data_17185
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Determination of the Binding Specificity of the Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3
;
_BMRB_accession_number 17185
_BMRB_flat_file_name bmr17185.str
_Entry_type new
_Submission_date 2010-09-10
_Accession_date 2010-09-10
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details .
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Meinecke Robert . .
2 Meyer Bernd . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
binding_constants 1
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2010-11-10 original author .
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'Determination of the Binding Specificity of an Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 11543674
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Meinecke Robert . .
2 Meyer Bernd . .
stop_
_Journal_abbreviation 'J. Med. Chem.'
_Journal_name_full 'Journal of Medicinal Chemistry'
_Journal_volume 44
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 3059
_Page_last 3065
_Year 2001
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 'cyclo/integrin complex'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
cyclo $cyclo
alphaIIb $alphaIIb
beta3 $beta3
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state ?
_System_paramagnetic no
_System_thiol_state .
_Database_query_date .
_Details 'cyclo bound to alphaIIb-beta integrin liposome construct'
save_
########################
# Monomeric polymers #
########################
save_cyclo
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common cyclo
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 5
_Mol_residue_sequence RGDXV
loop_
_Residue_seq_code
_Residue_label
1 ARG 2 GLY 3 ASP 4 DPN 5 VAL
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
save_alphaIIb
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common alphaIIb
_Molecular_mass .
_Mol_thiol_state 'not reported'
_Details .
_Residue_count 42
_Mol_residue_sequence
;
GALEERAIPIWWVLVGVLGG
LLLLTILVLAMWKVGFFKRN
RP
;
loop_
_Residue_seq_code
_Residue_label
1 GLY 2 ALA 3 LEU 4 GLU 5 GLU
6 ARG 7 ALA 8 ILE 9 PRO 10 ILE
11 TRP 12 TRP 13 VAL 14 LEU 15 VAL
16 GLY 17 VAL 18 LEU 19 GLY 20 GLY
21 LEU 22 LEU 23 LEU 24 LEU 25 THR
26 ILE 27 LEU 28 VAL 29 LEU 30 ALA
31 MET 32 TRP 33 LYS 34 VAL 35 GLY
36 PHE 37 PHE 38 LYS 39 ARG 40 ASN
41 ARG 42 PRO
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date 2015-01-30
loop_
_Database_name
_Database_accession_code
_Database_entry_mol_name
_Sequence_query_to_submitted_percentage
_Sequence_subject_length
_Sequence_identity
_Sequence_positive
_Sequence_homology_expectation_value
BMRB 16496 AIIbTMCD 92.86 54 100.00 100.00 3.55e-05
BMRB 16497 Integrin_aIIb_transmembrane_segment,_b3_complexed 100.00 42 100.00 100.00 1.41e-18
PDB 2K1A "Bicelle-Embedded Integrin Alpha(Iib) Transmembrane Segment" 100.00 42 100.00 100.00 1.41e-18
PDB 2K9J "Integrin Alphaiib-Beta3 Transmembrane Complex" 100.00 42 100.00 100.00 1.41e-18
PDB 2KNC "Platelet Integrin Alfaiib-Beta3 Transmembrane-Cytoplasmic Heterocomplex" 92.86 54 100.00 100.00 3.55e-05
DBJ BAG37735 "unnamed protein product [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18
DBJ BAI46167 "integrin, alpha 2b [synthetic construct]" 97.62 1039 100.00 100.00 1.96e-18
EMBL CAA29987 "platelet glycoprotein IIb (648 AA) [Homo sapiens]" 97.62 648 100.00 100.00 2.26e-19
GB AAA35926 "platelet glycoprotein IIb (GPIIb) [Homo sapiens]" 95.24 1039 100.00 100.00 5.44e-05
GB AAA52597 "glycoprotein IIb, partial [Homo sapiens]" 97.62 172 100.00 100.00 8.32e-18
GB AAA53150 "platelet Glycoprotein IIb (GPIIb), partial [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18
GB AAA60114 "platelet membrane glycoprotein IIb [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18
GB AAA65936 "glycoprotein IIb, partial [Papio cynocephalus]" 97.62 604 100.00 100.00 1.13e-19
PRF 1403305A "protein GPIIb" 97.62 649 100.00 100.00 2.60e-19
REF NP_000410 "integrin alpha-IIb preproprotein [Homo sapiens]" 97.62 1039 100.00 100.00 1.96e-18
REF XP_001114526 "PREDICTED: integrin alpha-IIb [Macaca mulatta]" 97.62 1039 100.00 100.00 7.03e-19
REF XP_001150497 "PREDICTED: integrin alpha-IIb isoform X2 [Pan troglodytes]" 97.62 1108 100.00 100.00 1.11e-18
REF XP_002827479 "PREDICTED: integrin alpha-IIb [Pongo abelii]" 97.62 1039 100.00 100.00 1.26e-18
REF XP_003282434 "PREDICTED: LOW QUALITY PROTEIN: integrin alpha-IIb [Nomascus leucogenys]" 97.62 1040 100.00 100.00 9.87e-19
SP P08514 "RecName: Full=Integrin alpha-IIb; AltName: Full=GPalpha IIb; Short=GPIIb; AltName: Full=Platelet membrane glycoprotein IIb; Alt" 97.62 1039 100.00 100.00 1.96e-18
SP P53711 "RecName: Full=Integrin alpha-IIb; AltName: Full=GPalpha IIb; Short=GPIIb; AltName: Full=Platelet membrane glycoprotein IIb; Alt" 97.62 604 100.00 100.00 1.13e-19
stop_
save_
save_beta3
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common beta3
_Molecular_mass .
_Mol_thiol_state 'not reported'
_Details .
_Residue_count 43
_Mol_residue_sequence
;
PESPKGPDILVVLLSVMGAI
LLIGLAALLIWKLLITIHDR
KEF
;
loop_
_Residue_seq_code
_Residue_label
1 PRO 2 GLU 3 SER 4 PRO 5 LYS
6 GLY 7 PRO 8 ASP 9 ILE 10 LEU
11 VAL 12 VAL 13 LEU 14 LEU 15 SER
16 VAL 17 MET 18 GLY 19 ALA 20 ILE
21 LEU 22 LEU 23 ILE 24 GLY 25 LEU
26 ALA 27 ALA 28 LEU 29 LEU 30 ILE
31 TRP 32 LYS 33 LEU 34 LEU 35 ILE
36 THR 37 ILE 38 HIS 39 ASP 40 ARG
41 LYS 42 GLU 43 PHE
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date 2015-01-30
loop_
_Database_name
_Database_accession_code
_Database_entry_mol_name
_Sequence_query_to_submitted_percentage
_Sequence_subject_length
_Sequence_identity
_Sequence_positive
_Sequence_homology_expectation_value
BMRB 16496 B3TMCD 90.70 79 100.00 100.00 6.87e-07
BMRB 16497 Integrin_b3_transmembrane_segment,_aIIb_complexed 100.00 43 100.00 100.00 2.90e-19
PDB 2K9J "Integrin Alphaiib-Beta3 Transmembrane Complex" 100.00 43 100.00 100.00 2.90e-19
PDB 2KNC "Platelet Integrin Alfaiib-Beta3 Transmembrane-Cytoplasmic Heterocomplex" 90.70 79 100.00 100.00 6.87e-07
PDB 2RMZ "Bicelle-Embedded Integrin Beta3 Transmembrane Segment" 100.00 43 100.00 100.00 2.90e-19
PDB 2RN0 "Micelle-Embedded Integrin Beta3 Transmembrane Segment" 100.00 43 100.00 100.00 2.90e-19
DBJ BAG62151 "unnamed protein product [Homo sapiens]" 100.00 751 97.67 97.67 8.70e-19
DBJ BAJ17755 "integrin, beta 3 [synthetic construct]" 100.00 788 97.67 97.67 9.15e-19
GB AAA35927 "plate glycoprotein IIIa (GPIIIa) [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19
GB AAA36121 "integrin beta-3, partial [Homo sapiens]" 100.00 74 97.67 97.67 9.82e-19
GB AAA52589 "glycoprotein IIIa precursor [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19
GB AAA52600 "platelet glycoprotein IIIa, partial [Homo sapiens]" 100.00 761 97.67 97.67 8.83e-19
GB AAA60122 "glycoprotein IIIa [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19
REF NP_000203 "integrin beta-3 precursor [Homo sapiens]" 100.00 788 97.67 97.67 9.15e-19
REF XP_002748172 "PREDICTED: integrin beta-3 [Callithrix jacchus]" 100.00 788 97.67 97.67 9.15e-19
REF XP_002834363 "PREDICTED: integrin beta-3 isoform X1 [Pongo abelii]" 100.00 788 97.67 97.67 9.15e-19
REF XP_003270746 "PREDICTED: integrin beta-3 [Nomascus leucogenys]" 100.00 788 97.67 97.67 9.15e-19
REF XP_004041501 "PREDICTED: integrin beta-3 [Gorilla gorilla gorilla]" 100.00 788 97.67 97.67 9.15e-19
SP P05106 "RecName: Full=Integrin beta-3; AltName: Full=Platelet membrane glycoprotein IIIa; Short=GPIIIa; AltName: CD_antigen=CD61; Flags" 100.00 788 97.67 97.67 9.15e-19
stop_
save_
######################
# Polymer residues #
######################
save_chem_comp_DPN
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-PHENYLALANINE
_BMRB_code .
_PDB_code DPN
_Standard_residue_derivative .
_Molecular_mass 165.189
_Mol_paramagnetic no
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jun 9 13:50:48 2009
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD1 CD1 C . 0 . ?
CD2 CD2 C . 0 . ?
CE1 CE1 C . 0 . ?
CE2 CE2 C . 0 . ?
CZ CZ C . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HXT HXT H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HD1 HD1 H . 0 . ?
HD2 HD2 H . 0 . ?
HE1 HE1 H . 0 . ?
HE2 HE2 H . 0 . ?
HZ HZ H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA C ? ?
SING CA CB ? ?
SING CA HA ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
DOUB CG CD1 ? ?
SING CG CD2 ? ?
SING CD1 CE1 ? ?
SING CD1 HD1 ? ?
DOUB CD2 CE2 ? ?
SING CD2 HD2 ? ?
DOUB CE1 CZ ? ?
SING CE1 HE1 ? ?
SING CE2 CZ ? ?
SING CE2 HE2 ? ?
SING CZ HZ ? ?
stop_
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$cyclo . . . . . .
$alphaIIb Human 9606 Eukaryota Metazoa . .
$beta3 Human 9606 Eukaryota Metazoa . .
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source
_Saveframe_category experimental_source
loop_
_Mol_label
_Production_method
_Host_organism_name_common
_Genus
_Species
_Strain
_Vector_name
$cyclo 'chemical synthesis' . . . . .
$alphaIIb 'purified from the natural source' . . . . .
$beta3 'purified from the natural source' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type solution
_Details 'cyclo titrated into integrin solution; two integrin parts were one unit; pD was adjusted with 100 mM DCl in D2O'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Concentration_min_value
_Concentration_max_value
_Isotopic_labeling
$cyclo . uM 0 275 'natural abundance'
$alphaIIb 5 uM . . 'natural abundance'
$beta3 5 uM . . 'natural abundance'
TRIS 10 mM . . 'natural abundance'
'sodium chloride' 10 mM . . 'natural abundance'
'sodium azide' 6 mM . . 'natural abundance'
'calcium chloride' 20.5 mM . . 'natural abundance'
D2O 99.9 % . . 'natural abundance'
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
RGD 274 mM 'natural abundance'
$cyclo 264 mM 'natural abundance'
$alphaIIb 5 uM 'natural abundance'
$beta3 5 uM 'natural abundance'
TRIS 10 mM 'natural abundance'
'sodium chloride' 10 mM 'natural abundance'
'sodium azide' 6 mM 'natural abundance'
'calcium chloride' 20.5 mM 'natural abundance'
D2O 99.9 % 'natural abundance'
stop_
save_
save_sample_3
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
RGD 274 mM 'natural abundance'
$cyclo 264 mM 'natural abundance'
$alphaIIb 5 uM 'natural abundance'
$beta3 5 uM 'natural abundance'
RGDS 264 mM 'natural abundance'
TRIS 10 mM 'natural abundance'
'sodium azide' 6 mM 'natural abundance'
'sodium chloride' 10 mM 'natural abundance'
'calcium chloride' 20.5 mM 'natural abundance'
D2O 99.9 % 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_xwinnmr
_Saveframe_category software
_Name xwinnmr
_Version 2.5
loop_
_Vendor
_Address
_Electronic_address
'Bruker Biospin' . .
stop_
loop_
_Task
processing
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model Avance
_Field_strength 500
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_STD_NMR_1
_Saveframe_category NMR_applied_experiment
_Experiment_name 'STD NMR'
_Sample_label $sample_1
save_
save_STD_NMR_2
_Saveframe_category NMR_applied_experiment
_Experiment_name 'STD NMR'
_Sample_label $sample_2
save_
save_STD_NMR_3
_Saveframe_category NMR_applied_experiment
_Experiment_name 'STD NMR'
_Sample_label $sample_3
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
temperature 283 . K
pD 7.4 . pH
pressure ambient . atm
stop_
save_