[English] 日本語
Yorodumi
- PDB-2k3u: Structure of the tyrosine-sulfated C5a receptor N-terminus in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k3u
TitleStructure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.
Components
  • C5a anaphylatoxin chemotactic receptor 1
  • Chemotaxis inhibitory protein
KeywordsIMMUNE SYSTEM / Chemotaxis Inhibitory Protein (CHIPS) / sulfated tyrosine / GPCR membrane protein C5aR / anaphylotoxin C5a / Staphylococcus Aureus / complement cascade / Secreted / Virulence
Function / homology
Function and homology information


complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance ...complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / response to peptidoglycan / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance / : / positive regulation of vascular endothelial growth factor production / cellular defense response / Peptide ligand-binding receptors / neutrophil chemotaxis / secretory granule membrane / Regulation of Complement cascade / G protein-coupled receptor activity / positive regulation of epithelial cell proliferation / astrocyte activation / microglial cell activation / mRNA transcription by RNA polymerase II / cognition / positive regulation of angiogenesis / chemotaxis / apical part of cell / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / immune response / Neutrophil degranulation / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Chemotaxis-inhibiting protein CHIPS / Chemotaxis inhibitory protein / FPRL1/chemotaxis inhibitory protein / FPRL1/chemotaxis inhibitory protein superfamily / Chemotaxis-inhibiting protein CHIPS / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Ubiquitin-like (UB roll) / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Chemotaxis-inhibiting protein CHIPS / Chemotaxis inhibitory protein / FPRL1/chemotaxis inhibitory protein / FPRL1/chemotaxis inhibitory protein superfamily / Chemotaxis-inhibiting protein CHIPS / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / Ubiquitin-like (UB roll) / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / Alpha Beta
Similarity search - Domain/homology
Chemotaxis inhibitory protein / C5a anaphylatoxin chemotactic receptor 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus str. Newman (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, simulated annealing docking, molecular dynamics
Model detailsChemotaxis Inhibitory Protein of Staphylococcus Aureus (CHIPS) complexed to the N-terminus (7-28) ...Chemotaxis Inhibitory Protein of Staphylococcus Aureus (CHIPS) complexed to the N-terminus (7-28) of the C5aR receptor.
AuthorsIppel, J.H. / Bunschoten, A. / Kemmink, J. / Liskamp, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of the Tyrosine-sulfated C5a Receptor N Terminus in Complex with Chemotaxis Inhibitory Protein of Staphylococcus aureus.
Authors: Ippel, J.H. / de Haas, C.J. / Bunschoten, A. / van Strijp, J.A. / Kruijtzer, J.A. / Liskamp, R.M. / Kemmink, J.
History
DepositionMay 16, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_mod_residue.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemotaxis inhibitory protein
B: C5a anaphylatoxin chemotactic receptor 1


Theoretical massNumber of molelcules
Total (without water)13,1872
Polymers13,1872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 130structures with the lowest energy
RepresentativeModel #1lowest energy and chemical shift difference

-
Components

#1: Protein Chemotaxis inhibitory protein


Mass: 10475.967 Da / Num. of mol.: 1 / Fragment: Chemotaxis inhibiting protein CHIPS(59-149).
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus str. Newman (bacteria)
Gene: chp / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: A6QIG7
#2: Protein/peptide C5a anaphylatoxin chemotactic receptor 1


Mass: 2710.813 Da / Num. of mol.: 1 / Fragment: C5aR(P7-28S) / Source method: obtained synthetically
Details: Fmoc/tBu-based peptide synthesis. Sulfated tyrosines 11 and 14 were introduced as Fmoc-2-chlorotrityl protected building blocks.
Source: (synth.) Homo sapiens (human) / References: UniProt: P21730
Compound detailsAMBIGUOUS CONFORMATIONAL STATES IN SLOW EXCHANGE ARE PRESENT FOR RESIDUES PRO25-VAL26-ASP27-LYS28 ...AMBIGUOUS CONFORMATIONAL STATES IN SLOW EXCHANGE ARE PRESENT FOR RESIDUES PRO25-VAL26-ASP27-LYS28 OF THE C5AR(P7-28S) PEPTIDE WHEN PRESENT IN THE COMPLEX, PROBABLY CAUSED BY CIS-TRANS ISOMERIZATION AT PRO25. THE RATIO OF THE TWO SLOWLY EXCHANGING CONFORMERS IS ABOUT 1:1. CHEMICAL SHIFTS OF RESIDUES IN CONFORMER A ARE ATTRIBUTED TO RESIDUES 25-28. CHEMICAL SHIFTS OF CONFORMER B ARE DESCRIBED BY RESIDUES 125-128 (OR 25'-28'). RESIDUES 25-28 OF THE C5AR(P7-28S) PEPTIDE ARE NOT IN DIRECT CONTACT TO THE CHIPS PROTEIN, ACCORDING TO EXPERIMENTAL NMR DATA, AND DO NOT CONTRIBUTE TO SPECIFIC BINDING PROPERTIES OF THE CHIPS COMPLEX. PEPTIDE N-TERMINAL END BLOCKED BY AN ACETYL GROUP. PEPTIDE C-TERMINAL END BLOCKED BY A NH2 GROUP. CONTAINS TWO SULFATED TYROSINES (TYS) AT POSITIONS 11 AND 14.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Chemotaxis Inhibitory Protein of Staphylococcus Aureus (CHIPS) complexed to the N-terminus (7-28) of the C5aR receptor.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-15N HSQC
2422D 1H-13C HSQC
2522D 1H-13C HSQC
2622D 1H-13C HSQC
2723D CBCA(CO)NH
2823D HN(CA)CB
2923D HNCO
21023D HBHACBCA(CO)NH
21123D (H)CCH-TOCSY
21223D (H)CCH-TOCSY
11313D 1H-15N NOESY
21423D 1H-15N NOESY
11513D 1H-15N TOCSY
21623D 1H-13C NOESY
21723D 1H-13C NOESY
21822D 1H-1H NOESY
21922D 1H-1H TOCSY
22023D COCA(HN)
22123D-CNH-NOESY
22222D-HBHD aromatic
22322D-HBHE aromatic
22422D-CBHD aromatic
22522D-CBHE aromatic
22623D HNHA
22723D HNHB
NMR detailsText: STANDARD TRIPLE RESONANCE EXPERIMENTS WERE USED FOR ASSIGNMENT AND STRUCTURE DETERMINATION OF THE CHIPS PROTEIN. THE UNLABELLED PEPTIDE C5AR(P7-28S) IN THE COMPLEX HAS BEEN SOLVED BY MEANS OF ...Text: STANDARD TRIPLE RESONANCE EXPERIMENTS WERE USED FOR ASSIGNMENT AND STRUCTURE DETERMINATION OF THE CHIPS PROTEIN. THE UNLABELLED PEPTIDE C5AR(P7-28S) IN THE COMPLEX HAS BEEN SOLVED BY MEANS OF ISOTOPE-FILTERED 2D SPECTRA. TO EXTRACT INTERMOLECULAR NOE'S BETWEEN [15N,13C] LABELLED CHIPS PROTEIN AND UNLABELLED C5AR(P7-28S) PEPTIDE, SEVERAL 2D-13C-FILTERED NOESY AND 3D 13C-EDITED-13C-FILTERED NOESY SPECTRA WERE RECORDED AT 900 MHZ. FOR THE 3D FILTERED SPECTRA THE 13C-HSQC DETECTION STEP WAS OPTIMIZED BY RECORDING TWO SPECTRA, ONE WITH THE 13C CARRIER FREQUENCY PLACED IN THE AROMATIC REGION, AND ONE WITH THE 13C CARRIER FREQUENCY SET TO THE ALIFATIC REGION. THE MIXING TIME USED WAS 200 MS, TO FORCE A GOOD SENSITIVITY NECESSARY FOR THE COLLECTION OF A SUFFICIENT NUMBER OF INTERMOLECULAR NOE'S.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1[U-99% 15N]1
0.5 mMentity_21
20 mMsodium phosphate1
0.1 %sodium azide1
90 %H2O1
10 %D2O1
1.0 mMentity_1[U-99% 13C; U-99% 15N]2
1.0 mMentity_22
20 mMsodium phosphate2
0.1 %sodium azide2
90 %H2O2
10 %D2O2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 6.5 ambient 298 K
220 6.5 ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Bruker AvanceBrukerAVANCE9003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Sparky3.112Goddardpeak picking
Sparky3.112Goddardchemical shift assignment
CARA1.3.2Keller and Wuthrichpeak picking
CARA1.3.2Keller and Wuthrichchemical shift assignment
VNMRVariancollection
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
YASARAYasara Structure 8.3.3/WHATIFKrieger and Vriendstructure solution
YASARAYasara Structure 8.3.3/WHATIFKrieger and Vriendrefinement
SHIFTCALC2004Williamson and Refaeechemical shift calculation
PACES(PACES) Coggins and Zhouchemical shift assignment
RefinementMethod: simulated annealing, torsion angle dynamics, simulated annealing docking, molecular dynamics
Software ordinal: 1
Details: THE ARIA1.2 / CNS1.1 SIMULATED ANNEALING PROTOCOL HAS BEEN APPLIED TO SOLVE THE NMR STRUCTURE SEPARATELY FOR BOTH THE CHIPS PROTEIN AND THE C5AR(P7-28S) PEPTIDE, WHEN BOUND IN THE COMPLEX. ...Details: THE ARIA1.2 / CNS1.1 SIMULATED ANNEALING PROTOCOL HAS BEEN APPLIED TO SOLVE THE NMR STRUCTURE SEPARATELY FOR BOTH THE CHIPS PROTEIN AND THE C5AR(P7-28S) PEPTIDE, WHEN BOUND IN THE COMPLEX. 160 STRUCTURES OF CHIPS AND P7-28S PEPTIDE (IN ITS DESULFATED STATE) WERE CALCULATED EACH. THE 60 LOWEST-ENERGY ARIA STRUCTURES WERE INITIALLY SELECTED FOR THE PROTEIN. COORDINATES OF THE 60 PROTEIN STRUCTURES ARE SUBSEQENTLY AVERAGED OVER THE ENSEMBLE (BACKBONE RMSD RESIDUE 36-113 = 0.275 ANGSTROM), WITH SIDECHAINS REGULARLIZED BY SIMULATED ANNEALING ENERGY- MINIMIZATION. THIS AVERAGE STRUCTURE IS USED AS REFERENCE FOR SUBSEQUENT DOCKING WITH THE THREE LOWEST ENERGY CONFORMERS OF THE P7-28 PEPTIDE. THE THREE LOW-ENERGY PEPTIDE STRUCTURES WERE TAKEN DIRECTLY FROM THE ARIA GENERATED ENSEMBLE CALCULATED BASED ON PEPTIDE-PEPTIDE NOES FROM THE 900 MHZ [15N,13C]-FILTERED 2D NOESY. DISTANCE RESTRAINT MD-DOCKING BETWEEN THE EXPERIMENTALLY DERIVED ARIA1.2 STRUCTURE OF THE (SULPHATE PATCHED) PEPTIDE AND THE AVERAGE CHIPS PROTEIN STRUCTURE WAS PERFORMED USING THE YASARA STRUCTURE/WHATIF 8.3.3 TWINSET SOFTWARE. DOCKING WAS DRIVEN BY A LARGE NUMBER OF INTERMOLECULAR NOES BETWEEN PROTEIN AND PEPTIDE, DERIVED FROM VARIOUS ISOTOPE-FILTERED 2D- AND 3D-NMR EXPERIMENTS RUN ON THE COMPLEX. 25 FINAL STRUCTURES WERE SELECTED, BASED ON THE CRITERIA OF A COMBINATION OF LOW RESTRAINT VIOLATION ENERGY AND BEST PREDICTED BACK-CALCULATED PROTON CHEMICAL SHIFTS AT THE PEPTIDE-PROTEIN BINDING INTERFACE. THE SELECTED STRUCTURES WERE REFINED IN EXPLICIT SOLVENT. STEREOSPECIFIC ASSIGNMENTS AND FLOATING ASSIGNMENTS ARE INDICATED IN THE B-FACTOR COLUMN OF THE PDB COORDINATES. A VALUE OF 50 MEANS A FLOATING ASSIGNMENT HAS BEEN APPLIED TO THIS PROTON PAIR. A VALUE OF 75 INDICATES A STEREOSPECIFIC ASSIGNMENT OF METHYL AND METHYLENE PROTON PAIRS IN THE CORRESPONDING STRUCTURE MODEL.
NMR constraintsNOE constraints total: 4162 / NOE intraresidue total count: 1191 / NOE long range total count: 889 / NOE medium range total count: 386 / NOE sequential total count: 772 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 10 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 56
NMR representativeSelection criteria: lowest energy and chemical shift difference
NMR ensembleAverage torsion angle constraint violation: 0.427 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 130 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0.23 Å / Maximum torsion angle constraint violation: 79.56 ° / Maximum upper distance constraint violation: 2.41 Å / Torsion angle constraint violation method: Yasara internal
NMR ensemble rmsDistance rms dev: 0.0167 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more