[日本語] English
万見
- PDB-2k3u: Structure of the tyrosine-sulfated C5a receptor N-terminus in com... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 2k3u
タイトルStructure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.
要素
  • C5a anaphylatoxin chemotactic receptor 1
  • Chemotaxis inhibitory protein
キーワードIMMUNE SYSTEM / Chemotaxis Inhibitory Protein (CHIPS) / sulfated tyrosine / GPCR membrane protein C5aR / anaphylotoxin C5a / Staphylococcus Aureus / complement cascade / Secreted / Virulence
機能・相同性
機能・相同性情報


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 / positive regulation of epithelial cell proliferation / Regulation of Complement cascade / astrocyte activation / G protein-coupled receptor activity / 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 / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / 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
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
Chemotaxis inhibitory protein / C5a anaphylatoxin chemotactic receptor 1
類似検索 - 構成要素
生物種Staphylococcus aureus subsp. aureus str. Newman (黄色ブドウ球菌)
Homo sapiens (ヒト)
手法溶液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.
データ登録者Ippel, J.H. / Bunschoten, A. / Kemmink, J. / Liskamp, R.
引用ジャーナル: J.Biol.Chem. / 年: 2009
タイトル: Structure of the Tyrosine-sulfated C5a Receptor N Terminus in Complex with Chemotaxis Inhibitory Protein of Staphylococcus aureus.
著者: Ippel, J.H. / de Haas, C.J. / Bunschoten, A. / van Strijp, J.A. / Kruijtzer, J.A. / Liskamp, R.M. / Kemmink, J.
履歴
登録2008年5月16日登録サイト: BMRB / 処理サイト: RCSB
改定 1.02009年3月10日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22020年2月19日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
カテゴリ: 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
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: 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

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: Chemotaxis inhibitory protein
B: C5a anaphylatoxin chemotactic receptor 1


分子量 (理論値)分子数
合計 (水以外)13,1872
ポリマ－13,1872
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)25 / 130structures with the lowest energy
代表モデルモデル #1lowest energy and chemical shift difference

-
要素

#1: タンパク質 Chemotaxis inhibitory protein


分子量: 10475.967 Da / 分子数: 1 / 断片: Chemotaxis inhibiting protein CHIPS(59-149). / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus subsp. aureus str. Newman (黄色ブドウ球菌)
遺伝子: chp / プラスミド: pRSET B / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): DE3 / 参照: UniProt: A6QIG7
#2: タンパク質・ペプチド C5a anaphylatoxin chemotactic receptor 1


分子量: 2710.813 Da / 分子数: 1 / 断片: C5aR(P7-28S) / 由来タイプ: 合成
詳細: Fmoc/tBu-based peptide synthesis. Sulfated tyrosines 11 and 14 were introduced as Fmoc-2-chlorotrityl protected building blocks.
由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P21730
構成要素の詳細AMBIGUOUS 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.

-
実験情報

-
実験

実験手法: 溶液NMR
詳細: Chemotaxis Inhibitory Protein of Staphylococcus Aureus (CHIPS) complexed to the N-terminus (7-28) of the C5aR receptor.
NMR実験
Conditions-IDExperiment-IDSolution-IDタイプ
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実験の詳細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 ...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.

-
試料調製

詳細
Solution-ID内容溶媒系
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
試料
濃度 (mg/ml)構成要素Isotopic 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
試料状態
Conditions-IDイオン強度pH圧 (kPa)温度 (K)
120 6.5 ambient 298 K
220 6.5 ambient 298 K

-
NMR測定

NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Bruker AvanceBrukerAVANCE9003

-
解析

NMR software
名称バージョン開発者分類
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospin解析
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax解析
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxデータ解析
ARIA1.2Linge, O'Donoghue and Nilges精密化
ARIA1.2Linge, O'Donoghue and Nilges構造決定
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Read構造決定
Sparky3.112Goddardpeak picking
Sparky3.112Goddardchemical shift assignment
CARA1.3.2Keller and Wuthrichpeak picking
CARA1.3.2Keller and Wuthrichchemical shift assignment
VNMRVariancollection
MOLMOLKoradi, Billeter and Wuthrichデータ解析
ProcheckNMRLaskowski and MacArthurデータ解析
TALOSCornilescu, Delaglio and Bax構造決定
TALOSCornilescu, Delaglio and Baxgeometry optimization
YASARAYasara Structure 8.3.3/WHATIFKrieger and Vriend構造決定
YASARAYasara Structure 8.3.3/WHATIFKrieger and Vriend精密化
SHIFTCALC2004Williamson and Refaeechemical shift calculation
PACES(PACES) Coggins and Zhouchemical shift assignment
精密化手法: simulated annealing, torsion angle dynamics, simulated annealing docking, molecular dynamics
ソフトェア番号: 1
詳細: 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. ...詳細: 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
代表構造選択基準: lowest energy and chemical shift difference
NMRアンサンブルAverage torsion angle constraint violation: 0.427 °
コンフォーマー選択の基準: structures with the lowest energy
計算したコンフォーマーの数: 130 / 登録したコンフォーマーの数: 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

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る