82 -46.83 REMARK 500 1 CYS A1930 33.44 176.32 REMARK 500 1 CYS A1937 -79.62 -148.33 REMARK 500 1 ALA A1938 -90.90 -152.91 REMARK 500 1 ASN A1939 -82.59 -123.94 REMARK 500 1 GLU A1973 -169.95 -114.67 REMARK 500 1 ASP A1974 78.49 63.29 REMARK 500 1 ASP A2001 67.85 69.64 REMARK 500 1 SER A2002 77.20 45.10 REMARK 500 1 GLU A2027 75.47 -155.39 REMARK 500 2 ASN A1891 -36.18 76.98 REMARK 500 2 LEU A1906 54.43 -91.88 REMARK 500 2 SER A1913 -63.94 -107.44 REMARK 500 2 HIS A1921 -27.85 -169.34 REMARK 500 2 CYS A1930 -30.98 73.37 REMARK 500 2 SER A1936 -1.85 -148.14 REMARK 500 2 ALA A1938 -92.22 79.07 REMARK 500 2 ASN A1939 -85.80 -123.29 REMARK 500 2 ALA A1942 -39.95 -139.63 REMARK 500 2 ASP A1974 129.92 73.18 REMARK 500 2 MET A1984 -158.77 -130.22 REMARK 500 2 ASP A2001 104.28 -170.43 REMARK 500 2 LEU A2007 -62.40 -91.82 REMARK 500 2 THR A2013 20.50 -147.65 REMARK 500 2 GLU A2028 40.72 -163.11 REMARK 500 3 LYS A1886 93.19 58.69 REMARK 500 3 SER A1887 -76.82 -67.91 REMARK 500 3 ARG A1911 -169.90 -176.24 REMARK 500 3 HIS A1921 -47.12 -157.27 REMARK 500 3 CYS A1930 42.27 -160.18 REMARK 500 3 SER A1935 -74.47 -159.23 REMARK 500 3 ALA A1938 -52.19 -136.01 REMARK 500 3 ASN A1939 -80.83 -111.28 REMARK 500 3 LYS A1959 74.87 -103.18 REMARK 500 3 GLN A1966 -11.73 71.92 REMARK 500 3 ASP A1974 90.49 55.06 REMARK 500 3 ASP A1997 49.57 -83.96 REMARK 500 3 ALA A1998 -49.01 -170.43 REMARK 500 3 SER A2002 123.13 56.63 REMARK 500 3 CYS A2014 65.97 63.16 REMARK 500 4 SER A1887 122.91 71.10 REMARK 500 4 ASP A1892 -86.85 -84.68 REMARK 500 4 CYS A1893 77.11 51.02 REMARK 500 4 ASP A1919 -156.06 -87.07 REMARK 500 4 HIS A1921 7.65 -171.40 REMARK 500 REMARK 500 THIS ENTRY HAS 317 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A1911 0.08 SIDE CHAIN REMARK 500 1 ARG A1923 0.09 SIDE CHAIN REMARK 500 2 TYR A1915 0.07 SIDE CHAIN REMARK 500 3 ARG A1911 0.08 SIDE CHAIN REMARK 500 6 TYR A1972 0.06 SIDE CHAIN REMARK 500 6 ARG A2032 0.08 SIDE CHAIN REMARK 500 7 ARG A1894 0.07 SIDE CHAIN REMARK 500 8 ARG A1923 0.07 SIDE CHAIN REMARK 500 11 ARG A1923 0.09 SIDE CHAIN REMARK 500 12 ARG A1911 0.09 SIDE CHAIN REMARK 500 14 ARG A1894 0.14 SIDE CHAIN REMARK 500 14 ARG A1923 0.09 SIDE CHAIN REMARK 500 15 ARG A1894 0.08 SIDE CHAIN REMARK 500 16 TYR A1972 0.05 SIDE CHAIN REMARK 500 17 ARG A1911 0.07 SIDE CHAIN REMARK 500 17 TYR A1989 0.06 SIDE CHAIN REMARK 500 20 TYR A1972 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CNJ RELATED DB: PDB REMARK 900 NMR STUDIES ON THE INTERACTION OF INSULIN-GROWTH FACTOR II (IGF-II) REMARK 900 WITH IGF2R DOMAIN 11 REMARK 900 RELATED ID: 1GP0 RELATED DB: PDB REMARK 900 HUMAN IGF2R DOMAIN 11 REMARK 900 RELATED ID: 2L29 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF E4 MUTANT HUMAN IGF2R DOMAIN 11 BOUND TO IGF-II REMARK 900 RELATED ID: 2L2A RELATED DB: PDB REMARK 900 MUTATED DOMAIN 11 OF THE CYTOPLASMIC REGION OF THE CATION- REMARK 900 INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR REMARK 900 RELATED ID: 17110 RELATED DB: BMRB DBREF 2L21 A 1885 2030 UNP Q90681 Q90681_CHICK 1485 1630 SEQADV 2L21 MET A 1885 UNP Q90681 LEU 1485 ENGINEERED MUTATION SEQADV 2L21 THR A 1896 UNP Q90681 MET 1496 ENGINEERED MUTATION SEQADV 2L21 MET A 1984 UNP Q90681 THR 1584 ENGINEERED MUTATION SEQADV 2L21 PRO A 2031 UNP Q90681 EXPRESSION TAG SEQADV 2L21 ARG A 2032 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2033 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2034 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2035 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2036 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2037 UNP Q90681 EXPRESSION TAG SEQADV 2L21 HIS A 2038 UNP Q90681 EXPRESSION TAG SEQRES 1 A 154 MET LYS SER ASN VAL GLN ASN ASP CYS ARG VAL THR ASN SEQRES 2 A 154 PRO ALA THR GLY HIS LEU PHE ASP LEU THR SER LEU LYS SEQRES 3 A 154 ARG GLU SER GLY TYR THR ILE THR ASP SER HIS ASN ARG SEQRES 4 A 154 LYS ILE GLU LEU ASN VAL CYS ALA GLU ALA LYS SER SER SEQRES 5 A 154 CYS ALA ASN GLY ALA ALA VAL CYS ILE THR ASP GLY PRO SEQRES 6 A 154 LYS THR LEU ASN ALA GLY LYS LEU SER LYS THR LEU THR SEQRES 7 A 154 TYR GLU ASP GLN VAL LEU LYS LEU VAL TYR GLU ASP GLY SEQRES 8 A 154 ASP PRO CYS PRO THR ASP LEU LYS MET LYS HIS LYS SER SEQRES 9 A 154 TYR PHE SER PHE VAL CYS LYS SER ASP ALA GLY ASP ASP SEQRES 10 A 154 SER GLN PRO VAL PHE LEU SER PHE ASP GLU GLN THR CYS SEQRES 11 A 154 THR SER TYR PHE SER TRP HIS THR SER LEU ALA CYS GLU SEQRES 12 A 154 GLU GLU VAL PRO ARG HIS HIS HIS HIS HIS HIS SHEET 1 A 2 ARG A1894 THR A1896 0 SHEET 2 A 2 LEU A1903 ASP A1905 -1 O PHE A1904 N VAL A1895 SHEET 1 B 4 TYR A1915 THR A1918 0 SHEET 2 B 4 LYS A1924 LEU A1927 -1 O LEU A1927 N TYR A1915 SHEET 3 B 4 ALA A1941 ASP A1947 -1 O THR A1946 N LYS A1924 SHEET 4 B 4 LYS A1950 LYS A1956 -1 O LEU A1952 N ILE A1945 SHEET 1 C 5 THR A1962 GLU A1964 0 SHEET 2 C 5 VAL A1967 GLU A1973 -1 O LYS A1969 N THR A1962 SHEET 3 C 5 LYS A1987 VAL A1993 -1 O PHE A1992 N LEU A1968 SHEET 4 C 5 THR A2015 HIS A2021 1 O PHE A2018 N SER A1991 SHEET 5 C 5 PRO A2004 ASP A2010 -1 N SER A2008 O TYR A2017 SSBOND 1 CYS A 1893 CYS A 1930 1555 1555 2.01 SSBOND 2 CYS A 1937 CYS A 1944 1555 1555 2.03 SSBOND 3 CYS A 1978 CYS A 2014 1555 1555 2.00 SSBOND 4 CYS A 1994 CYS A 2026 1555 1555 2.05 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