HEADER SIGNALING PROTEIN, PROTEIN BINDING 11-MAY-07 2JPH TITLE NMR SOLUTION STRUCTURE OF THE RHO GTPASE BINDING DOMAIN OF HUMAN TITLE 2 PLEXIN-B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 1743-1862; COMPND 5 SYNONYM: SEMAPHORIN RECEPTOR SEP; COMPND 6 ENGINEERED: YES; COMPND 7 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: PLXNB1, KIAA0407, SEP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS PROTEIN, UBIQUITIN FOLD, SIGNALING PROTEIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.TONG,M.BUCK REVDAT 3 20-OCT-21 2JPH 1 REMARK SEQADV REVDAT 2 24-FEB-09 2JPH 1 VERSN REVDAT 1 18-MAR-08 2JPH 0 JRNL AUTH Y.TONG,P.K.HOTA,M.B.HAMANEH,M.BUCK JRNL TITL INSIGHTS INTO ONCOGENIC MUTATIONS OF PLEXIN-B1 BASED ON THE JRNL TITL 2 SOLUTION STRUCTURE OF THE RHO GTPASE BINDING DOMAIN JRNL REF STRUCTURE V. 16 246 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18275816 JRNL DOI 10.1016/J.STR.2007.12.012 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.TONG,D.HUGHES,L.PLACANICA,M.BUCK REMARK 1 TITL WHEN MONOMERS ARE PREFERRED: A STRATEGY FOR THE REMARK 1 TITL 2 IDENTIFICATION AND DISRUPTION OF WEAKLY OLIGOMERIZED REMARK 1 TITL 3 PROTEINS. REMARK 1 REF STRUCTURE V. 13 7 2005 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 15642257 REMARK 1 DOI 10.1016/J.STR.2004.10.018 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.TONG,M.BUCK REMARK 1 TITL 1H, 15N AND 13C RESONANCE ASSIGNMENTS AND SECONDARY REMARK 1 TITL 2 STRUCTURE DETERMINATION REVEAL THAT THE MINIMAL RAC1 GTPASE REMARK 1 TITL 3 BINDING DOMAIN OF PLEXIN-B1 HAS A UBIQUITIN FOLD. REMARK 1 REF J.BIOMOL.NMR V. 31 369 2005 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 15929008 REMARK 1 DOI 10.1007/S10858-005-0943-9 REMARK 1 REFERENCE 3 REMARK 1 AUTH I.OINUMA,Y.ISHIKAWA,H.KATOH,M.NEGISHI REMARK 1 TITL THE SEMAPHORIN 4D RECEPTOR PLEXIN-B1 IS A GTPASE ACTIVATING REMARK 1 TITL 2 PROTEIN FOR R-RAS. REMARK 1 REF SCIENCE V. 305 862 2004 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 15297673 REMARK 1 DOI 10.1126/SCIENCE.1097545 REMARK 1 REFERENCE 4 REMARK 1 AUTH H.G.VIKIS,W.LI,Z.HE,K.L.GUAN REMARK 1 TITL THE SEMAPHORIN RECEPTOR PLEXIN-B1 SPECIFICALLY INTERACTS REMARK 1 TITL 2 WITH ACTIVE RAC IN A LIGAND-DEPENDENT MANNER. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 12457 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 11035813 REMARK 1 DOI 10.1073/PNAS.220421797 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.H.DRIESSENS,C.D.NOBES,A.SELF,I.JORDENS,C.S.GOODMAN,A.HALL REMARK 1 TITL PLEXIN-B SEMAPHORIN RECEPTORS INTERACT DIRECTLY WITH ACTIVE REMARK 1 TITL 2 RAC AND REGULATE THE ACTIN CYTOSKELETON BY ACTIVATING RHO. REMARK 1 REF CURR.BIOL. V. 11 339 2001 REMARK 1 REFN ISSN 0960-9822 REMARK 1 PMID 11267870 REMARK 1 DOI 10.1016/S0960-9822(01)00092-6 REMARK 1 REFERENCE 6 REMARK 1 AUTH Y.TONG,P.CHUGHA,P.K.HOTA,R.S.ALVIANI,M.LI,W.TEMPEL,L.SHEN, REMARK 1 AUTH 2 H.W.PARK,M.BUCK REMARK 1 TITL BINDING OF RAC1, RND1, AND RHOD TO A NOVEL RHO GTPASE REMARK 1 TITL 2 INTERACTION MOTIF DESTABILIZES DIMERIZATION OF THE PLEXIN-B1 REMARK 1 TITL 3 EFFECTOR DOMAIN REMARK 1 REF J.BIOL.CHEM. V. 282 37215 2007 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17916560 REMARK 1 DOI 10.1074/JBC.M703800200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEW, X-PLOR NIH 2.17.0 REMARK 3 AUTHORS : JOHNSON, ONE MOON SCIENTIFIC (NMRVIEW), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FOLLOWING NEDERVEEN AJ ET AL., PROTEINS REMARK 3 2005, 59: 662-672 BUT IN PRESENCE OF A 10ANGSTROM EXPLICIT WATER REMARK 3 SHELL, FINAL MINIMIZATION IN PRESENCE OF 4.5 ANGSTROM EXPLICIT REMARK 3 WATER SHELL REMARK 4 REMARK 4 2JPH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000100125. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.75 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 90%H2O/10% D2O; 1.25 MM REMARK 210 [U-100% 13C; U-100% 15N; 80% 2H] REMARK 210 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, NMRPIPE, CYANA 2.3, X REMARK 210 -PLOR NIH 2.17.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 0 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 PRO A 8 109.18 -57.38 REMARK 500 1 ALA A 21 48.97 -69.68 REMARK 500 1 ALA A 24 -76.03 -81.96 REMARK 500 1 GLN A 25 -63.83 -140.76 REMARK 500 1 ASP A 35 -165.76 -71.58 REMARK 500 1 TYR A 49 32.51 -96.48 REMARK 500 1 ASP A 81 -82.92 -116.30 REMARK 500 1 GLN A 87 -19.59 -143.03 REMARK 500 2 PRO A 8 104.82 -58.32 REMARK 500 2 ALA A 21 48.51 -70.58 REMARK 500 2 ALA A 24 -77.38 -79.80 REMARK 500 2 GLN A 25 -58.77 -129.56 REMARK 500 2 ASP A 35 -161.44 -71.83 REMARK 500 2 ASP A 81 -87.26 -134.90 REMARK 500 2 GLN A 87 -14.11 -151.81 REMARK 500 2 CYS A 112 76.85 45.49 REMARK 500 2 LEU A 113 -40.12 -143.08 REMARK 500 3 ALA A 21 79.09 -69.19 REMARK 500 3 GLU A 23 30.75 -149.90 REMARK 500 3 ALA A 24 -75.37 -88.37 REMARK 500 3 GLN A 25 -67.43 -139.87 REMARK 500 3 GLU A 80 63.63 -153.05 REMARK 500 3 ASP A 81 -103.84 -143.92 REMARK 500 3 VAL A 86 77.56 -103.87 REMARK 500 3 GLN A 87 21.30 -141.22 REMARK 500 3 LEU A 118 -162.31 -122.43 REMARK 500 4 ALA A 21 39.80 -70.33 REMARK 500 4 ALA A 24 -83.08 -106.07 REMARK 500 4 ASP A 35 -166.39 -74.61 REMARK 500 4 ASP A 81 -79.38 -140.19 REMARK 500 4 ARG A 91 94.03 -64.88 REMARK 500 4 LEU A 113 -49.27 -130.25 REMARK 500 5 ALA A 16 50.10 -114.41 REMARK 500 5 ALA A 21 29.03 -74.14 REMARK 500 5 ALA A 24 -73.85 -66.60 REMARK 500 5 GLN A 25 -61.80 -129.91 REMARK 500 5 ASP A 81 -89.63 -102.17 REMARK 500 5 CYS A 112 93.97 50.15 REMARK 500 5 HIS A 116 95.61 -62.87 REMARK 500 6 VAL A 4 -163.73 -123.95 REMARK 500 6 ALA A 21 24.22 -71.75 REMARK 500 6 ALA A 24 -78.25 -88.99 REMARK 500 6 GLN A 25 -64.67 -125.32 REMARK 500 6 ASP A 81 -90.43 -102.40 REMARK 500 6 CYS A 112 85.21 50.40 REMARK 500 7 GLU A 5 79.38 -108.08 REMARK 500 7 ALA A 24 -93.21 -83.82 REMARK 500 7 ASP A 81 -151.85 -154.89 REMARK 500 7 ARG A 92 -67.86 -131.22 REMARK 500 7 CYS A 112 76.91 52.47 REMARK 500 REMARK 500 THIS ENTRY HAS 147 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 14 ARG A 57 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6346 RELATED DB: BMRB REMARK 900 CHEM. SHIFT ASSIGNMENTS DBREF 2JPH A 3 122 UNP O43157 PLXB1_HUMAN 1743 1862 SEQADV 2JPH MET A 0 UNP O43157 INITIATING METHIONINE SEQADV 2JPH LYS A 1 UNP O43157 EXPRESSION TAG SEQADV 2JPH LYS A 2 UNP O43157 EXPRESSION TAG SEQADV 2JPH PHE A 90 UNP O43157 TRP 1830 ENGINEERED MUTATION SEQRES 1 A 123 MET LYS LYS ASP VAL GLU TYR ARG PRO LEU THR LEU ASN SEQRES 2 A 123 ALA LEU LEU ALA VAL GLY PRO GLY ALA GLY GLU ALA GLN SEQRES 3 A 123 GLY VAL PRO VAL LYS VAL LEU ASP CYS ASP THR ILE SER SEQRES 4 A 123 GLN ALA LYS GLU LYS MET LEU ASP GLN LEU TYR LYS GLY SEQRES 5 A 123 VAL PRO LEU THR GLN ARG PRO ASP PRO ARG THR LEU ASP SEQRES 6 A 123 VAL GLU TRP ARG SER GLY VAL ALA GLY HIS LEU ILE LEU SEQRES 7 A 123 SER ASP GLU ASP VAL THR SER GLU VAL GLN GLY LEU PHE SEQRES 8 A 123 ARG ARG LEU ASN THR LEU GLN HIS TYR LYS VAL PRO ASP SEQRES 9 A 123 GLY ALA THR VAL ALA LEU VAL PRO CYS LEU THR LYS HIS SEQRES 10 A 123 VAL LEU ARG GLU ASN GLN HELIX 1 1 THR A 36 GLN A 47 1 12 HELIX 2 2 THR A 95 LYS A 100 1 6 SHEET 1 A 5 VAL A 27 VAL A 31 0 SHEET 2 A 5 LEU A 9 ALA A 13 -1 N ALA A 13 O VAL A 27 SHEET 3 A 5 ALA A 105 VAL A 110 1 O ALA A 105 N ASN A 12 SHEET 4 A 5 ASP A 64 ARG A 68 -1 N ARG A 68 O THR A 106 SHEET 5 A 5 HIS A 74 LEU A 77 -1 O LEU A 75 N TRP A 67 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