HEADER SIGNALING PROTEIN/GROWTH FACTOR RECEPTOR13-OCT-04 1XR0 TITLE STRUCTURAL BASIS OF SNT PTB DOMAIN INTERACTIONS WITH DISTINCT TITLE 2 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 JUXTAMEMBRANE COMPND 5 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 SEQUENCE SOURCE 4 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 MOTIF, KEYWDS 2 SIGNALING PROTEIN-GROWTH FACTOR RECEPTOR COMPLEX EXPDTA SOLUTION NMR AUTHOR C.DHALLUIN,K.S.YAN,O.PLOTNIKOVA,K.W.LEE,L.ZENG,M.KUTI,S.MUJTABA, AUTHOR 2 M.P.GOLDFARB,M.-M.ZHOU REVDAT 3 02-MAR-22 1XR0 1 REMARK SEQADV 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,M.KUTI, JRNL AUTH 2 S.MUJTABA,M.P.GOLDFARB,M.-M.ZHOU JRNL TITL STRUCTURAL BASIS OF SNT PTB DOMAIN INTERACTIONS WITH JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, ARIA 1.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR), M. NILGES AND S. O'DONOGHUE REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030666. 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 EDTA00 REMARK 210 MM PHOSPHATE BUFFER, REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : SNT-1 PTB DOMAIN/HFGFR1 PEPTIDE REMARK 210 COMPLEX (1:1) OF ~0.5 MM IN 100 REMARK 210 MM PHOSPHATE BUFFER OF PH 6.5, 5 REMARK 210 MM DTT-D10, AND 0.5 MM EDTA IN REMARK 210 H2O/2H2O (9/1) OR 2H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA; 3D_13C-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; 2D 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 : NULL 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 BY REMARK 210 USING THE X-PLOR PROGRAM ([4]). REMARK 210 NOE DISTANCE AND DIHEDRAL ANGLE REMARK 210 RESTRAINTS WERE TREATED WITH A REMARK 210 SQUARE-WELL POTENTIAL OF 50 KCAL REMARK 210 MOL?1 ?2. A TOTAL OF 2448 REMARK 210 MANUALLY ASSIGNED NOE-DERIVED REMARK 210 DISTANCE RESTRAINTS WERE REMARK 210 OBTAINED FROM THE 15N- OR 13C- REMARK 210 EDITED NOESY DATA. INCLUDED IN REMARK 210 THIS FIGURE ARE 251 INTRAPEPTIDE REMARK 210 AND 258 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 BY REMARK 210 USING ARIA. THE FINAL STRUCTURE REMARK 210 CALCULATIONS EMPLOYED A TOTAL OF REMARK 210 2755 NOE RESTRAINTS OBTAINED REMARK 210 FROM THE MANUAL AND THE ARIA- REMARK 210 ASSISTED ASSIGNMENTS, 2703 OF REMARK 210 WHICH WERE UNAMBIGUOUSLY REMARK 210 ASSIGNED 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 BONDS REMARK 210 AND 19 -ANGLE RESTRAINTS WERE REMARK 210 ALSO USED IN THE STRUCTURE REMARK 210 CALCULATIONS. FOR THE ENSEMBLE REMARK 210 OF THE FINAL 20 STRUCTURES, NO REMARK 210 DISTANCE OR TORSIONAL ANGLE REMARK 210 RESTRAINT WAS VIOLATED BY MORE REMARK 210 THAN 0.4 OR 5, RESPECTIVELY. THE REMARK 210 DISTANCE-VIOLATION, DIHEDRAL- REMARK 210 VIOLATION, AND TOTAL ENERGIES REMARK 210 WERE 74.4 1.7 KCAL MOL/1, 0.82 REMARK 210 0.08 KCAL MOL/1, AND 262.0 6.0 REMARK 210 KCAL MOL/1, RESPECTIVELY. THE REMARK 210 LENNARD-JONES POTENTIAL, WHICH REMARK 210 WAS NOT USED DURING ANY REMARK 210 REFINEMENT STAGE, WAS 659.3 23.1 REMARK 210 KCAL MOL/1 FOR THE FINAL REMARK 210 STRUCTURES. RAMACHANDRAN PLOT REMARK 210 ANALYSIS BY PROCHECK-NMR SHOWED REMARK 210 THAT IN THE FINAL STRUCTURES OF REMARK 210 THE COMPLEX, 98.1% OF THE REMARK 210 BACKBONE GEOMETRIES OF THE NON- REMARK 210 GLY AND NON-PRO RESIDUES IN THE REMARK 210 COMPLEX (PROTEIN RESIDUES 18-116 REMARK 210 AND PEPTIDE RESIDUES (412-430) REMARK 210 AND NEARLY 100% IN THE SECONDARY REMARK 210 STRUCTURE (PROTEIN RESIDUES 19- REMARK 210 24, 35-40, 45-49, 52-57, 63-68, REMARK 210 71-76, 85-90, 94-107, AND 111- REMARK 210 115 AND PEPTIDE RESIDUES 426-430) REMARK 210 LIE WITHIN ENERGETICALLY REMARK 210 FAVORABLE 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: REMARK 210 NMR SPECTRA WERE ACQUIRED AT 30C ON A BRUKER DRX600 OR DRX500 REMARK 210 SPECTROMETER. THE BACKBONE AND REMARK 210 SIDE CHAIN 1H, 13C, AND 15N RESONANCES OF THE PROTEIN WERE REMARK 210 ASSIGNED USING DEUTERIUM-DECOUPLED REMARK 210 TRIPLE-RESONANCE EXPERIMENTS OF HNCA, HN(CO)CA, HNCACB, HN(CO) REMARK 210 CACB, AND REMARK 210 (H)C(CO)NH-TOCSY ([34 AND 30]) RECORDED BY USING UNIFORMLY 15N/ REMARK 210 13C-LABELED AND FRACTIONALLY REMARK 210 DEUTERATED PROTEIN IN COMPLEX WITH A NONISOTOPICALLY LABELED REMARK 210 HFGFR1 PEPTIDE. THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED USING 3D HCCH-TOCSY ([7]) DATA REMARK 210 COLLECTED FROM A UNIFORMLY 15N/13C REMARK 210 LABELED-PROTEIN/NONLABELED-PEPTIDE COMPLEX. NOE-DERIVED REMARK 210 DISTANCE RESTRAINTS WERE OBTAINED FROM REMARK 210 15N- OR 13C-EDITED 3D NOESY SPECTRA ([7]). -ANGLE RESTRAINTS REMARK 210 WERE DETERMINED FROM 3JHN,H REMARK 210 COUPLING CONSTANTS MEASURED IN A 3D HNHA-J SPECTRUM ([7]). REMARK 210 SLOWLY EXCHANGING AMIDE PROTONS WERE REMARK 210 IDENTIFIED FROM A SERIES OF 2D 15N-HSQC SPECTRA RECORDED AFTER REMARK 210 THE H2O BUFFER WAS CHANGED TO 2H2O REMARK 210 BUFFER. THE PEPTIDE RESONANCES WERE ASSIGNED USING 13C/15N- REMARK 210 FILTERED 2D NOESY AND TOCSY SPECTRA REMARK 210 ([30]) COLLECTED FROM A 15N/13C LABELED-PROTEIN/NONLABELED- REMARK 210 PEPTIDE COMPLEX. THE INTERMOLECULAR NOES REMARK 210 USED IN DEFINING THE STRUCTURE OF THE SNT-1 PTB DOMAIN/HFGFR1 REMARK 210 COMPLEX WERE DETECTED IN 13C- OR REMARK 210 15N-EDITED (F 1), 13C/15N-FILTERED (F 3) 3D NOESY SPECTRA. ALL REMARK 210 NMR SPECTRA WERE PROCESSED WITH REMARK 210 NMRPIPE/NMRDRAW ([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 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: 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