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- PDB-2xkx: Single particle analysis of PSD-95 in negative stain -

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基本情報

登録情報
データベース: PDB / ID: 2xkx
タイトルSingle particle analysis of PSD-95 in negative stain
要素DISKS LARGE HOMOLOG 4
キーワードSTRUCTURAL PROTEIN / SCAFFOLD PROTEIN / MEMBRANE ASSOCIATED GUANYLATE KINASE
機能・相同性
機能・相同性情報


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / protein localization to synapse / vocalization behavior / cerebellar mossy fiber / proximal dendrite / LGI-ADAM interactions / cellular response to potassium ion / Trafficking of AMPA receptors / dendritic branch / neuron spine / negative regulation of receptor internalization / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / frizzled binding / juxtaparanode region of axon / dendritic spine organization / neuron projection terminus / postsynaptic neurotransmitter receptor diffusion trapping / acetylcholine receptor binding / Synaptic adhesion-like molecules / positive regulation of synapse assembly / regulation of NMDA receptor activity / RAF/MAP kinase cascade / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / extrinsic component of cytoplasmic side of plasma membrane / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / AMPA glutamate receptor complex / social behavior / excitatory synapse / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / dendrite cytoplasm / cell periphery / synaptic membrane / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / kinase binding / cerebral cortex development / cell-cell adhesion / cell-cell junction / cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / protein-containing complex assembly / basolateral plasma membrane / chemical synaptic transmission / protein phosphatase binding / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Disks large homolog 4
類似検索 - 構成要素
生物種RATTUS NORVEGICUS (ドブネズミ)
手法電子顕微鏡法 / 溶液散乱 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 22.9 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B
データ登録者Fomina, S. / Howard, T.D. / Sleator, O.K. / Golovanova, M. / O'Ryan, L. / Leyland, M.L. / Grossmann, J.G. / Collins, R.F. / Prince, S.M.
引用
ジャーナル: Biochim Biophys Acta / 年: 2011
タイトル: Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95.
著者: Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince /
要旨: The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using ...The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron micrographs corresponding to a 1:1 complex, a large self-enclosed tetrad complex and extended chains of linked channel domains. Using models derived from small angle X-ray scattering experiments in which high resolution structures from X-ray crystallographic and Nuclear Magnetic Resonance studies are positioned, the envelopes from single particle analysis can be resolved as a Kir2.1NC(4):PSD-95 complex and a tetrad of this unit (Kir2.1NC(4):PSD-95)(4). The tetrad complex shows the close association of the Kir2.1 cytoplasmic domains and the influence of PSD-95 mediated self-assembly on the clustering of these channels.
#1: ジャーナル: J Mol Biol / 年: 2003
タイトル: Supramodular structure and synergistic target binding of the N-terminal tandem PDZ domains of PSD-95.
著者: Jia-Fu Long / Hidehito Tochio / Ping Wang / Jing-Song Fan / Carlo Sala / Martin Niethammer / Morgan Sheng / Mingjie Zhang /
要旨: PDZ domain proteins play critical roles in binding, clustering and subcellular targeting of membrane receptors and ion channels. PDZ domains in multi-PDZ proteins often are arranged in groups with ...PDZ domain proteins play critical roles in binding, clustering and subcellular targeting of membrane receptors and ion channels. PDZ domains in multi-PDZ proteins often are arranged in groups with highly conserved spacing and intervening sequences; however, the functional significance of such tandem arrangements of PDZs is unclear. We have solved the three-dimensional structure of the first two PDZ domains of postsynaptic density protein-95 (PSD-95 PDZ1 and PDZ2), which are closely linked to each other in the PSD-95 family of scaffold proteins. The two PDZs have limited freedom of rotation and their C-terminal peptide-binding grooves are aligned with each other with an orientation preference for binding to pairs of C termini extending in the same direction. Increasing the spacing between PDZ1 and PDZ2 resulted in decreased binding between PDZ12 and its dimeric targets. The same mutation impaired the functional ability of PSD-95 to cluster Kv1.4 potassium channels in heterologous cells. The data presented provide a molecular basis for preferential binding of PSD-95 to multimeric membrane proteins with appropriate C-terminal sequences.
#2: ジャーナル: J Mol Biol / 年: 2000
タイトル: Solution structure and backbone dynamics of the second PDZ domain of postsynaptic density-95.
著者: H Tochio / F Hung / M Li / D S Bredt / M Zhang /
要旨: The second PDZ domain of postsynaptic density-95 (PSD-95 PDZ2) plays a critical role in coupling N-methyl-D-aspartate receptors to neuronal nitric oxide synthase (nNOS). In this work, the solution ...The second PDZ domain of postsynaptic density-95 (PSD-95 PDZ2) plays a critical role in coupling N-methyl-D-aspartate receptors to neuronal nitric oxide synthase (nNOS). In this work, the solution structure of PSD-95 PDZ2 was determined to high resolution by NMR spectroscopy. The structure of PSD-95 PDZ2 was compared in detail with that of alpha1-syntrophin PDZ domain, as the PDZ domains share similar target interaction properties. The interaction of the PSD-95 PDZ2 with a carboxyl-terminal peptide derived from a cytoplasmic protein CAPON was studied by NMR titration experiments. Complex formation between PSD-95 PDZ2 and the nNOS PDZ was modelled on the basis of the crystal structure of the alpha1-syntrophin PDZ/nNOS PDZ dimer. We found that the prolonged loop connecting the betaB and betaC strands of PSD-95 PDZ2 is likely to play a role in both the binding of the carboxyl-terminal peptide and the nNOS beta-finger. Finally, the backbone dynamics of the PSD-95 PDZ2 in the absence of bound peptide were studied using a model-free approach. The "GLGF"-loop and the loop connecting alphaB and betaF of the protein display some degree of flexibility in solution. The rest of the protein is rigid and lacks detectable slow time-scale (microseconds to milliseconds) motions. In particular, the loop connecting betaB and betaC loop adopts a well-defined, rigid structure in solution. It appears that the loop adopts a pre-aligned conformation for the PDZ domain to interact with its targets.
#3: ジャーナル: To be Published
タイトル: Structure of the Third Pdz Domain of Psd-95 Protein Complexed with Kketwv Peptide Ligand
著者: Saro, D. / Wawrzak, Z. / Martin, P. / Vickrey, J. / Paredes, A. / Kovari, L. / Spaller, M.
#4: ジャーナル: Mol Cell / 年: 2001
タイトル: Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins.
著者: A W McGee / S R Dakoji / O Olsen / D S Bredt / W A Lim / K E Prehoda /
要旨: Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit ...Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit signaling proteins, as well as a Src homology 3 (SH3) and a guanylate kinase-like (GK) domain, implicated in scaffold oligomerization. The crystal structure of the SH3-GK module from PSD-95 reveals that these domains form an integrated unit: the SH3 fold comprises noncontiguous sequence elements divided by a hinge region and the GK domain. These elements compose two subdomains that can assemble in either an intra- or intermolecular fashion to complete the SH3 fold. We propose a model for MAGUK oligomerization in which complementary SH3 subdomains associate by 3D domain swapping. This model provides a possible mechanism for ligand regulation of oligomerization.
履歴
登録2010年7月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02011年7月20日Provider: repository / タイプ: Initial release
改定 1.12011年8月10日Group: Database references
改定 1.22017年8月30日Group: Data collection / カテゴリ: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
改定 1.32019年11月13日Group: Data collection / Other / カテゴリ: cell / Item: _cell.Z_PDB
改定 1.42024年5月8日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-1761
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: DISKS LARGE HOMOLOG 4
B: DISKS LARGE HOMOLOG 4


分子量 (理論値)分子数
合計 (水以外)160,4062
ポリマ－160,4062
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA

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要素

#1: タンパク質 DISKS LARGE HOMOLOG 4 / POSTSYNAPTIC DENSITY PROTEIN 95 / PSD-95 / SYNAPSE-ASSOCIATED PROTEIN 90 / SAP-90 / SAP90 / 座標モデル: Cα原子のみ


分子量: 80203.047 Da / 分子数: 2 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) RATTUS NORVEGICUS (ドブネズミ) / プラスミド: PGEX-6P / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P31016
構成要素の詳細ENGINEERED RESIDUE IN CHAIN A, THR 9 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 23 TO LYS ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, THR 9 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 23 TO LYS ENGINEERED RESIDUE IN CHAIN A, GLN 594 TO ARG

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実験情報

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実験

実験
手法
電子顕微鏡法
溶液散乱
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: RAT PSD-95 / タイプ: COMPLEX
緩衝液名称: 20MM TRIS/HCL, 5MM DTT, 1MM EDTA, / pH: 7.5 / 詳細: 20MM TRIS/HCL, 5MM DTT, 1MM EDTA,
試料濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO
染色タイプ: NEGATIVE / 染色剤: Uranyl Acetate
試料支持詳細: CARBON

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データ収集

顕微鏡モデル: FEI TECNAI 10 / 詳細: LOW DOSE
電子銃電子線源: TUNGSTEN HAIRPIN / 加速電圧: 100 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 43000 X / 最大 デフォーカス（公称値）: 2250 nm / 最小 デフォーカス（公称値）: 900 nm / Cs: 3.6 mm
試料ホルダ傾斜角・最大: 0.1 ° / 傾斜角・最小: 0 °
撮影フィルム・検出器のモデル: GENERIC FILM
画像スキャンデジタル画像の数: 2
放射波長相対比: 1
Soln scatter
タイプIDBuffer nameConc. range (mg/ml)Data reduction software list検出器タイプMean guiner radius (nm)Num. of time framesProtein lengthSource beamlineSource classSource type温度 (K)
x-ray120MM TRIS/HCL, 5MM DTT, 1MM EDTA, PH 7.5, 50MM NACL1-8OTOKO/GNOMMULTIWIRE 2-D4.366414STATION 2.1YSRS277
modelling2

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解析

EMソフトウェア
ID名称カテゴリ
1UCSF Chimeraモデルフィッティング
2EMAN３次元再構成
CTF補正詳細: PARAMETERS DETERMINED USING SCATTERING CURVE
対称性点対称性: C1 (非対称)
3次元再構成解像度: 22.9 Å / 粒子像の数: 7854 / ピクセルサイズ（公称値）: 3.667 Å / ピクセルサイズ（実測値）: 3.667 Å
詳細: THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, ...詳細: THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, THIS COMPOSITE STRUCTURE IS THEN FITTED INTO AN EM MAP. DOMAINS PROVIDED BY X-RAY, NMR POSITIONED BY BUNCH ( PETOUKHOV, M. V. & SVERGUN, D. I. (2005). GLOBAL RIGID BODY MODELING OF MACROMOLECULAR COMPLEXES AGAINST SMALL- ANGLE SCATTERING DATA. BIOPHYS J 89, 1237-50.) REFINEMENT SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1761. (DEPOSITION ID: 7384).
対称性のタイプ: POINT
原子モデル構築プロトコル: RIGID BODY FIT / 空間: REAL
詳細: METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS- ...詳細: METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS-CORRELATION WITH THE EXPERIMENTAL MAP. THE COORDINATES WERE THEN REPLACED IN THE CALCULATED MAP TO GENERATE THE FINAL ENTRY. REFINEMENT PROTOCOL--DOCKED USING CHIMERA
原子モデル構築
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameタイプ
11IU0

1iu0

11IU01PDBexperimental model
21QLC

1qlc

11QLC2PDBexperimental model
31TP5

1tp5

11TP53PDBexperimental model
41KJW

1kjw

11KJW4PDBexperimental model
精密化最高解像度: 22.9 Å
精密化ステップサイクル: LAST / 最高解像度: 22.9 Å
タンパク質核酸リガンド溶媒全体
原子数1439 0 0 0 1439
Soln scatter model手法: RIGID BODY MODELLING
コンフォーマー選択の基準: TWO MAJOR CONFORMERS WERE PRESENT IN THE POOL OF REFINED SAXS MODELS CHAIN A REPRESENTS THE BEST AGREEMENT WITH THE EXPERIMENTAL SAXS DATA (CHI=3.3). CHAIN B IS ...コンフォーマー選択の基準: TWO MAJOR CONFORMERS WERE PRESENT IN THE POOL OF REFINED SAXS MODELS CHAIN A REPRESENTS THE BEST AGREEMENT WITH THE EXPERIMENTAL SAXS DATA (CHI=3.3). CHAIN B IS REPRESENTATIVE OF THE SECOND CONFORMATION (CHI=3.8).
詳細: NUMBER OF TIME FRAMES USED 24 (60S, 4.25M CAMERA), 40(60S, 1M CAMERA). PROTEIN CONCENTRATION 1 MG/ML (4.25M CAMERA) 8 MG/ML (1M CAMERA)
Entry fitting list: PROGRAM PRE-BUNCH 1IU0/1QLC/1TP5/1KJW + SEQUENCE DATA
Num. of conformers calculated: 20 / Num. of conformers submitted: 2 / Software author list: PETOUKHOV, M. V. & SVERGUN, D. I. / Software list: SASREF7/BUNCH8

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