HEADER TRANSPORT PROTEIN 13-AUG-10 2L2A TITLE MUTATED DOMAIN 11 OF THE CYTOPLASMIC REGION OF THE CATION-INDEPENDENT TITLE 2 MANNOSE-6-PHOSPHATE RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR VARIANT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 11, RESIDUES 1431-1570; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; 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 MANNOSE 6 PHOSPHATE RECEPTOR, PROTEIN EVOLUTION, INSULIN-LIKE GROWTH KEYWDS 2 FACTOR 2, GENOMIC IMPRINTING, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.WILLIAMS,H.HOPPE,D.REZGUI,M.STRICKLAND,S.FRAGO,R.Z.ELLIS,P.WATTANA- AUTHOR 2 AMORN,S.N.PRINCE,O.J.ZACCHEO,B.FORBES,E.Y.JONES,M.P.CRUMP,A.B.HASSAN REVDAT 2 12-DEC-12 2L2A 1 JRNL REVDAT 1 15-FEB-12 2L2A 0 JRNL AUTH C.WILLIAMS,H.J.HOPPE,D.REZGUI,M.STRICKLAND,B.E.FORBES, JRNL AUTH 2 F.GRUTZNER,S.FRAGO,R.Z.ELLIS,P.WATTANA-AMORN,S.N.PRINCE, JRNL AUTH 3 O.J.ZACCHEO,C.M.NOLAN,A.J.MUNGALL,E.Y.JONES,M.P.CRUMP, JRNL AUTH 4 A.B.HASSAN JRNL TITL AN EXON SPLICE ENHANCER PRIMES IGF2:IGF2R BINDING SITE JRNL TITL 2 STRUCTURE AND FUNCTION EVOLUTION. JRNL REF SCIENCE V. 338 1209 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 23197533 JRNL DOI 10.1126/SCIENCE.1228633 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, ICING R765, ARIA 2.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 , VUISTER, DORELEIJERS, SOUSA DA SILVA (ICING), REMARK 3 LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARIA2.2 PROTOCOL. COOL_1 AND COOL_2 REMARK 3 STEPS INCREASED TO 40K AND COOL_2, ARIA2.2 WATER REFINEMENT REMARK 3 MODIFIED WITH RECOORD WATER REFINEMENT PARAMETERS REMARK 4 REMARK 4 2L2A 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 RCSB ID CODE IS RCSB101866. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 4.2 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5% D2O, 10 MM [U-99% 2H] SODIUM REMARK 210 ACETATE, 0.5-1 MM [U-98% 13C; U- REMARK 210 98% 15N] IGF2R, 100 UM EDTA, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D HCCH-TOCSY; 3D REMARK 210 H(CCO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ, ANALYSIS 2.13, CNS, REMARK 210 NMRPIPE, TALOS, ARIA 2.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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: 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 2 TYR A1592 CE1 TYR A1592 CZ -0.109 REMARK 500 2 TYR A1592 CZ TYR A1592 CE2 0.095 REMARK 500 3 TYR A1549 CE1 TYR A1549 CZ -0.092 REMARK 500 3 TYR A1549 CZ TYR A1549 CE2 0.095 REMARK 500 3 TYR A1592 CE1 TYR A1592 CZ -0.085 REMARK 500 5 TYR A1549 CE1 TYR A1549 CZ 0.105 REMARK 500 5 TYR A1549 CZ TYR A1549 CE2 -0.117 REMARK 500 12 TYR A1606 CE1 TYR A1606 CZ -0.093 REMARK 500 12 TYR A1606 CZ TYR A1606 CE2 0.087 REMARK 500 15 TYR A1583 CE1 TYR A1583 CZ -0.092 REMARK 500 15 TYR A1583 CZ TYR A1583 CE2 0.082 REMARK 500 16 TYR A1606 CE1 TYR A1606 CZ 0.116 REMARK 500 16 TYR A1606 CZ TYR A1606 CE2 -0.113 REMARK 500 18 TYR A1592 CE1 TYR A1592 CZ 0.086 REMARK 500 18 TYR A1592 CZ TYR A1592 CE2 -0.102 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 A1543 -153.60 -40.85 REMARK 500 1 PRO A1560 109.21 -52.18 REMARK 500 1 SER A1600 -74.24 -79.61 REMARK 500 1 LYS A1601 -87.11 -98.13 REMARK 500 2 ASP A1514 -72.30 -45.53 REMARK 500 2 ASP A1515 -94.19 45.73 REMARK 500 2 SER A1543 -151.14 -47.47 REMARK 500 2 LYS A1544 -26.42 -39.69 REMARK 500 2 LYS A1579 89.99 -163.87 REMARK 500 2 GLN A1586 -1.63 64.63 REMARK 500 2 LYS A1601 81.58 68.49 REMARK 500 3 LYS A1509 -29.87 79.37 REMARK 500 3 ASN A1511 -28.39 -141.09 REMARK 500 3 SER A1543 -151.00 -46.62 REMARK 500 3 GLU A1557 39.57 -91.87 REMARK 500 3 ALA A1577 102.33 -56.22 REMARK 500 3 LYS A1601 -97.93 66.02 REMARK 500 3 GLU A1617 40.48 -94.01 REMARK 500 3 ASN A1622 53.14 -91.46 REMARK 500 4 GLU A1512 1.11 -64.52 REMARK 500 4 ASP A1514 -42.16 -140.37 REMARK 500 4 ASP A1515 -168.41 -125.58 REMARK 500 4 SER A1543 -152.20 -37.58 REMARK 500 4 GLU A1557 -158.99 54.82 REMARK 500 4 ASN A1558 -8.95 69.93 REMARK 500 4 PRO A1560 137.30 -37.80 REMARK 500 4 ALA A1577 88.67 -67.10 REMARK 500 4 GLN A1586 -7.10 68.56 REMARK 500 4 PRO A1616 64.45 -69.75 REMARK 500 4 ALA A1618 -43.14 70.34 REMARK 500 4 THR A1621 -52.45 -132.00 REMARK 500 4 ASN A1622 -68.92 -138.03 REMARK 500 5 SER A1543 -150.79 -45.67 REMARK 500 5 LYS A1544 -37.22 -39.55 REMARK 500 5 PRO A1560 112.59 -24.24 REMARK 500 5 ALA A1577 79.16 -68.92 REMARK 500 5 ASP A1585 75.57 54.72 REMARK 500 5 GLN A1586 -14.67 68.16 REMARK 500 5 LYS A1601 116.64 -162.33 REMARK 500 5 GLU A1617 40.77 -81.01 REMARK 500 6 ASP A1514 -79.73 -49.47 REMARK 500 6 ASP A1515 -88.31 62.16 REMARK 500 6 SER A1543 -150.46 -49.57 REMARK 500 6 LYS A1544 -28.12 -39.81 REMARK 500 6 PRO A1560 122.16 -29.88 REMARK 500 6 GLN A1586 -14.43 73.78 REMARK 500 7 LYS A1509 117.68 69.29 REMARK 500 7 SER A1543 -152.15 -46.50 REMARK 500 7 ASN A1558 -43.94 -146.82 REMARK 500 7 PRO A1560 113.11 -32.95 REMARK 500 REMARK 500 THIS ENTRY HAS 169 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 PHE A1567 0.06 SIDE CHAIN REMARK 500 2 ARG A1580 0.09 SIDE CHAIN REMARK 500 3 TYR A1549 0.06 SIDE CHAIN REMARK 500 3 TYR A1606 0.07 SIDE CHAIN REMARK 500 4 ARG A1615 0.08 SIDE CHAIN REMARK 500 6 TYR A1592 0.09 SIDE CHAIN REMARK 500 7 TYR A1549 0.07 SIDE CHAIN REMARK 500 7 TYR A1583 0.05 SIDE CHAIN REMARK 500 8 TYR A1606 0.07 SIDE CHAIN REMARK 500 12 PHE A1567 0.07 SIDE CHAIN REMARK 500 12 TYR A1592 0.07 SIDE CHAIN REMARK 500 12 TYR A1606 0.05 SIDE CHAIN REMARK 500 14 TYR A1542 0.07 SIDE CHAIN REMARK 500 14 PHE A1612 0.07 SIDE CHAIN REMARK 500 15 TYR A1549 0.05 SIDE CHAIN REMARK 500 16 TYR A1592 0.06 SIDE CHAIN REMARK 500 16 TYR A1606 0.05 SIDE CHAIN REMARK 500 18 TYR A1592 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 13 GLU A1557 24.6 L L OUTSIDE RANGE 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 REMARK 900 (IGF-II) WITH IGF2R DOMAIN 11 REMARK 900 RELATED ID: 1GP0 RELATED DB: PDB REMARK 900 HUMAN IGF2R DOMAIN 11 REMARK 900 RELATED ID: 2L21 RELATED DB: PDB REMARK 900 CHICKEN IGF2R DOMAIN 11 REMARK 900 RELATED ID: 2L29 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF E4 MUTANT HUMAN IGF2R DOMAIN 11 BOUND REMARK 900 TO IGF-II REMARK 900 RELATED ID: 17128 RELATED DB: BMRB DBREF 2L2A A 1508 1647 UNP Q59EZ3 Q59EZ3_HUMAN 1431 1570 SEQADV 2L2A LYS A 1544 UNP Q59EZ3 GLU 1467 ENGINEERED MUTATION SEQADV 2L2A SER A 1545 UNP Q59EZ3 LYS 1468 ENGINEERED MUTATION SEQADV 2L2A VAL A 1547 UNP Q59EZ3 LEU 1470 ENGINEERED MUTATION SEQADV 2L2A PRO A 1648 UNP Q59EZ3 EXPRESSION TAG SEQADV 2L2A GLU A 1649 UNP Q59EZ3 EXPRESSION TAG SEQRES 1 A 142 MET LYS SER ASN GLU HIS ASP ASP CYS GLN VAL THR ASN SEQRES 2 A 142 PRO SER THR GLY HIS LEU PHE ASP LEU SER SER LEU SER SEQRES 3 A 142 GLY ARG ALA GLY PHE THR ALA ALA TYR SER LYS SER GLY SEQRES 4 A 142 VAL VAL TYR MET SER ILE CYS GLY GLU ASN GLU ASN CYS SEQRES 5 A 142 PRO PRO GLY VAL GLY ALA CYS PHE GLY GLN THR ARG ILE SEQRES 6 A 142 SER VAL GLY LYS ALA ASN LYS ARG LEU ARG TYR VAL ASP SEQRES 7 A 142 GLN VAL LEU GLN LEU VAL TYR LYS ASP GLY SER PRO CYS SEQRES 8 A 142 PRO SER LYS SER GLY LEU SER TYR LYS SER VAL ILE SER SEQRES 9 A 142 PHE VAL CYS ARG PRO GLU ALA GLY PRO THR ASN ARG PRO SEQRES 10 A 142 MET LEU ILE SER LEU ASP LYS GLN THR CYS THR LEU PHE SEQRES 11 A 142 PHE SER TRP HIS THR PRO LEU ALA CYS GLU PRO GLU SHEET 1 A 2 GLN A1517 THR A1519 0 SHEET 2 A 2 LEU A1526 ASP A1528 -1 O PHE A1527 N VAL A1518 SHEET 1 B 4 PHE A1538 ALA A1540 0 SHEET 2 B 4 VAL A1548 MET A1550 -1 O MET A1550 N PHE A1538 SHEET 3 B 4 ALA A1565 PHE A1567 -1 O CYS A1566 N TYR A1549 SHEET 4 B 4 ILE A1572 SER A1573 -1 O ILE A1572 N PHE A1567 SHEET 1 C 5 LEU A1581 VAL A1584 0 SHEET 2 C 5 VAL A1587 TYR A1592 -1 O GLN A1589 N ARG A1582 SHEET 3 C 5 LYS A1607 VAL A1613 -1 O SER A1608 N TYR A1592 SHEET 4 C 5 THR A1635 HIS A1641 1 O PHE A1638 N VAL A1609 SHEET 5 C 5 MET A1625 ASP A1630 -1 N ASP A1630 O THR A1635 SHEET 1 D 2 PRO A1597 CYS A1598 0 SHEET 2 D 2 LEU A1604 SER A1605 -1 O LEU A1604 N CYS A1598 SSBOND 1 CYS A 1516 CYS A 1553 1555 1555 2.02 SSBOND 2 CYS A 1559 CYS A 1566 1555 1555 2.03 SSBOND 3 CYS A 1598 CYS A 1634 1555 1555 2.01 SSBOND 4 CYS A 1614 CYS A 1646 1555 1555 2.03 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