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- PDB-5v6y: Crystal structure of the human CLR:RAMP1 extracellular domain het... -

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基本情報

登録情報
データベース: PDB / ID: 5v6y
タイトルCrystal structure of the human CLR:RAMP1 extracellular domain heterodimer with bound high-affinity and altered selectivity adrenomedullin variant
要素
  • ADM
  • Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
キーワードTRANSPORT PROTEIN / MEMBRANE PROTEIN / class B G protein-coupled receptor / GPCR / calcitonin family peptide / TRANSPORT PROTEIN - MEMBRANE PROTEIN complex
機能・相同性
機能・相同性情報


adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / calcitonin gene-related peptide binding / vascular associated smooth muscle cell development / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity ...adrenomedullin receptor binding / positive regulation of progesterone biosynthetic process / calcitonin gene-related peptide binding / vascular associated smooth muscle cell development / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / neuron projection regeneration / adrenomedullin receptor signaling pathway / amylin receptor activity / calcitonin receptor activity / spongiotrophoblast layer development / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / branching involved in labyrinthine layer morphogenesis / positive regulation of vasculogenesis / regulation of systemic arterial blood pressure / regulation of the force of heart contraction / regulation of G protein-coupled receptor signaling pathway / regulation of urine volume / G protein-coupled receptor internalization / negative regulation of vascular permeability / negative regulation of vasoconstriction / positive regulation of heart rate / response to starvation / odontogenesis of dentin-containing tooth / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / androgen metabolic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / developmental growth / maltodextrin transmembrane transport / vasculogenesis / animal organ regeneration / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to glucocorticoid / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / cAMP-mediated signaling / neural tube closure / protein localization to plasma membrane / G protein-coupled receptor activity / female pregnancy / intracellular protein transport / response to insulin / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / receptor internalization / positive regulation of angiogenesis / calcium ion transport / protein transport / heart development / positive regulation of cytosolic calcium ion concentration / outer membrane-bounded periplasmic space / G alpha (s) signalling events / angiogenesis / cell population proliferation / response to lipopolysaccharide / cell surface receptor signaling pathway / lysosome / receptor complex / response to hypoxia / endosome / inflammatory response / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of cell population proliferation / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / plasma membrane / cytoplasm
類似検索 - 分子機能
Pro-adrenomedullin / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain ...Pro-adrenomedullin / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
類似検索 - ドメイン・相同性
alpha-maltose / Receptor activity-modifying protein 1 / Maltose/maltodextrin-binding periplasmic protein / Pro-adrenomedullin / Calcitonin gene-related peptide type 1 receptor
類似検索 - 構成要素
生物種Escherichia coli O157:H7 (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Pioszak, A. / Booe, J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104251 米国
引用ジャーナル: Mol. Pharmacol. / 年: 2018
タイトル: Probing the Mechanism of Receptor Activity-Modifying Protein Modulation of GPCR Ligand Selectivity through Rational Design of Potent Adrenomedullin and Calcitonin Gene-Related Peptide Antagonists.
著者: Booe, J.M. / Warner, M.L. / Roehrkasse, A.M. / Hay, D.L. / Pioszak, A.A.
履歴
登録2017年3月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年1月31日Provider: repository / タイプ: Initial release
改定 1.12018年2月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22018年3月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.32020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年3月4日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
改定 3.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 3.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
B: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
C: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
D: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
E: ADM
F: ADM
G: ADM
H: ADM
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)274,19212
ポリマ－272,8238
非ポリマー1,3694
水543
1
A: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
E: ADM
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,5483
ポリマ－68,2062
非ポリマー3421
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-10 kcal/mol
Surface area24950 Å2
手法PISA
2
B: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
F: ADM
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,5483
ポリマ－68,2062
非ポリマー3421
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-9 kcal/mol
Surface area24990 Å2
手法PISA
3
C: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
G: ADM
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,5483
ポリマ－68,2062
非ポリマー3421
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-11 kcal/mol
Surface area25130 Å2
手法PISA
4
D: Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor
H: ADM
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,5483
ポリマ－68,2062
非ポリマー3421
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-8 kcal/mol
Surface area25000 Å2
手法PISA
単位格子
Length a, b, c (Å)195.496, 69.436, 200.000
Angle α, β, γ (deg.)90.000, 99.430, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain F and (resseq 38:43 or (resid 44 and (name...
21(chain E and (resseq 38:44 or resseq 46:53))
12(chain H and (resseq 40:45 or (resid 46 and (name...
22(chain G and ((resid 40 and (name O or name...
13(chain A and ((resid 4 and (name O or name...
23(chain B and ((resid 4 and (name N or name...
33(chain D and ((resid 4 and (name O or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain F and (resseq 38:43 or (resid 44 and (name...F38 - 43
121(chain F and (resseq 38:43 or (resid 44 and (name...F44
131(chain F and (resseq 38:43 or (resid 44 and (name...F38 - 52
141(chain F and (resseq 38:43 or (resid 44 and (name...F38 - 52
151(chain F and (resseq 38:43 or (resid 44 and (name...F38 - 52
161(chain F and (resseq 38:43 or (resid 44 and (name...F38 - 52
211(chain E and (resseq 38:44 or resseq 46:53))E38 - 44
221(chain E and (resseq 38:44 or resseq 46:53))E46 - 53
112(chain H and (resseq 40:45 or (resid 46 and (name...H40 - 45
122(chain H and (resseq 40:45 or (resid 46 and (name...H46
132(chain H and (resseq 40:45 or (resid 46 and (name...H40 - 52
142(chain H and (resseq 40:45 or (resid 46 and (name...H40 - 52
152(chain H and (resseq 40:45 or (resid 46 and (name...H40 - 52
212(chain G and ((resid 40 and (name O or name...G40
222(chain G and ((resid 40 and (name O or name...G40 - 52
232(chain G and ((resid 40 and (name O or name...G40 - 52
242(chain G and ((resid 40 and (name O or name...G40 - 52
252(chain G and ((resid 40 and (name O or name...G40 - 52
113(chain A and ((resid 4 and (name O or name...A4
123(chain A and ((resid 4 and (name O or name...A2 - 2129
133(chain A and ((resid 4 and (name O or name...A2 - 2129
143(chain A and ((resid 4 and (name O or name...A2 - 2129
153(chain A and ((resid 4 and (name O or name...A2 - 2129
163(chain A and ((resid 4 and (name O or name...A2 - 2129
173(chain A and ((resid 4 and (name O or name...A2 - 2129
213(chain B and ((resid 4 and (name N or name...B4
223(chain B and ((resid 4 and (name N or name...B3 - 2129
233(chain B and ((resid 4 and (name N or name...B3 - 2129
243(chain B and ((resid 4 and (name N or name...B3 - 2129
253(chain B and ((resid 4 and (name N or name...B3 - 2129
263(chain B and ((resid 4 and (name N or name...B3 - 2129
273(chain B and ((resid 4 and (name N or name...B3 - 2129
313(chain D and ((resid 4 and (name O or name...D4
323(chain D and ((resid 4 and (name O or name...D4 - 2201
333(chain D and ((resid 4 and (name O or name...D4 - 2201
343(chain D and ((resid 4 and (name O or name...D4 - 2201
353(chain D and ((resid 4 and (name O or name...D4 - 2201
363(chain D and ((resid 4 and (name O or name...D4 - 2201
373(chain D and ((resid 4 and (name O or name...D4 - 2201

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcitonin-receptor-like ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Calcitonin-receptor-like receptor activity-modifying protein 1 / CRLR activity-modifying protein 1 / CGRP type 1 receptor / Calcitonin receptor-like receptor


分子量: 66304.562 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli O157:H7 (大腸菌), (組換発現) Homo sapiens (ヒト)
遺伝子: malE, Z5632, ECs5017, RAMP1, CALCRL, CGRPR / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Origami B (DE3) / 参照: UniProt: P0AEY0, UniProt: O60894, UniProt: Q16602
#2: タンパク質・ペプチド
ADM


分子量: 1901.152 Da / 分子数: 4 / Mutation: S45W, K46L, Q50W, Y52F / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P35318
#3: 多糖
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


タイプ: oligosaccharide, Oligosaccharide / クラス: 栄養素 / 分子量: 342.297 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: oligosaccharide / 参照: alpha-maltose
記述子タイププログラム
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3 / 由来タイプ: 天然 / 式: H2O

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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: 2.63 Å3/Da / 溶媒含有率: 53.27 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6
詳細: 15% PEG3350, 0.1 M Sodium Malonate pH 6.0, 50 mM Potassium/Sodium tartrate, 1% Cadaverine

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データ収集

回折平均測定温度: 105 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-G / 波長: 0.9786 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2016年6月18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: 0.9786 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 61924 / % possible obs: 94.3 % / 冗長度: 6.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.56
反射 シェル解像度: 2.8→2.85 Å / 冗長度: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2927 / CC1/2: 0.517 / % possible all: 91.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.22データ抽出
HKL-2000データ削減
HKL-2000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: 4RWG

4rwg


解像度: 2.8→45.114 Å / SU ML: 0.4 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.56
Rfactor反射数%反射
Rfree0.2445 2000 3.23 %
Rwork0.212 --
obs0.2131 61912 94.14 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 257.75 Å2 / Biso mean: 118.0399 Å2 / Biso min: 44.62 Å2
精密化ステップサイクル: final / 解像度: 2.8→45.114 Å
タンパク質核酸リガンド溶媒全体
原子数17742 0 96 3 17841
Biso mean--82.64 74.97 -
残基数----2253
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00218348
X-RAY DIFFRACTIONf_angle_d0.44124975
X-RAY DIFFRACTIONf_chiral_restr0.0382663
X-RAY DIFFRACTIONf_plane_restr0.0033227
X-RAY DIFFRACTIONf_dihedral_angle_d13.28510809
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11F110X-RAY DIFFRACTION5.502TORSIONAL
12E110X-RAY DIFFRACTION5.502TORSIONAL
21H98X-RAY DIFFRACTION5.502TORSIONAL
22G98X-RAY DIFFRACTION5.502TORSIONAL
31A7299X-RAY DIFFRACTION5.502TORSIONAL
32B7299X-RAY DIFFRACTION5.502TORSIONAL
33D7299X-RAY DIFFRACTION5.502TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7997-2.86970.39941330.36283977411089
2.8697-2.94730.38511380.32514143428192
2.9473-3.0340.33241390.30014151429091
3.034-3.13190.30641390.29924184432393
3.1319-3.24380.30911440.29174298444295
3.2438-3.37360.3371450.27644346449197
3.3736-3.52710.2881470.24794403455098
3.5271-3.7130.28411500.23634479462998
3.713-3.94550.27921490.21414488463799
3.9455-4.24990.24191500.19364486463699
4.2499-4.67720.1991510.17224530468199
4.6772-5.35310.2031500.16844502465299
5.3531-6.74070.24071480.20014410455896
6.7407-45.11960.19051170.18613515363274
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)
13.1187-0.02550.97192.8947-2.227.88930.0145-0.47910.42440.102-0.40080.3506-0.0139-0.26540.33240.56440.0569-0.00170.86-0.32190.6733207.10373.73892.491
24.7703-1.28730.5584.88111.88628.599-0.2897-1.5279-0.61390.19540.4417-0.19540.49750.1359-0.06460.8230.30130.13481.47140.46120.891247.037-16.506377.9324
36.08080.2436-1.19222.20270.16113.0742-0.2955-0.5688-0.24060.04730.01850.0790.3744-0.53550.26680.72630.22250.1051.28440.27680.6166229.8053-11.243371.8967
43.8465-0.6437-0.12954.36041.27789.45690.02810.31520.4559-0.0661-0.4462-0.8465-0.63421.29860.23860.54360.01-0.12190.68350.21610.7708165.9396-28.01236.7128
55.28911.21960.66962.7873-1.47937.29130.2647-0.4807-1.10310.1528-0.42550.75930.6689-0.93710.1820.8836-0.33390.09651.0142-0.1031.2211136.4841-61.025923.216
66.7652-1.15220.90768.9507-0.99884.5312-0.1044-0.3169-0.4210.90040.04470.64290.1278-0.23140.08370.7052-0.08850.04240.6264-0.07220.5108150.4948-49.585227.937
73.78731.06170.89757.56580.22893.90770.17740.1020.1210.52310.4252-0.2097-0.2190.3548-0.55210.50710.04310.12340.598-0.18540.6068182.1832-20.416270.7648
89.25061.43090.78363.7244-2.13318.8579-0.21070.2752-0.8624-0.60590.363-0.22420.77860.3017-0.12620.53980.0583-0.01130.4782-0.08290.4887165.6813-51.497141.557
94.55391.45451.13087.45041.39216.255-0.161-0.33190.23880.09890.32130.3332-0.2064-0.3359-0.13410.33460.09680.04570.62030.11890.5034156.9353-40.149253.969
108.1615-1.86040.98797.2145-1.57062.2262-0.65031.1094-0.3972-0.13490.78460.36990.6665-0.7546-0.13051.232-0.30210.11471.73060.16680.8442216.2664-18.882357.9148
112.8351.4605-0.27764.4064-1.43254.05130.5217-0.6128-0.3188-0.0093-0.34820.1707-0.08010.0965-0.21390.7981-0.3453-0.20751.45980.28630.901195.740813.782929.9655
124.3655-1.25582.46192.5155-2.35564.198-0.75362.11820.1269-0.64190.97040.45950.6422-0.6675-0.11830.9345-0.40580.03982.20750.3290.8989220.2579-5.14644.8279
132.5033-1.8193-1.41973.1185.07219.7984-0.2866-0.8707-0.4571.20210.56420.45861.2206-1.37850.4671.01130.23840.27732.18280.57630.7715225.9784-17.246584.3287
148.3233-5.04310.17069.4977-5.01198.16190.78590.6973-0.4317-2.2854-0.99460.22860.3868-0.13980.17481.05250.0208-0.08080.6277-0.16210.5743155.8621-53.826915.0464
152.17871.6793-1.38848.99022.20397.8245-0.1717-1.2285-1.16721.43820.0315-0.98120.2220.28250.05990.54650.0715-0.07020.72540.17620.7562169.5391-39.132660.4515
166.24780.2181-1.4453.6734-4.93286.8291-0.96382.88560.7368-1.43590.2601-0.07610.31161.73290.00491.2314-0.6476-0.29123.37570.72551.1619207.4937-9.241939.0522
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 2:374) or (resid 2201))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 1024:1105))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 2035:2129))A0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 3:374) or (resid 2201))B0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 1024:1106))B0
6X-RAY DIFFRACTION6chain 'B' and ((resseq 2034:2129))B0
7X-RAY DIFFRACTION7chain 'C' and ((resseq 5:374) or (resid 2201))C0
8X-RAY DIFFRACTION8chain 'C' and ((resseq 1024:1106))C0
9X-RAY DIFFRACTION9chain 'C' and ((resseq 2034:2129))C0
10X-RAY DIFFRACTION10chain 'D' and ((resseq 1024:1106))D0
11X-RAY DIFFRACTION11chain 'D' and ((resseq 4:374) or (resid 2201))D0
12X-RAY DIFFRACTION12chain 'D' and ((resseq 2036:2128))D0
13X-RAY DIFFRACTION13chain 'E'E38 - 52
14X-RAY DIFFRACTION14chain 'F'F38 - 52
15X-RAY DIFFRACTION15chain 'G'G40 - 52
16X-RAY DIFFRACTION16chain 'H'H40 - 52

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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://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

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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