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- PDB-2jkr: AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE -

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基本情報

登録情報
データベース: PDB / ID: 2jkr
タイトルAP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE
要素
  • (AP-2 COMPLEX SUBUNIT ...) x 4
  • CD4 PEPTIDE
キーワードENDOCYTOSIS / ALTERNATIVE SPLICING / PHOSPHOPROTEIN / PHOSPHORYLATION / PROTEIN TRANSPORT / ADAPTOR / MEMBRANE / TRANSPORT / COATED PIT / CELL MEMBRANE / LIPID-BINDING
機能・相同性
機能・相同性情報


LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling ...LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / T cell selection / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / MHC class II protein binding / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / positive regulation of kinase activity / signal sequence binding / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / Alpha-defensins / neurotransmitter secretion / endolysosome membrane / regulation of hematopoietic stem cell differentiation / regulation of T cell activation / response to vitamin D / extracellular matrix structural constituent / aorta development / Other interleukin signaling / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of calcium ion transport into cytosol / positive regulation of receptor internalization / macrophage differentiation / Generation of second messenger molecules / immunoglobulin binding / positive regulation of endocytosis / T cell differentiation / Co-inhibition by PD-1 / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / Binding and entry of HIV virion / negative regulation of protein localization to plasma membrane / coreceptor activity / vesicle-mediated transport / clathrin-coated pit / positive regulation of T cell proliferation / Neutrophil degranulation / positive regulation of interleukin-2 production / MHC class II antigen presentation / positive regulation of calcium-mediated signaling / VLDLR internalisation and degradation / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / secretory granule
類似検索 - 分子機能
Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Immunoglobulin C2-set / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Immunoglobulin C2-set domain / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Immunoglobulin / Immunoglobulin domain / Beta-Lactamase / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Armadillo-like helical / Alpha Horseshoe / Immunoglobulin subtype / Immunoglobulin / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
cDNA, FLJ79547, highly similar to T-cell surface glycoprotein CD4 / T-cell surface glycoprotein CD4 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu
類似検索 - 構成要素
生物種MUS MUSCULUS (ハツカネズミ)
HOMO SAPIENS (ヒト)
RATTUS NORVEGICUS (ドブネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.98 Å
データ登録者Owen, D.J. / McCoy, A.J. / Kelly, B.T. / Evans, P.R.
引用ジャーナル: Nature / 年: 2008
タイトル: A Structural Explanation for the Binding of Endocytic Dileucine Motifs by the Ap2 Complex.
著者: Kelly, B.T. / Mccoy, A.J. / Spaete, K. / Miller, S.E. / Evans, P.R. / Hoening, S. / Owen, D.J.
履歴
登録2008年8月29日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02008年10月28日Provider: repository / タイプ: Initial release
改定 1.12012年6月20日Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
改定 1.22023年12月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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

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集合体

登録構造単位
A: AP-2 COMPLEX SUBUNIT ALPHA-2
B: AP-2 COMPLEX SUBUNIT BETA-1
E: AP-2 COMPLEX SUBUNIT BETA-1
I: AP-2 COMPLEX SUBUNIT SIGMA-1
L: AP-2 COMPLEX SUBUNIT ALPHA-2
M: AP-2 COMPLEX SUBUNIT MU-1
P: CD4 PEPTIDE
Q: CD4 PEPTIDE
S: AP-2 COMPLEX SUBUNIT SIGMA-1
U: AP-2 COMPLEX SUBUNIT MU-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)412,87541
ポリマ－409,89710
非ポリマー2,97831
水34219
1
A: AP-2 COMPLEX SUBUNIT ALPHA-2
B: AP-2 COMPLEX SUBUNIT BETA-1
M: AP-2 COMPLEX SUBUNIT MU-1
P: CD4 PEPTIDE
S: AP-2 COMPLEX SUBUNIT SIGMA-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,29319
ポリマ－204,9495
非ポリマー1,34514
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area23280 Å2
ΔGint-260.1 kcal/mol
Surface area68870 Å2
手法PISA
2
E: AP-2 COMPLEX SUBUNIT BETA-1
I: AP-2 COMPLEX SUBUNIT SIGMA-1
L: AP-2 COMPLEX SUBUNIT ALPHA-2
Q: CD4 PEPTIDE
U: AP-2 COMPLEX SUBUNIT MU-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,58222
ポリマ－204,9495
非ポリマー1,63317
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area24020 Å2
ΔGint-303.8 kcal/mol
Surface area68680 Å2
手法PISA
単位格子
Length a, b, c (Å)169.900, 169.900, 321.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:623 )
211CHAIN L AND (RESSEQ 3:623 )
112CHAIN B AND (RESSEQ 12:582 )
212CHAIN E AND (RESSEQ 12:582 )
113CHAIN M AND (RESSEQ 1:141 OR RESSEQ 159:222 OR RESSEQ 232:435 )
213CHAIN U AND (RESSEQ 1:141 OR RESSEQ 159:222 OR RESSEQ 232:435 )
114CHAIN S AND (RESSEQ 1:142 )
214CHAIN I AND (RESSEQ 1:142 )
115CHAIN P AND (RESSEQ 2:10 )
215CHAIN Q AND (RESSEQ 2:10 )

NCSアンサンブル:
ID
1
2
3
4
5

NCS oper: (Code: given
Matrix: (0.005, 0.998, 0.062), (0.998, -0.009, 0.056), (0.057, 0.062, -0.996)
ベクター: 6.985, 2.861, -160.492)

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要素

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AP-2 COMPLEX SUBUNIT ... , 4種, 8分子 ALBEISMU

#1: タンパク質 AP-2 COMPLEX SUBUNIT ALPHA-2 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT ALPHA-2 / ALPHA2-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN ALPHA C SUBUNIT / ALPHA-ADAPTIN C / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 ALPHA-C LARGE CHAIN / 100 KDA COATED VESICLE PROTEIN C


分子量: 69786.406 Da / 分子数: 2 / 断片: ALPHA CHAIN, RESIDUES 1-620 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / プラスミド: PMW172K / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P17427
#2: タンパク質 AP-2 COMPLEX SUBUNIT BETA-1 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA2-ADAPTIN / BETA-ADAPTIN / PLASMA ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA2-ADAPTIN / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B


分子量: 66953.195 Da / 分子数: 2 / 断片: BETA2 CHAIN, RESIDUES 1-591 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PMW172H6 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P63010
#3: タンパク質 AP-2 COMPLEX SUBUNIT SIGMA-1 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA2-ADAPTIN / SIGMA-ADAPTIN 3B / ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA2-ADAPTIN / SIGMA-ADAPTIN 3B / PLASMA MEMBRANE ADAPTOR AP-2 17 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN 2 SMALL CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP17 / CLATHRIN COAT-ASSOCIATED PROTEIN AP17


分子量: 17038.688 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / プラスミド: PMW172K / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62743
#4: タンパク質 AP-2 COMPLEX SUBUNIT MU-1 / AP2 / MU2-ADAPTIN / AP-2 MU-2 CHAIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ...AP2 / MU2-ADAPTIN / AP-2 MU-2 CHAIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED PROTEIN AP50


分子量: 49726.641 Da / 分子数: 2 / 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: PMW172H6 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P84092

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タンパク質・ペプチド , 1種, 2分子 PQ

#5: タンパク質・ペプチド CD4 PEPTIDE / CDNA / FLJ79547 / HIGHLY SIMILAR TO T-CELL SURFACE GLYCOPROTEIN CD4


分子量: 1443.629 Da / 分子数: 2 / 断片: RESIDUES 252-262 / 由来タイプ: 合成
詳細: RMS(P)EIKRLLSE. RESIDUE 3 IS PHOSPHOSERINE THOUGH NO PHOSPHORYL GROUP WAS VISIBLE IN THE STRUCTURE
由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: B0AZV7, UniProt: P01730*PLUS

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非ポリマー , 2種, 50分子

#6: 化合物...
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 31 / 由来タイプ: 合成 / 式: SO4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 19 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
配列の詳細SEQUENCE OF CHAINS A AND L IS FROM MOUSE BUT HAS GLU INSERTED AT POSITION 272

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.95 Å3/Da / 溶媒含有率: 57.96 % / 解説: NONE
結晶化pH: 6.5
詳細: 1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE ...詳細: 1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.976
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2008年5月23日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.976 Å / 相対比: 1
反射解像度: 3→51 Å / Num. obs: 96683 / % possible obs: 100 % / Observed criterion σ(I): -9 / 冗長度: 8.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.6
反射 シェル解像度: 3→3.16 Å / 冗長度: 9 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
MOSFLMデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2VGL

2vgl


解像度: 2.98→50.95 Å / SU ML: 0.44 / σ(F): 1.23 / 位相誤差: 27.79 / 立体化学のターゲット値: ML
詳細: 28 TLS GROUPS. THE PHOSPHATE OF THE PHOSPHOSERINE RESIDUES P3 AND Q3 WERE NOT VISIBLE, SO THE RESIDUE WAS MODELLED AS SERINE
Rfactor反射数%反射
Rfree0.26 9168 5 %
Rwork0.199 --
obs0.202 183747 99.9 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 50.75 Å2 / ksol: 0.33 e/Å3
精密化ステップサイクル: LAST / 解像度: 2.98→50.95 Å
タンパク質核酸リガンド溶媒全体
原子数27946 0 155 19 28120
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0128556
X-RAY DIFFRACTIONf_angle_d1.37738646
X-RAY DIFFRACTIONf_dihedral_angle_d23.57317614
X-RAY DIFFRACTIONf_chiral_restr0.0914472
X-RAY DIFFRACTIONf_plane_restr0.0054892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A4885X-RAY DIFFRACTIONPOSITIONAL
12L4885X-RAY DIFFRACTIONPOSITIONAL0.054
21B4527X-RAY DIFFRACTIONPOSITIONAL
22E4527X-RAY DIFFRACTIONPOSITIONAL0.05
31M3288X-RAY DIFFRACTIONPOSITIONAL
32U3288X-RAY DIFFRACTIONPOSITIONAL0.046
41S1200X-RAY DIFFRACTIONPOSITIONAL
42I1200X-RAY DIFFRACTIONPOSITIONAL0.048
51P73X-RAY DIFFRACTIONPOSITIONAL
52Q73X-RAY DIFFRACTIONPOSITIONAL0.042
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9782-3.0120.39162930.3645640X-RAY DIFFRACTION97
3.012-3.04750.3972960.33755855X-RAY DIFFRACTION100
3.0475-3.08460.34233050.32475834X-RAY DIFFRACTION100
3.0846-3.12370.38073020.32315817X-RAY DIFFRACTION100
3.1237-3.16480.37052770.30915873X-RAY DIFFRACTION100
3.1648-3.20810.36942860.2955848X-RAY DIFFRACTION100
3.2081-3.25390.34983300.29825806X-RAY DIFFRACTION100
3.2539-3.30250.39422840.28115816X-RAY DIFFRACTION100
3.3025-3.35410.32562410.2635863X-RAY DIFFRACTION100
3.3541-3.40910.34473120.26345878X-RAY DIFFRACTION100
3.4091-3.46780.30683250.24655802X-RAY DIFFRACTION100
3.4678-3.53090.29963370.22725799X-RAY DIFFRACTION100
3.5309-3.59880.28072950.20745821X-RAY DIFFRACTION100
3.5988-3.67220.28393480.20775782X-RAY DIFFRACTION100
3.6722-3.7520.25953130.19275857X-RAY DIFFRACTION100
3.752-3.83930.26672740.17685832X-RAY DIFFRACTION100
3.8393-3.93530.27083240.17565837X-RAY DIFFRACTION100
3.9353-4.04160.20952800.1585868X-RAY DIFFRACTION100
4.0416-4.16050.24362970.15865777X-RAY DIFFRACTION100
4.1605-4.29470.22883300.14725844X-RAY DIFFRACTION100
4.2947-4.44810.19942910.13125834X-RAY DIFFRACTION100
4.4481-4.62610.17553420.12245760X-RAY DIFFRACTION100
4.6261-4.83650.20482670.13825877X-RAY DIFFRACTION100
4.8365-5.09130.22952910.14625827X-RAY DIFFRACTION100
5.0913-5.40990.24383150.15415840X-RAY DIFFRACTION100
5.4099-5.82710.24383720.16895753X-RAY DIFFRACTION100
5.8271-6.41250.27022950.17315820X-RAY DIFFRACTION100
6.4125-7.3380.24153130.16965836X-RAY DIFFRACTION100
7.338-9.23620.1723430.12685791X-RAY DIFFRACTION100
9.2362-50.96110.16112900.16535792X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3979-0.4871-1.16950.41150.18960.92440.57280.1508-0.3755-0.274-0.0735-0.08130.25260.8258-0.27840.62370.1645-0.27181.01150.01540.77681.1375-24.6458-97.352
21.7507-0.6169-0.95280.46180.29571.29640.4661-0.27580.2028-0.0290.1067-0.4784-0.12190.1249-0.46310.2835-0.04570.03880.2809-0.05610.498873.0662-4.1883-107.4668
34.7861-0.8613-1.6220.7166-0.36860.28460.76661.69220.9211-0.7854-0.5567-0.4753-0.6777-0.3769-0.22870.25960.20520.15480.58240.21770.2348.71841.704-118.5513
42.2981-0.2301-1.30910.99481.17992.13610.12890.4202-0.2870.1036-0.305-0.0272-0.1116-0.38030.12670.1643-0.0183-0.0310.2699-0.06170.08329.4186-8.1405-98.005
51.90140.0486-1.14831.12861.5634-1.2848-0.4165-0.102-0.00810.3680.1277-0.0971-0.09230.07630.18990.55790.1455-0.08370.3820.05670.04715.0284-0.5358-54.7729
60.9429-0.51370.77421.08010.1994-3.34940.7190.4488-0.3502-0.8104-0.80390.0480.23720.19450.0330.36740.4745-0.6170.02520.8954-0.745630.21425.3706-88.5266
73.049-0.00350.31240.47120.14410.26910.64640.0449-1.06180.1143-0.67820.3507-0.3008-0.1605-0.00060.5851-0.2091-0.04180.7488-0.191.059667.8467-46.5462-83.0508
80.91050.0887-0.4512-0.70010.01650.9763-0.29430.0986-0.59110.16790.04040.1017-0.0604-0.05250.20150.53170.0148-0.04180.3198-0.08420.553355.3141-52.0918-58.2339
9-0.0629-0.5540.57522.09330.79161.5757-0.0951-0.09520.16020.00140.2234-0.42690.1634-0.13720.02020.29730.0671-0.19080.04370.05490.324152.9595-16.2654-37.402
101.702-0.8694-1.35730.8040.8576-0.0397-0.00430.0040.14470.14990.1782-0.13180.0134-0.0475-0.08510.4563-0.0283-0.21190.23730.05540.151229.145116.5102-48.4585
111.7532-0.5229-1.21080.7455-1.15221.21170.2901-0.2806-0.15710.29750.15930.9488-0.19560.1203-0.32050.4496-0.1338-0.00170.32110.02460.514340.8097-22.4292-43.4284
121.6178-0.49730.32380.7797-0.51870.80920.19050.3609-0.26030.1812-0.0081-0.2244-0.1181-0.1318-0.14250.36150.042-0.19150.2913-0.01350.416760.5843-29.2918-61.9924
131.1112-0.46881.37830.18230.10431.44980.00020.27830.23930.0994-0.123-0.16980.11610.2560.09270.4021-0.0685-0.11520.41970.14470.393253.70714.8797-70.8161
142.8539-0.057-1.25890.38961.13150.86090.1005-0.429-0.3942-0.34820.1062-0.04510.02810.1148-0.15360.38080.013-0.05710.3080.02330.266357.0681-17.3492-101.2189
150.13060.5086-0.35120.65031.1506-0.1725-0.0608-0.0127-0.20050.56250.06840.2717-0.4156-0.0101-0.01860.5670.20920.10760.19570.25340.404-23.50178.1872-59.7796
160.6949-0.6894-0.52361.36860.76431.50650.00770.03590.2584-0.03540.3777-0.4167-0.04230.08-0.31190.1397-0.06620.03620.1726-0.01360.2961-3.822269.2143-48.8999
170.7297-0.5557-0.27781.49571.43752.8217-0.7695-0.8087-0.2970.81220.881-0.13810.94390.2259-0.16720.43360.1056-0.23280.0404-0.2486-0.20181.134744.1123-39.1287
181.2283-0.1305-0.91.71890.68921.1289-0.36770.0621-0.08820.32170.09920.09570.41980.15780.20930.3671-0.01550.05770.1970.04920.0559-7.442826.3393-61.5406
192.1135-1.1347-1.26562.06750.6304-1.69050.19410.2998-0.08140.0851-0.35780.0487-0.217-0.06380.08510.43410.10050.01930.48380.07010.02522.901414.7442-105.0478
20-0.8858-0.145-1.90961.9407-0.5779-3.3138-0.32610.0897-0.13031.05340.18820.1218-0.27371.35770.19870.43880.0784-0.39870.48540.098-0.182826.63227.3865-68.7498
212.54611.0449-0.4632-0.90220.90220.4119-1.01060.4564-0.9398-0.10230.30970.39480.0250.29350.49160.9314-0.23510.01770.80340.05011.2685-44.435766.0929-76.0369
22-0.473-0.251-0.18310.99360.90751.3751-0.07780.0335-0.03140.1569-0.1870.81420.09880.04270.19770.28970.05560.13980.53310.05250.4539-48.825454.9892-101.7502
231.8030.0112-0.83660.1264-0.48160.83570.1562-0.0750.147-0.0357-0.022-0.02160.0546-0.1639-0.09510.2070.10530.0450.30390.21010.2956-12.035253.544-120.9226
241.0904-0.2726-0.82451.67831.5007-0.48880.17020.40960.1464-0.1174-0.0473-0.3012-0.1497-0.016-0.07930.28130.0512-0.00030.30590.17990.124520.10328.9414-109.635
256.64912.03860.171.62910.31782.357-0.05010.2088-2.0182-0.16660.3924-0.3015-0.51430.1852-0.15060.363-0.2080.13590.5325-0.03650.7368-18.539741.1319-115.8811
260.5803-0.46030.10041.1594-0.60491.1153-0.01470.16140.35230.48350.14780.11820.05520.02580.07220.22540.0440.1270.21440.19390.2245-26.095760.0578-96.6076
270.6043-0.38490.33350.1575-0.2656-0.3765-0.07950.11370.03390.31670.122-0.0418-0.2762-0.0448-0.04250.43430.0055-0.02660.31460.07490.14217.499952.1163-86.5212
280.4308-0.578-0.74341.54680.37040.36290.2232-0.15980.0725-0.5117-0.0260.2333-0.12750.1307-0.13720.3225-0.03550.02530.34370.05810.1367-16.610853.958-57.0629
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:50)
2X-RAY DIFFRACTION2CHAIN A AND RESID 51:186)
3X-RAY DIFFRACTION3CHAIN A AND RESID 187:245)
4X-RAY DIFFRACTION4CHAIN A AND RESID 246:457)
5X-RAY DIFFRACTION5CHAIN A AND RESID 458:610)
6X-RAY DIFFRACTION6CHAIN A AND RESID 611:999)
7X-RAY DIFFRACTION7CHAIN B AND RESID 1:51)
8X-RAY DIFFRACTION8CHAIN B AND RESID 52:206)
9X-RAY DIFFRACTION9CHAIN B AND RESID 207:414)
10X-RAY DIFFRACTION10CHAIN B AND RESID 415:549)
11X-RAY DIFFRACTION11CHAIN B AND RESID 550:999)
12X-RAY DIFFRACTION12CHAIN M AND RESID 1:159)
13X-RAY DIFFRACTION13CHAIN M AND RESID 160:435)
14X-RAY DIFFRACTION14CHAIN S AND RESID 1:142) OR CHAIN P
15X-RAY DIFFRACTION15CHAIN L AND RESID 1:50)
16X-RAY DIFFRACTION16CHAIN L AND RESID 51:186)
17X-RAY DIFFRACTION17CHAIN L AND RESID 187:245)
18X-RAY DIFFRACTION18CHAIN L AND RESID 246:457)
19X-RAY DIFFRACTION19CHAIN L AND RESID 458:610)
20X-RAY DIFFRACTION20CHAIN L AND RESID 611:999)
21X-RAY DIFFRACTION21CHAIN E AND RESID 1:51)
22X-RAY DIFFRACTION22CHAIN E AND RESID 52:206)
23X-RAY DIFFRACTION23CHAIN E AND RESID 207:414)
24X-RAY DIFFRACTION24CHAIN E AND RESID 415:549)
25X-RAY DIFFRACTION25CHAIN E AND RESID 550:999)
26X-RAY DIFFRACTION26CHAIN U AND RESID 1:159)
27X-RAY DIFFRACTION27CHAIN U AND RESID 160:435)
28X-RAY DIFFRACTION28CHAIN I AND RESID 1:142) OR CHAIN Q

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万見について

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お知らせ

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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

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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

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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

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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

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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。

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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