BMRB Entry 15778

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15778
MolProbity Validation Chart

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Title:
Structure of the tyrosine-O-sulfated C5a receptor N-terminus in complex with the immune evasive protein CHIPS.
Deposition date:
2008-05-16
Original release date:
2009-04-03
Authors:
Ippel, Johannes; Bunschoten, Anton; Kemmink, Johan; Liskamp, Rob
Citation:

Citation: Ippel, Johannes; de Haas, Carla; Bunschoten, Anton; van Strijp, Jos; Kruijtzer, John; Liskamp, Rob; Kemmink, Johan. "Structure of the tyrosine-sulfated C5a receptor N-terminus in complex with chemotaxis inhibitory protein of Staphylococcus aureus"  J. Biol. Chem. 284, 12363-12372 (2009).
PubMed: 19251703

Assembly members:

Assembly members:
CHIPS protein, polymer, 91 residues, 10476.059 Da.
C5aR(P7-28S) peptide, polymer, 24 residues, 2710.827 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pRSET B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CHIPS protein: NSGLPTTLGKLDERLRNYLK KGTKNSAQFEKMVILTENKG YYTVYLNTPLAEDRKNVELL GKMYKTYFFKKGESKSSYVI NGPGKTNEYAY
C5aR(P7-28S) peptide: XTTPDXGHXDDKDTLDLNTP VDKX

Data sets:
Data typeCount
13C chemical shifts416
15N chemical shifts102
1H chemical shifts830

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1CHIPS protein1
2C5aR(P7-28S) peptide2

Entities:

Entity 1, CHIPS protein 91 residues - 10476.059 Da.

CHIPS sequence N31 to Y121 represent the truncated variant of CHIPS(1-121), minus the signal peptide part, derived from Staphylococcus Aureus. The truncated CHIPS variant shows full inhibition against C5a-activation of the human C5aR receptor.

1   ASNSERGLYLEUPROTHRTHRLEUGLYLYS
2   LEUASPGLUARGLEUARGASNTYRLEULYS
3   LYSGLYTHRLYSASNSERALAGLNPHEGLU
4   LYSMETVALILELEUTHRGLUASNLYSGLY
5   TYRTYRTHRVALTYRLEUASNTHRPROLEU
6   ALAGLUASPARGLYSASNVALGLULEULEU
7   GLYLYSMETTYRLYSTHRTYRPHEPHELYS
8   LYSGLYGLUSERLYSSERSERTYRVALILE
9   ASNGLYPROGLYLYSTHRASNGLUTYRALA
10   TYR

Entity 2, C5aR(P7-28S) peptide 24 residues - 2710.827 Da.

Synthetic peptide containing the amino acid sequence part (7-28) of the extracellular N-terminus of the human C5aR (CD88) receptor, including the two O-sulfated tyrosines at positions 11 and 14, natively present in the C5aR receptor.

1   ACETHRTHRPROASPTYSGLYHISTYSASP
2   ASPLYSASPTHRLEUASPLEUASNTHRPRO
3   VALASPLYSNH2

Samples:

sample_1: entity_1, [U-99% 15N], 0.5 mM; entity_2 0.5 mM; sodium phosphate 20 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_2: entity_1, [U-99% 13C; U-99% 15N], 1.0 mM; entity_2 1.0 mM; sodium phosphate 20 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
3D CBCA(CO)NHsample_2isotropicsample_conditions_2
3D HNCACBsample_2isotropicsample_conditions_2
3D HNCOsample_2isotropicsample_conditions_2
3D HBHACBCA(CO)NHsample_2isotropicsample_conditions_2
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_2
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_2
3D 1H-13C NOESYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
3D COCA(HN)sample_2isotropicsample_conditions_2
3D-CNH-NOESYsample_2isotropicsample_conditions_2
2D-HBHD aromaticsample_2isotropicsample_conditions_2
2D-HBHE aromaticsample_2isotropicsample_conditions_2
2D-CBHD aromaticsample_2isotropicsample_conditions_2
2D-CBHE aromaticsample_2isotropicsample_conditions_2
3D HNHAsample_2isotropicsample_conditions_2
3D HNHBsample_2isotropicsample_conditions_2

Software:

xwinnmr v3.5, Bruker Biospin - collection, processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

ARIA v1.2, Linge, O'Donoghue and Nilges - refinement, structure solution

CNSSOLVE v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

SPARKY v3.112, Goddard - chemical shift assignment, peak picking

CARA v1.3.2, Keller and Wuthrich - chemical shift assignment, peak picking

VNMR, Varian - collection

Molmol, Koradi, Billeter and Wuthrich - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

TALOS, Cornilescu, Delaglio and Bax - geometry optimization, structure solution

YASARA vYasara Structure 8.3.3/WHATIF, Krieger and Vriend - refinement, structure solution

ShiftCalc v2004, Williamson and Refaee - chemical shift calculation

PACES, (PACES) Coggins and Zhou - chemical shift assignment

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz
  • Bruker Avance 900 MHz

Related Database Links:

UniProtKB A6QIG7 P21730
PDB
DBJ BAB43029 BAF68149 BAR09439 BAR12163
EMBL CAG41022 CAQ06479 CBX35158 CCG16570 CDP41562
GB AAQ14339 ABD22075 ABD31214 ABF73223 ABQ49784
REF NP_835578 WP_000727643 WP_000727645 WP_000727649 WP_000727650
SP A6QIG7 Q2FFF7 Q2FWV5 Q6GFB3 Q99SU8
AlphaFold A6QIG7 Q2FFF7 Q2FWV5 Q6GFB3 Q99SU8

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks