10 20 30 40 50 60 70 80 1XR0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN/GROWTH FACTOR RECEPTOR13-OCT-04 1XR0
TITLE STRUCTURAL BASIS OF SNT PTB DOMAIN INTERACTIONS WITH TITLE 2 DISTINCT NEUROTROPHIC RECEPTORS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 409-430 FROM THE COMPND 5 JUXTAMEMBRANE REGION OF HFGFR1; COMPND 6 SYNONYM: FGFR-1, BFGF-R, FMS-LIKE TYROSINE KINASE-2, C-FGR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: FGFR SIGNALLING ADAPTOR SNT-1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: PTB DOMAIN AT THE N TERMINUS; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SOURCE 4 SEQUENCE IS TAKEN FROM HOMO SAPIENS (HUMAN).; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS FGFR, SNT, PHOSPHOTYROSINE BINDING DOMAIN, PTB, TRK, NPXPY KEYWDS 2 MOTIF,, SIGNALING PROTEIN/GROWTH FACTOR RECEPTOR COMPLEX
EXPDTA SOLUTION NMR
AUTHOR C.DHALLUIN,K.S.YAN,O.PLOTNIKOVA,K.W.LEE,L.ZENG,M.KUTI, AUTHOR 2 S.MUJTABA,M.P.GOLDFARB,M.-M.ZHOU
REVDAT 2 24-FEB-09 1XR0 1 VERSN REVDAT 1 02-NOV-04 1XR0 0
JRNL AUTH C.DHALLUIN,K.S.YAN,O.PLOTNIKOVA,K.W.LEE,L.ZENG, JRNL AUTH 2 M.KUTI,S.MUJTABA,M.P.GOLDFARB,M.-M.ZHOU JRNL TITL STRUCTURAL BASIS OF SNT PTB DOMAIN INTERACTIONS JRNL TITL 2 WITH DISTINCT NEUROTROPHIC RECEPTORS JRNL REF MOL.CELL V. 6 921 2000 JRNL REFN ISSN 1097-2765 JRNL PMID 11090629 JRNL DOI 10.1016/S1097-2765(05)00087-0
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.1 REMARK 3 AUTHORS : M. NILGES AND S. O'DONOGHUE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1XR0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030666.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 15 MM DTT-D10, AND 0.5 MM REMARK 210 EDTA00 MM PHOSPHATE BUFFER, REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : SNT-1 PTB DOMAIN/HFGFR1 REMARK 210 PEPTIDE COMPLEX (1:1) OF ~0.5 REMARK 210 MM IN 100 MM PHOSPHATE BUFFER REMARK 210 OF PH 6.5, 5 MM DTT-D10, AND REMARK 210 0.5 MM EDTA IN H2O/2H2O (9/1) REMARK 210 OR 2H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA, 3D_13C-SEPARATED_NOESY, REMARK 210 3D_15N-SEPARATED_NOESY, 2D REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : STRUCTURES OF THE SNT-1 PTB REMARK 210 DOMAIN IN COMPLEX WITH THE REMARK 210 HFGFR1 PEPTIDE WERE CALCULATED REMARK 210 WITH A DISTANCE GEOMETRY AND REMARK 210 SIMULATED ANNEALING PROTOCOL REMARK 210 BY USING THE X-PLOR PROGRAM REMARK 210 ([4]). NOE DISTANCE AND REMARK 210 DIHEDRAL ANGLE RESTRAINTS WERE REMARK 210 TREATED WITH A SQUARE-WELL REMARK 210 POTENTIAL OF 50 KCAL MOL?1 ?2. REMARK 210 A TOTAL OF 2448 MANUALLY REMARK 210 ASSIGNED NOE-DERIVED DISTANCE REMARK 210 RESTRAINTS WERE OBTAINED FROM REMARK 210 THE 15N- OR 13C-EDITED NOESY REMARK 210 DATA. INCLUDED IN THIS FIGURE REMARK 210 ARE 251 INTRAPEPTIDE AND 258 REMARK 210 INTERMOLECULAR DISTANCE REMARK 210 RESTRAINTS. ADDITIONALLY, 255 REMARK 210 UNAMBIGUOUS AND 52 AMBIGUOUS REMARK 210 DISTANCE RESTRAINTS WERE REMARK 210 IDENTIFIED FROM THE NOE DATA REMARK 210 BY USING ARIA. THE FINAL REMARK 210 STRUCTURE CALCULATIONS REMARK 210 EMPLOYED A TOTAL OF 2755 NOE REMARK 210 RESTRAINTS OBTAINED FROM THE REMARK 210 MANUAL AND THE ARIA-ASSISTED REMARK 210 ASSIGNMENTS, 2703 OF WHICH REMARK 210 WERE UNAMBIGUOUSLY ASSIGNED REMARK 210 NOE-DERIVED DISTANCE REMARK 210 RESTRAINTS THAT COMPRISE 1072 REMARK 210 INTRARESIDUE, 466 SEQUENTIAL, REMARK 210 216 MEDIUM-RANGE, AND 949 LONG REMARK 210 -RANGE NOES. IN ADDITION, 70 REMARK 210 HYDROGEN-BOND DISTANCE REMARK 210 RESTRAINTS FOR 35 HYDROGEN REMARK 210 BONDS AND 19 -ANGLE RESTRAINTS REMARK 210 WERE ALSO USED IN THE REMARK 210 STRUCTURE CALCULATIONS. FOR REMARK 210 THE ENSEMBLE OF THE FINAL 20 REMARK 210 STRUCTURES, NO DISTANCE OR REMARK 210 TORSIONAL ANGLE RESTRAINT WAS REMARK 210 VIOLATED BY MORE THAN 0.4 OR REMARK 210 5, RESPECTIVELY. THE DISTANCE- REMARK 210 VIOLATION, DIHEDRAL-VIOLATION, REMARK 210 AND TOTAL ENERGIES WERE 74.4 REMARK 210 1.7 KCAL MOL/1, 0.82 0.08 KCAL REMARK 210 MOL/1, AND 262.0 6.0 KCAL MOL/ REMARK 210 1, RESPECTIVELY. THE LENNARD- REMARK 210 JONES POTENTIAL, WHICH WAS NOT REMARK 210 USED DURING ANY REFINEMENT REMARK 210 STAGE, WAS 659.3 23.1 KCAL REMARK 210 MOL/1 FOR THE FINAL REMARK 210 STRUCTURES. RAMACHANDRAN PLOT REMARK 210 ANALYSIS BY PROCHECK-NMR REMARK 210 SHOWED THAT IN THE FINAL REMARK 210 STRUCTURES OF THE COMPLEX, REMARK 210 98.1% OF THE BACKBONE REMARK 210 GEOMETRIES OF THE NON-GLY AND REMARK 210 NON-PRO RESIDUES IN THE REMARK 210 COMPLEX (PROTEIN RESIDUES 18- REMARK 210 116 AND PEPTIDE RESIDUES (412- REMARK 210 430) AND NEARLY 100% IN THE REMARK 210 SECONDARY STRUCTURE (PROTEIN REMARK 210 RESIDUES 19-24, 35-40, 45-49, REMARK 210 52-57, 63-68, 71-76, 85-90, REMARK 210 94-107, AND 111-115 AND REMARK 210 PEPTIDE RESIDUES 426-430) LIE REMARK 210 WITHIN ENERGETICALLY FAVORABLE REMARK 210 OR ALLOWED REGIONS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NMR SPECTRA WERE ACQUIRED AT 30C ON A BRUKER DRX600 OR REMARK 210 DRX500 SPECTROMETER. THE BACKBONE AND SIDE CHAIN 1H, 13C, AND REMARK 210 15N RESONANCES OF THE PROTEIN WERE ASSIGNED USING DEUTERIUM- REMARK 210 DECOUPLED TRIPLE-RESONANCE EXPERIMENTS OF HNCA, HN(CO)CA, REMARK 210 HNCACB, HN(CO)CACB, AND (H)C(CO)NH-TOCSY ([34 AND 30]) REMARK 210 RECORDED BY USING UNIFORMLY 15N/13C-LABELED AND FRACTIONALLY REMARK 210 DEUTERATED PROTEIN IN COMPLEX WITH A NONISOTOPICALLY LABELED REMARK 210 HFGFR1 PEPTIDE. THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 USING 3D HCCH-TOCSY ([7]) DATA COLLECTED FROM A UNIFORMLY 15N/ REMARK 210 13C LABELED-PROTEIN/NONLABELED-PEPTIDE COMPLEX. NOE-DERIVED REMARK 210 DISTANCE RESTRAINTS WERE OBTAINED FROM 15N- OR 13C-EDITED 3D REMARK 210 NOESY SPECTRA ([7]). -ANGLE RESTRAINTS WERE DETERMINED FROM REMARK 210 3JHN,H COUPLING CONSTANTS MEASURED IN A 3D HNHA-J SPECTRUM REMARK 210 ([7]). SLOWLY EXCHANGING AMIDE PROTONS WERE IDENTIFIED FROM A REMARK 210 SERIES OF 2D 15N-HSQC SPECTRA RECORDED AFTER THE H2O BUFFER REMARK 210 WAS CHANGED TO 2H2O BUFFER. THE PEPTIDE RESONANCES WERE REMARK 210 ASSIGNED USING 13C/15N-FILTERED 2D NOESY AND TOCSY SPECTRA REMARK 210 ([30]) COLLECTED FROM A 15N/13C LABELED-PROTEIN/NONLABELED- REMARK 210 PEPTIDE COMPLEX. THE INTERMOLECULAR NOES USED IN DEFINING THE REMARK 210 STRUCTURE OF THE SNT-1 PTB DOMAIN/HFGFR1 COMPLEX WERE DETECTED REMARK 210 IN 13C- OR 15N-EDITED (F 1), 13C/15N-FILTERED (F 3) 3D NOESY REMARK 210 SPECTRA. ALL NMR SPECTRA WERE PROCESSED WITH NMRPIPE/NMRDRAW REMARK 210 ([8]) AND ANALYZED USING NMRVIEW.
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 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 GLN A 411 -86.34 61.86 REMARK 500 MET A 412 -178.00 50.11 REMARK 500 VAL A 414 95.77 -42.03 REMARK 500 HIS A 415 -173.67 -65.40 REMARK 500 PRO A 422 75.09 -64.72 REMARK 500 GLN A 426 73.55 -161.08 REMARK 500 ASP B 11 33.08 -161.25 REMARK 500 ASN B 16 74.34 -64.62 REMARK 500 HIS B 17 54.30 -160.75 REMARK 500 LYS B 22 82.99 -59.15 REMARK 500 GLU B 32 141.03 60.75 REMARK 500 SER B 35 122.05 167.68 REMARK 500 LEU B 40 66.83 -119.24 REMARK 500 THR B 41 -167.57 -54.15 REMARK 500 THR B 43 54.06 -163.83 REMARK 500 GLU B 44 139.61 178.49 REMARK 500 LEU B 45 67.50 -101.64 REMARK 500 LYS B 51 27.05 47.92 REMARK 500 ARG B 52 -52.35 -152.46 REMARK 500 HIS B 58 32.03 -96.59 REMARK 500 TYR B 59 -80.57 70.02 REMARK 500 LEU B 62 -152.33 -59.81 REMARK 500 ARG B 63 -44.63 -151.73 REMARK 500 SER B 69 -84.68 56.85 REMARK 500 ARG B 79 -74.75 -156.49 REMARK 500 CYS B 80 -155.55 178.88 REMARK 500 GLN B 81 -85.89 69.85 REMARK 500 PHE B 98 -70.83 -49.11 REMARK 500 VAL B 112 54.28 -143.95 REMARK 500 VAL B 113 99.72 -44.22 REMARK 500 VAL B 117 34.88 -146.65 REMARK 500 VAL B 118 96.12 41.10 REMARK 500 ASN B 121 -80.70 61.70 REMARK 500 ASN B 122 119.78 179.43 REMARK 500 GLU B 128 -49.25 -166.21 REMARK 500 THR B 135 79.25 66.04 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1XR0 A 409 430 UNP P11362 FGFR1_HUMAN 409 430 DBREF 1XR0 B 11 136 UNP Q8WU20 FRS2_HUMAN 11 136
SEQADV 1XR0 MET B 8 UNP Q8WU20 CLONING ARTIFACT SEQADV 1XR0 GLY B 9 UNP Q8WU20 CLONING ARTIFACT SEQADV 1XR0 SER B 10 UNP Q8WU20 CLONING ARTIFACT
SEQRES 1 A 22 HIS SER GLN MET ALA VAL HIS LYS LEU ALA LYS SER ILE SEQRES 2 A 22 PRO LEU ARG ARG GLN VAL THR VAL SER SEQRES 1 B 129 MET GLY SER ASP THR VAL PRO ASP ASN HIS ARG ASN LYS SEQRES 2 B 129 PHE LYS VAL ILE ASN VAL ASP ASP ASP GLY ASN GLU LEU SEQRES 3 B 129 GLY SER GLY ILE MET GLU LEU THR ASP THR GLU LEU ILE SEQRES 4 B 129 LEU TYR THR ARG LYS ARG ASP SER VAL LYS TRP HIS TYR SEQRES 5 B 129 LEU CYS LEU ARG ARG TYR GLY TYR ASP SER ASN LEU PHE SEQRES 6 B 129 SER PHE GLU SER GLY ARG ARG CYS GLN THR GLY GLN GLY SEQRES 7 B 129 ILE PHE ALA PHE LYS CYS ALA ARG ALA GLU GLU LEU PHE SEQRES 8 B 129 ASN MET LEU GLN GLU ILE MET GLN ASN ASN SER ILE ASN SEQRES 9 B 129 VAL VAL GLU GLU PRO VAL VAL GLU ARG ASN ASN HIS GLN SEQRES 10 B 129 THR GLU LEU GLU VAL PRO ARG THR PRO ARG THR PRO
HELIX 1 1 ARG B 93 ASN B 108 1 16
SHEET 1 A 2 VAL A 427 THR A 428 0 SHEET 2 A 2 VAL B 113 GLU B 114 -1 O VAL B 113 N THR A 428 SHEET 1 B 7 ASP B 53 TRP B 57 0 SHEET 2 B 7 LEU B 45 THR B 49 -1 N LEU B 47 O VAL B 55 SHEET 3 B 7 GLY B 36 LEU B 40 -1 N ILE B 37 O TYR B 48 SHEET 4 B 7 LYS B 20 VAL B 26 -1 N VAL B 23 O GLY B 36 SHEET 5 B 7 GLY B 85 LYS B 90 -1 O ALA B 88 N VAL B 26 SHEET 6 B 7 LEU B 71 SER B 76 -1 N PHE B 74 O PHE B 87 SHEET 7 B 7 LEU B 62 TYR B 67 -1 N GLY B 66 O SER B 73
CISPEP 1 VAL B 129 PRO B 130 0 0.34
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