HEADER ANTITUMOR PROTEIN 27-MAR-13 2M68 TITLE NMR SOLUTION STRUCTURE ENSEMBLE OF 3-4D MUTANT DOMAIN 11 IGF2R IN TITLE 2 COMPLEX WITH IGF2 (DOMAIN 11 STRUCTURE ONLY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR VARIANT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 11; 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: DOMAIN 11 IGF2R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET26A KEYWDS ANTITUMOR, DIRECTED EVOLUTION, HIGH AFFINITY, ANTITUMOR PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.STRICKLAND,C.WILLIAMS,E.RICHARDS,L.MINNALL,M.P.CRUMP,S.FRAGO, AUTHOR 2 J.HUGHES,L.GARNER,H.HOPPE,D.REZGUI,O.J.ZACCHEO,S.N.PRINCE, AUTHOR 3 A.B.HASSAN,S.WHITTAKER REVDAT 5 14-JUN-23 2M68 1 REMARK SEQADV REVDAT 4 01-JUN-16 2M68 1 JRNL REVDAT 3 18-MAY-16 2M68 1 JRNL REVDAT 2 04-MAY-16 2M68 1 JRNL REVDAT 1 15-OCT-14 2M68 0 JRNL AUTH S.FRAGO,R.D.NICHOLLS,M.STRICKLAND,J.HUGHES,C.WILLIAMS, JRNL AUTH 2 L.GARNER,M.SURAKHY,R.MACLEAN,D.REZGUI,S.N.PRINCE, JRNL AUTH 3 O.J.ZACCHEO,D.EBNER,S.SANEGRE,S.YU,F.M.BUFFA,M.P.CRUMP, JRNL AUTH 4 A.B.HASSAN JRNL TITL FUNCTIONAL EVOLUTION OF IGF2:IGF2R DOMAIN 11 BINDING JRNL TITL 2 GENERATES NOVEL STRUCTURAL INTERACTIONS AND A SPECIFIC IGF2 JRNL TITL 3 ANTAGONIST. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 E2766 2016 JRNL REFN ISSN 0027-8424 JRNL PMID 27140600 JRNL DOI 10.1073/PNAS.1513023113 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2, ARIA 2.2, CING ICING REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA), DORELEIJERS (CING) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000103260. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.15; 298.15 REMARK 210 PH : 4; 4 REMARK 210 IONIC STRENGTH : 0.005; 0.005 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : STRUCTURAL STUDIES: LYOPHILISED REMARK 210 IGF2 WAS ADDED TO SOLUTION STATE REMARK 210 DOMAIN 11 AT PH 4 IN A 1:1 REMARK 210 RATIO.; DYNAMICS STUDIES: REMARK 210 LYOPHILISED IGF2 WAS ADDED TO REMARK 210 SOLUTION STATE DOMAIN 11 AT PH 4 REMARK 210 IN A 1:1 RATIO. 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 HN(CO)CA; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; REMARK 210 HETERONUCLEAR NOE RATIO; T1 REMARK 210 EXPERIMENTS; T2 EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.2, NMRPIPE, NMRDRAW, REMARK 210 RELAX 1.3.9, SPARKY 2.6, VNMRJ REMARK 210 0.4, CCPN_ANALYSIS 2.1, TALOS REMARK 210 TALOS+ REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY 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 LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 HIS A1513 -22.01 -161.47 REMARK 500 1 ASP A1514 -69.69 -90.23 REMARK 500 1 SER A1533 35.00 -76.76 REMARK 500 1 CYS A1553 92.30 65.54 REMARK 500 1 THR A1570 -83.56 -83.99 REMARK 500 1 ARG A1571 32.12 -168.28 REMARK 500 1 ASP A1594 71.24 59.35 REMARK 500 1 PRO A1597 47.75 -79.69 REMARK 500 1 LEU A1604 -80.14 -71.08 REMARK 500 1 TYR A1606 49.32 -69.74 REMARK 500 1 ARG A1615 100.98 -163.64 REMARK 500 1 ALA A1618 42.17 -93.73 REMARK 500 2 SER A1533 33.30 -80.76 REMARK 500 2 CYS A1553 88.57 58.68 REMARK 500 2 THR A1570 -83.83 -86.19 REMARK 500 2 ARG A1571 34.80 -169.43 REMARK 500 2 PRO A1597 48.32 -79.62 REMARK 500 2 LEU A1604 -102.15 -89.53 REMARK 500 2 TYR A1606 47.47 -86.67 REMARK 500 2 ALA A1618 42.29 -82.81 REMARK 500 3 CYS A1516 71.90 -112.53 REMARK 500 3 SER A1533 32.75 -81.62 REMARK 500 3 CYS A1553 89.15 58.70 REMARK 500 3 THR A1570 -83.59 -88.86 REMARK 500 3 ARG A1571 32.71 -169.88 REMARK 500 3 LYS A1579 36.36 -93.35 REMARK 500 3 ASP A1594 62.75 62.07 REMARK 500 3 PRO A1597 47.54 -82.73 REMARK 500 3 LEU A1604 -84.72 -82.56 REMARK 500 3 TYR A1606 48.44 -68.96 REMARK 500 3 GLU A1617 33.06 -96.28 REMARK 500 3 ALA A1618 42.05 -77.57 REMARK 500 3 CYS A1634 65.70 65.23 REMARK 500 4 LYS A1509 24.34 -150.03 REMARK 500 4 ASP A1514 -63.97 -144.53 REMARK 500 4 CYS A1516 64.75 -100.87 REMARK 500 4 SER A1533 34.18 -77.99 REMARK 500 4 CYS A1553 89.12 59.27 REMARK 500 4 THR A1570 -84.63 -80.75 REMARK 500 4 ARG A1571 31.64 -171.48 REMARK 500 4 PRO A1597 48.04 -79.85 REMARK 500 4 PRO A1599 96.08 -57.08 REMARK 500 4 LEU A1604 -101.09 -80.06 REMARK 500 4 TYR A1606 47.24 -80.50 REMARK 500 4 ALA A1618 41.40 -79.50 REMARK 500 5 SER A1533 34.16 -73.63 REMARK 500 5 CYS A1553 95.81 60.90 REMARK 500 5 GLU A1555 106.92 -47.47 REMARK 500 5 THR A1570 -84.02 -83.17 REMARK 500 5 ARG A1571 32.25 -170.62 REMARK 500 REMARK 500 THIS ENTRY HAS 225 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 10 ARG A1571 0.09 SIDE CHAIN REMARK 500 10 ARG A1580 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CNJ RELATED DB: PDB REMARK 900 RELATED ID: 2L2A RELATED DB: PDB REMARK 900 RELATED ID: 2L29 RELATED DB: PDB REMARK 900 RELATED ID: 19117 RELATED DB: BMRB REMARK 900 RELATED ID: 2M6T RELATED DB: PDB DBREF 2M68 A 1508 1649 UNP Q59EZ3 Q59EZ3_HUMAN 1431 1572 SEQADV 2M68 ALA A 1543 UNP Q59EZ3 SER 1466 ENGINEERED MUTATION SEQADV 2M68 LYS A 1544 UNP Q59EZ3 GLU 1467 ENGINEERED MUTATION SEQADV 2M68 GLY A 1545 UNP Q59EZ3 LYS 1468 ENGINEERED MUTATION SEQADV 2M68 TRP A 1546 UNP Q59EZ3 GLY 1469 ENGINEERED MUTATION SEQADV 2M68 GLY A 1547 UNP Q59EZ3 LEU 1470 ENGINEERED MUTATION SEQADV 2M68 LEU A 1648 UNP Q59EZ3 GLN 1571 CLONING ARTIFACT 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 ALA LYS GLY TRP SEQRES 4 A 142 GLY 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 LEU ALA HELIX 1 1 SER A 1530 SER A 1533 5 4 HELIX 2 2 PRO A 1643 CYS A 1646 5 4 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 A1543 0 SHEET 2 B 4 TRP A1546 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 ARG A1582 VAL A1584 0 SHEET 2 C 5 VAL A1587 TYR A1592 -1 O GLN A1589 N ARG A1582 SHEET 3 C 5 SER A1608 CYS A1614 -1 O PHE A1612 N LEU A1588 SHEET 4 C 5 THR A1635 THR A1642 1 O PHE A1638 N SER A1611 SHEET 5 C 5 PRO A1624 ASP A1630 -1 N ILE A1627 O PHE A1637 SSBOND 1 CYS A 1516 CYS A 1553 1555 1555 2.01 SSBOND 2 CYS A 1559 CYS A 1566 1555 1555 2.03 SSBOND 3 CYS A 1598 CYS A 1634 1555 1555 2.03 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20