HEADER TRANSFERASE 27-OCT-08 2K9Y TITLE EPHA2 DIMERIC STRUCTURE IN THE LIPIDIC BICELLE AT PH 5.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EPHA2_TM, RESIDUES 523-563; COMPND 5 SYNONYM: TYROSINE-PROTEIN KINASE RECEPTOR ECK, EPITHELIAL CELL COMPND 6 KINASE; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: EPHA2, ECK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEMEX1 KEYWDS RECEPTOR TYROSINE KINASE, MEMBRANE PROTEIN, DIMERIC TRANSMEMBRANE KEYWDS 2 DOMAIN, EPHRIN RECEPTOR, ATP-BINDING, GLYCOPROTEIN, KINASE, KEYWDS 3 MEMBRANE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 RECEPTOR, TRANSFERASE, TRANSMEMBRANE, TYROSINE-PROTEIN KINASE EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR M.L.MAYZEL,E.V.BOCHAROV,P.E.VOLYNSKY,A.S.ARSENIEV REVDAT 3 16-MAR-22 2K9Y 1 REMARK REVDAT 2 16-MAR-10 2K9Y 1 JRNL REVDAT 1 11-AUG-09 2K9Y 0 JRNL AUTH E.V.BOCHAROV,M.L.MAYZEL,P.E.VOLYNSKY,K.S.MINEEV,E.N.TKACH, JRNL AUTH 2 Y.S.ERMOLYUK,A.A.SCHULGA,R.G.EFREMOV,A.S.ARSENIEV JRNL TITL LEFT-HANDED DIMER OF EPHA2 TRANSMEMBRANE DOMAIN: HELIX JRNL TITL 2 PACKING DIVERSITY AMONG RECEPTOR TYROSINE KINASES JRNL REF BIOPHYS.J. V. 98 881 2010 JRNL REFN ISSN 0006-3495 JRNL PMID 20197042 JRNL DOI 10.1016/J.BPJ.2009.11.008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, GROMACS 3.3.2 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), ERIK LINDAHL (GROMACS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FIRST 15 MODELS REPRESENTS TORSION REMARK 3 ANGLE DYNAMICS WITH APPLIED NMR RESTRAINS USING CYANA SOFTWARE, REMARK 3 LAST TWO MODELS (16 AND 17) REPRESENTS MD RELAXATION IN THE REMARK 3 EXPLICIT HYDRATED DPPC BILAYER WITH NMR RESTRAINS USING GROMACS REMARK 3 SOFTWARE REMARK 4 REMARK 4 2K9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000100861. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3 MM [U-95% 13C; U-95% 15N] REMARK 210 EPHA2_TM 15N,13C, 96 MM [U-2H] REMARK 210 DHPC, 24 MM [U-2H] DMPC, 1.5 MM REMARK 210 NAN3, 1 MM EDTA, 10 MM PHOSPHATE REMARK 210 BUFFER, 95% H2O/5% D2O; 3 MM [U- REMARK 210 95% 15N] EPHA2_TM 15N, 96 MM [U- REMARK 210 2H] DHPC, 24 MM [U-2H] DMPC, 1.5 REMARK 210 MM NAN3, 1 MM EDTA, 10 MM REMARK 210 PHOSPHATE BUFFER, 90% H2O/10% REMARK 210 D2O; 1.5 MM [U-95% 13C; U-95% REMARK 210 15N] EPHA2_TM 15N,13C, 96 MM [U- REMARK 210 2H] DHPC, 24 MM [U-2H] DMPC, 1.5 REMARK 210 MM NAN3, 1 MM EDTA, 10 MM REMARK 210 PHOSPHATE BUFFER, 1.5 MM EPHA2_ REMARK 210 TM, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 3D 1H-13C NOESY; 3D HNHB; 3D REMARK 210 HNHA; 2D 1H-1H NOESY; 13C F1- REMARK 210 FILTERED/F3-EDITED-NOESY; 15N-T2; REMARK 210 15N-T1; 15N-NOE; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.5.5, 1.8, CYANA 2.1, REMARK 210 VNMR, GROMACS 3.3.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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: DIMERIC 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 16 THR A 526 CA - CB - OG1 ANGL. DEV. = 12.7 DEGREES REMARK 500 16 VAL A 554 CA - CB - CG2 ANGL. DEV. = 9.6 DEGREES REMARK 500 16 ARG A 560 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 16 ARG A 561 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 16 ARG A 562 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 562 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 16 THR B 526 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 16 VAL B 543 CA - CB - CG2 ANGL. DEV. = 14.6 DEGREES REMARK 500 16 ARG B 562 CD - NE - CZ ANGL. DEV. = 10.5 DEGREES REMARK 500 16 ARG B 562 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 VAL A 546 CG1 - CB - CG2 ANGL. DEV. = -10.4 DEGREES REMARK 500 17 ARG A 562 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 17 PHE B 524 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 17 SER B 528 N - CA - CB ANGL. DEV. = -9.2 DEGREES REMARK 500 17 ARG B 560 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 17 ARG B 560 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 17 ARG B 561 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 17 ARG B 562 NE - CZ - NH1 ANGL. DEV. = -4.0 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 ALA A 552 -73.55 -62.49 REMARK 500 1 ARG A 562 -178.59 55.99 REMARK 500 1 THR B 526 81.85 46.19 REMARK 500 1 SER B 532 49.98 -96.45 REMARK 500 1 ALA B 552 -73.36 -62.68 REMARK 500 1 HIS B 559 29.94 -143.14 REMARK 500 1 ARG B 562 -82.76 63.25 REMARK 500 2 THR A 526 -42.61 -155.41 REMARK 500 2 SER A 532 -46.13 -152.36 REMARK 500 2 ALA A 552 -75.79 -60.05 REMARK 500 2 THR B 526 -42.14 -133.69 REMARK 500 2 LEU B 527 -175.11 56.87 REMARK 500 2 ALA B 552 -72.72 -62.86 REMARK 500 2 ARG B 562 -175.34 55.29 REMARK 500 3 THR A 526 25.06 -155.91 REMARK 500 3 SER A 532 -70.32 -159.22 REMARK 500 3 ALA A 552 -74.11 -62.24 REMARK 500 3 ARG A 562 165.96 62.00 REMARK 500 3 THR B 526 84.73 46.61 REMARK 500 3 ALA B 552 -74.52 -62.61 REMARK 500 3 ARG B 562 77.87 54.10 REMARK 500 4 SER A 532 -47.57 -138.35 REMARK 500 4 ALA A 552 -72.12 -62.78 REMARK 500 4 ARG A 562 102.36 63.18 REMARK 500 4 SER B 532 61.44 -102.91 REMARK 500 4 ALA B 552 -76.01 -68.22 REMARK 500 4 ARG B 562 -174.03 57.22 REMARK 500 5 THR A 526 80.79 -151.87 REMARK 500 5 ALA A 552 -75.51 -67.92 REMARK 500 5 ARG A 562 -171.40 52.90 REMARK 500 5 LEU B 527 -179.75 56.72 REMARK 500 5 ALA B 552 -71.96 -60.11 REMARK 500 5 ARG B 561 -50.91 -137.18 REMARK 500 6 THR B 526 72.50 -150.07 REMARK 500 6 ALA B 552 -73.83 -60.34 REMARK 500 6 ARG B 561 -51.48 -134.71 REMARK 500 7 THR A 526 -73.91 -130.63 REMARK 500 7 LEU A 527 82.34 54.22 REMARK 500 7 SER A 532 -40.19 -163.13 REMARK 500 7 THR B 526 25.96 -153.07 REMARK 500 7 GLU B 530 117.74 -162.74 REMARK 500 7 ALA B 552 -72.38 -62.21 REMARK 500 7 ARG B 562 77.05 63.36 REMARK 500 8 GLU A 530 113.97 -165.57 REMARK 500 8 ALA A 552 -71.71 -64.29 REMARK 500 8 SER B 532 28.48 -148.52 REMARK 500 8 ALA B 552 -72.99 -63.11 REMARK 500 8 ARG B 560 100.89 -49.78 REMARK 500 8 ARG B 561 -62.29 72.96 REMARK 500 8 ARG B 562 173.45 175.36 REMARK 500 REMARK 500 THIS ENTRY HAS 112 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 16 ARG A 560 0.09 SIDE CHAIN REMARK 500 17 PHE A 557 0.08 SIDE CHAIN REMARK 500 17 ARG B 561 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 17 ASN A 534 -10.51 REMARK 500 17 GLU B 530 -10.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K1K RELATED DB: PDB REMARK 900 EPHA1 PH 4.3 REMARK 900 RELATED ID: 2K1L RELATED DB: PDB REMARK 900 EPHA1 PH 6.3 REMARK 900 RELATED ID: 16005 RELATED DB: BMRB DBREF 2K9Y A 523 563 UNP P29317 EPHA2_HUMAN 523 563 DBREF 2K9Y B 523 563 UNP P29317 EPHA2_HUMAN 523 563 SEQRES 1 A 41 GLU PHE GLN THR LEU SER PRO GLU GLY SER GLY ASN LEU SEQRES 2 A 41 ALA VAL ILE GLY GLY VAL ALA VAL GLY VAL VAL LEU LEU SEQRES 3 A 41 LEU VAL LEU ALA GLY VAL GLY PHE PHE ILE HIS ARG ARG SEQRES 4 A 41 ARG LYS SEQRES 1 B 41 GLU PHE GLN THR LEU SER PRO GLU GLY SER GLY ASN LEU SEQRES 2 B 41 ALA VAL ILE GLY GLY VAL ALA VAL GLY VAL VAL LEU LEU SEQRES 3 B 41 LEU VAL LEU ALA GLY VAL GLY PHE PHE ILE HIS ARG ARG SEQRES 4 B 41 ARG LYS HELIX 1 1 LEU A 535 PHE A 557 1 23 HELIX 2 2 LEU B 535 PHE B 557 1 23 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