HEADER SIGNALING PROTEIN 11-DEC-12 2M20 TITLE EGFR TRANSMEMBRANE - JUXTAMEMBRANE (TM-JM) SEGMENT IN BICELLES: MD TITLE 2 GUIDED NMR REFINED STRUCTURE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EGFR TRANSMEMBRANE-JUXTAMEMBRANE SEGMENT, UNP RESIDUES 642- COMPND 5 697; COMPND 6 SYNONYM: PROTO-ONCOGENE C-ERBB-1, RECEPTOR TYROSINE-PROTEIN KINASE COMPND 7 ERBB-1; COMPND 8 ENGINEERED: YES; COMPND 9 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: EGFR, ERBB, ERBB1, HER1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMMHB KEYWDS TRANSMEMBRANE, CELL SIGNALING, JUXTAMEMBRANE, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.F.ENDRES,R.DAS,A.SMITH,A.ARKHIPOV,E.KOVACS,Y.HUANG,J.G.PELTON, AUTHOR 2 Y.SHAN,D.E.SHAW,D.E.WEMMER,J.T.GROVES,J.KURIYAN REVDAT 1 20-FEB-13 2M20 0 JRNL AUTH N.F.ENDRES,R.DAS,A.W.SMITH,A.ARKHIPOV,E.KOVACS,Y.HUANG, JRNL AUTH 2 J.G.PELTON,Y.SHAN,D.E.SHAW,D.E.WEMMER,J.T.GROVES,J.KURIYAN JRNL TITL CONFORMATIONAL COUPLING ACROSS THE PLASMA MEMBRANE IN JRNL TITL 2 ACTIVATION OF THE EGF RECEPTOR. JRNL REF CELL(CAMBRIDGE,MASS.) V. 152 543 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23374349 JRNL DOI 10.1016/J.CELL.2012.12.032 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.F.ENDRES,R.DAS,A.SMITH,A.ARKHIPOV,E.KOVACS,Y.HUANG, REMARK 1 AUTH 2 J.G.PELTON,Y.SHAN,D.E.SHAW,D.E.WEMMER,J.T.GROVES,J.KURIYAN REMARK 1 TITL ARCHITECTURE AND MEMBRANE INTERACTIONS OF THE EGF RECEPTOR. REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS V1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. THE TM-JM DIMER STRUCTURE WAS REMARK 3 CALCULATED WITH 38 INTERCHAIN NOES (19 INTERCHAIN NOE RESTRAINT REMARK 3 PER MONOMER). THERE ARE TOO FEW INTERCHAIN NOES TO DETERMINE THE REMARK 3 CONFIGURATION OF THE TM-JM DIMER UNAMBIGUOUSLY. THEREFORE, WE REMARK 3 USED OBSERVATIONS FROM MOLECULAR DYNAMICS SIMULATIONS OF THE TM- REMARK 3 JM SEGMENT IN DMPC LIPID BILAYERS (SEE ARKHIPOV ET AL. 2013, CELL REMARK 3 IN PRESS; COMPANION PAPER TO THE PAPER DESCRIBING THE ANALYSIS OF REMARK 3 THE TM-JM STRUCTURE IN AN EXPERIMENTAL CONTEXT), AND SELECTED A REMARK 3 INITIAL STRUCTURE OF THE TM-JM DIMER WITH A DIMERIC CONFORMATION REMARK 3 OF RIGHT HANDED CROSSING ANGLES THAT WAS STABLE DURING THE MD REMARK 3 SIMULATIONS. IT WAS THEN REFINED USING NMR RESTRAINTS. 2. THE REMARK 3 SECONDARY STRUCTURE ANALYSIS SUGGESTED THAT THE JUXTAMEMBRANE -A REMARK 3 SEGMENT HAS A 30% PROBABILITY OF HELIX FORMATION. IN ORDER TO REMARK 3 MODEL THE JUXTAMEMBRANE DIMER WE ASSUMED THAT THE JUXTAMEMBRANE-A REMARK 3 SEGMENT ONLY FORMS A DIMER WHEN BOTH JUXTAMEMBRANE SEGMENTS ARE REMARK 3 HELICAL. REMARK 4 REMARK 4 2M20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-12. REMARK 100 THE RCSB ID CODE IS RCSB103108. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 312 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.300 MM [U-100% 13C; U-100% REMARK 210 15N; U-80% 2H] EGFR TM-JM, 50 MM REMARK 210 MES, 5 MM TCEP, 1 MM EDTA, 0.05 REMARK 210 MM AMESF, 10 % [U-2H] D2O, 0.02 % REMARK 210 SODIUM AZIDE, 9.4 MM [U-99% 2H] REMARK 210 DMPC (D54), 37.98 MM [U-99% 2H] REMARK 210 DHPC (D22), 90% H2O/10% D2O; REMARK 210 0.300 MM [U-100% 13C; U-100% 15N] REMARK 210 EGFR TM-JM, 50 MM MES, 5 MM TCEP, REMARK 210 1 MM EDTA, 0.05 MM AMESF, 10 % [U REMARK 210 -2H] D2O, 0.02 % SODIUM AZIDE, REMARK 210 9.4 MM [U-99% 2H] DMPC (D54), REMARK 210 37.98 MM [U-99% 2H] DHPC (D22), REMARK 210 90% H2O/10% D2O; 0.300 MM EGFR TM REMARK 210 -JM, 50 MM MES, 5 MM TCEP, 1 MM REMARK 210 EDTA, 0.05 MM AMESF, 10 % [U-2H] REMARK 210 D2O, 0.02 % SODIUM AZIDE, 18.8 MM REMARK 210 [U-99% 2H] DMPC (D54), 77.86 MM REMARK 210 [U-99% 2H] DHPC (D22), 0.300 MM REMARK 210 EGFR TM-JM, 90% H2O/10% 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 HN(CO)CA; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 3D 15N-13C F1 FILTERED/F3 REMARK 210 EDITED NOESY-HSQC; 2D 1H-15N TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE-II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN V1.3, NMRDRAW V3.0, REMARK 210 NMRPIPE V3.0, SPARKY V3.114, REMARK 210 TALOS+, CNS V1.3, PROCHECKNMR, REMARK 210 PSVS, MOLMOL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 1476 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12144 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.6 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 O LEU B 98 HB2 LEU B 102 1.54 REMARK 500 O LEU A 38 HB2 LEU A 42 1.54 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 LEU A 47 27.38 -146.50 REMARK 500 1 LEU B 107 27.34 -146.43 REMARK 500 2 LYS A 35 -43.85 -132.05 REMARK 500 2 LYS B 95 -43.90 -132.01 REMARK 500 3 LEU A 47 27.17 -150.13 REMARK 500 3 LEU B 107 27.22 -150.06 REMARK 500 5 ARG A 36 34.89 -88.55 REMARK 500 5 ARG B 96 35.05 -88.58 REMARK 500 6 TRP A 59 121.89 62.23 REMARK 500 6 TRP B 119 121.79 62.35 REMARK 500 7 LYS A 35 -45.27 -130.78 REMARK 500 7 LYS B 95 -45.10 -130.73 REMARK 500 10 GLU A 56 127.66 63.37 REMARK 500 10 GLU B 116 127.57 63.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18888 RELATED DB: BMRB DBREF 2M20 A 1 56 UNP P00533 EGFR_HUMAN 642 697 DBREF 2M20 B 61 116 UNP P00533 EGFR_HUMAN 642 697 SEQADV 2M20 LEU A 9 UNP P00533 MET 650 ENGINEERED MUTATION SEQADV 2M20 ILE A 27 UNP P00533 MET 668 ENGINEERED MUTATION SEQADV 2M20 LYS A 57 UNP P00533 EXPRESSION TAG SEQADV 2M20 LEU A 58 UNP P00533 EXPRESSION TAG SEQADV 2M20 TRP A 59 UNP P00533 EXPRESSION TAG SEQADV 2M20 SER A 60 UNP P00533 EXPRESSION TAG SEQADV 2M20 LEU B 69 UNP P00533 MET 650 ENGINEERED MUTATION SEQADV 2M20 ILE B 87 UNP P00533 MET 668 ENGINEERED MUTATION SEQADV 2M20 LYS B 117 UNP P00533 EXPRESSION TAG SEQADV 2M20 LEU B 118 UNP P00533 EXPRESSION TAG SEQADV 2M20 TRP B 119 UNP P00533 EXPRESSION TAG SEQADV 2M20 SER B 120 UNP P00533 EXPRESSION TAG SEQRES 1 A 60 LYS ILE PRO SER ILE ALA THR GLY LEU VAL GLY ALA LEU SEQRES 2 A 60 LEU LEU LEU LEU VAL VAL ALA LEU GLY ILE GLY LEU PHE SEQRES 3 A 60 ILE ARG ARG ARG HIS ILE VAL ARG LYS ARG THR LEU ARG SEQRES 4 A 60 ARG LEU LEU GLN GLU ARG GLU LEU VAL GLU PRO LEU THR SEQRES 5 A 60 PRO SER GLY GLU LYS LEU TRP SER SEQRES 1 B 60 LYS ILE PRO SER ILE ALA THR GLY LEU VAL GLY ALA LEU SEQRES 2 B 60 LEU LEU LEU LEU VAL VAL ALA LEU GLY ILE GLY LEU PHE SEQRES 3 B 60 ILE ARG ARG ARG HIS ILE VAL ARG LYS ARG THR LEU ARG SEQRES 4 B 60 ARG LEU LEU GLN GLU ARG GLU LEU VAL GLU PRO LEU THR SEQRES 5 B 60 PRO SER GLY GLU LYS LEU TRP SER HELIX 1 1 PRO A 3 ARG A 29 1 27 HELIX 2 2 ARG A 29 ARG A 34 1 6 HELIX 3 3 GLN A 43 VAL A 48 1 6 HELIX 4 4 PRO B 63 ARG B 89 1 27 HELIX 5 5 ARG B 89 ARG B 94 1 6 HELIX 6 6 GLN B 103 VAL B 108 1 6 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