10 20 30 40 50 60 70 80 2OTK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DE NOVO PROTEIN, PEPTIDE BINDING PROTEIN08-FEB-07 2OTK
TITLE STRUCTURE OF ALZHEIMER AB PEPTIDE IN COMPLEX WITH AN TITLE 2 ENGINEERED BINDING PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RESIDUES 672-711; COMPND 5 SYNONYM: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ZAB3 AFFIBODY DIMER; COMPND 8 CHAIN: E, F; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ENGINEERED BINDING PROTEIN; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEIN-PEPTIDE COMPLEX, BETA-HAIRPIN, INTERMOLECULAR BETA- KEYWDS 2 SHEET, DE NOVO PROTEIN, PEPTIDE BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 24
AUTHOR W.HOYER,T.HARD
REVDAT 3 24-FEB-09 2OTK 1 VERSN REVDAT 2 22-APR-08 2OTK 1 JRNL REVDAT 1 12-FEB-08 2OTK 0
JRNL AUTH W.HOYER,C.GRONWALL,A.JONSSON,S.STAHL,T.HARD JRNL TITL STABILIZATION OF A BETA-HAIRPIN IN MONOMERIC JRNL TITL 2 ALZHEIMER'S AMYLOID-BETA PEPTIDE INHIBITS AMYLOID JRNL TITL 3 FORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 5099 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18375754 JRNL DOI 10.1073/PNAS.0711731105
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.GRONWALL,A.JONSSON,S.LINDSTROM,E.GUNNERIUSSON, REMARK 1 AUTH 2 S.STAHL,N.HERNE REMARK 1 TITL SELECTION AND CHARACTERIZATION OF AFFIBODY LIGANDS REMARK 1 TITL 2 BINDING TO ALZHEIMER AMYLOID BETA PEPTIDES REMARK 1 REF J.BIOTECHNOL. V. 128 162 2007 REMARK 1 REFN ISSN 0168-1656 REMARK 1 PMID 17088007 REMARK 1 DOI 10.1016/J.JBIOTEC.2006.09.013
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.15.0 REMARK 3 AUTHORS : KUSZEWSKI ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2OTK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-07. REMARK 100 THE RCSB ID CODE IS RCSB041567.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 398; 398 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOPHATE; 20 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 400 UM 13C,15N ABETA PEPTIDE REMARK 210 460 UM NONLABELED ZAB3 DIMERS, REMARK 210 90% H2O, 10% D2O; 460 UM REMARK 210 NONLABELED ABETA PEPTIDE 400 REMARK 210 UM 13C,15N ZAB3 DIMERS, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH 2.15.0, CCPNMR REMARK 210 ANALYSIS 1.10, NMRPIPE 2.3 REMARK 210 METHOD USED : AB INITIO SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: INTERMOLECULAR NOES ASSIGNED BASED ON 3D F1 (13C,15N)- REMARK 210 FILTERED, F2 (13C OR 15N)-EDITED NOESY EXPERIMENTS
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 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 1-24 REMARK 465 RES C SSSEQI REMARK 465 ASP C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 PHE C 4 REMARK 465 ARG C 5 REMARK 465 HIS C 6 REMARK 465 ASP C 7 REMARK 465 SER C 8 REMARK 465 GLY C 9 REMARK 465 TYR C 10 REMARK 465 GLU C 11 REMARK 465 VAL C 12 REMARK 465 HIS C 13 REMARK 465 HIS C 14 REMARK 465 GLN C 15 REMARK 465 GLY E -10 REMARK 465 SER E -9 REMARK 465 SER E -8 REMARK 465 HIS E -7 REMARK 465 HIS E -6 REMARK 465 HIS E -5 REMARK 465 HIS E -4 REMARK 465 HIS E -3 REMARK 465 HIS E -2 REMARK 465 LEU E -1 REMARK 465 GLN E 0 REMARK 465 VAL E 1 REMARK 465 ASP E 2 REMARK 465 ASN E 3 REMARK 465 LYS E 4 REMARK 465 PHE E 5 REMARK 465 ASN E 6 REMARK 465 LYS E 7 REMARK 465 GLU E 8 REMARK 465 MET E 9 REMARK 465 ALA E 10 REMARK 465 SER E 11 REMARK 465 ALA E 12 REMARK 465 GLY E 13 REMARK 465 PRO E 57 REMARK 465 LYS E 58 REMARK 465 VAL E 59 REMARK 465 ASP E 60 REMARK 465 GLY F -10 REMARK 465 SER F -9 REMARK 465 SER F -8 REMARK 465 HIS F -7 REMARK 465 HIS F -6 REMARK 465 HIS F -5 REMARK 465 HIS F -4 REMARK 465 HIS F -3 REMARK 465 HIS F -2 REMARK 465 LEU F -1 REMARK 465 GLN F 0 REMARK 465 VAL F 1 REMARK 465 ASP F 2 REMARK 465 ASN F 3 REMARK 465 LYS F 4 REMARK 465 PHE F 5 REMARK 465 ASN F 6 REMARK 465 LYS F 7 REMARK 465 GLU F 8 REMARK 465 MET F 9 REMARK 465 ALA F 10 REMARK 465 SER F 11 REMARK 465 ALA F 12 REMARK 465 GLY F 13 REMARK 465 PRO F 57 REMARK 465 LYS F 58 REMARK 465 VAL F 59 REMARK 465 ASP F 60
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 SER C 26 -167.33 53.57 REMARK 500 1 LEU F 19 72.56 -116.35 REMARK 500 2 SER C 26 28.22 49.57 REMARK 500 2 ASP E 37 95.83 -162.80 REMARK 500 3 SER C 26 28.39 48.78 REMARK 500 4 SER C 26 174.25 -56.72 REMARK 500 5 LYS C 28 -23.51 -145.55 REMARK 500 6 LEU F 19 72.26 -116.00 REMARK 500 7 SER C 26 47.60 -78.96 REMARK 500 7 LYS C 28 -1.31 -142.02 REMARK 500 8 SER C 26 28.30 49.36 REMARK 500 8 ASP E 37 75.27 -116.77 REMARK 500 8 LEU F 19 72.35 -117.36 REMARK 500 8 ASP F 37 84.47 -151.62 REMARK 500 9 LEU F 19 78.07 -117.76 REMARK 500 10 SER C 26 28.79 48.47 REMARK 500 11 SER C 26 35.73 38.00 REMARK 500 11 LEU F 19 72.11 -115.59 REMARK 500 13 LEU F 19 71.06 -117.70 REMARK 500 14 SER C 26 28.50 47.07 REMARK 500 14 ASN C 27 -5.38 69.94 REMARK 500 15 GLN E 55 -68.86 -91.00 REMARK 500 16 SER C 26 28.22 48.20 REMARK 500 17 SER C 26 43.49 -79.30 REMARK 500 17 LEU F 19 72.91 -116.86 REMARK 500 18 SER C 26 27.87 49.06 REMARK 500 18 LEU E 19 60.07 -118.36 REMARK 500 19 LEU F 19 74.38 -118.74 REMARK 500 20 LEU F 19 72.12 -116.61 REMARK 500 21 SER C 26 28.82 49.42 REMARK 500 22 SER C 26 -169.83 54.18 REMARK 500 24 LEU F 19 77.33 -118.49 REMARK 500 REMARK 500 REMARK: NULL
REMARK 999 REMARK 999 SEQUENCE REMARK 999 FRAGMENTS E AND F IS A DIMER OF AN ENGINEERED BINDING REMARK 999 PROTEIN, DECRIBED IN THE GRONWALL ET AL (2007) J. REMARK 999 BIOTECHNOL.
DBREF 2OTK C 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2OTK E -10 60 PDB 2OTK 2OTK -10 60 DBREF 2OTK F -10 60 PDB 2OTK 2OTK -10 60
SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 40 VAL SEQRES 1 E 71 GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP SEQRES 2 E 71 ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU SEQRES 3 E 71 ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS SEQRES 4 E 71 ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER SEQRES 5 E 71 ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA SEQRES 6 E 71 GLN ALA PRO LYS VAL ASP SEQRES 1 F 71 GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP SEQRES 2 F 71 ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU SEQRES 3 F 71 ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS SEQRES 4 F 71 ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER SEQRES 5 F 71 ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA SEQRES 6 F 71 GLN ALA PRO LYS VAL ASP
HELIX 1 1 SER C 26 LYS C 28 5 3 HELIX 2 2 ASN E 23 ASP E 37 1 15 HELIX 3 3 GLN E 40 GLN E 55 1 16 HELIX 4 4 ASN F 23 ASP F 37 1 15 HELIX 5 5 ASP F 37 GLN F 55 1 19
SHEET 1 A 4 GLU E 15 TYR E 18 0 SHEET 2 A 4 GLY C 29 VAL C 36 -1 N LEU C 34 O VAL E 17 SHEET 3 A 4 LEU C 17 GLY C 25 -1 N PHE C 20 O GLY C 33 SHEET 4 A 4 ILE F 16 LEU F 19 -1 O LEU F 19 N PHE C 19
SSBOND 1 CYS E 28 CYS F 28 1555 1555 2.02
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