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- PDB-4uow: Crystal structure of the titin M10-Obscurin Ig domain 1 complex -

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基本情報

登録情報
データベース: PDB / ID: 4uow
タイトルCrystal structure of the titin M10-Obscurin Ig domain 1 complex
要素
  • Obscurin
  • Titin
キーワードTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / TRANSFERASE / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY
機能・相同性
機能・相同性情報


protein localization to M-band / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / phosphatidylinositol-5-phosphate binding / detection of muscle stretch / muscle alpha-actinin binding / protein kinase A signaling ...protein localization to M-band / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / phosphatidylinositol-5-phosphate binding / detection of muscle stretch / muscle alpha-actinin binding / protein kinase A signaling / cardiac myofibril assembly / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / phosphatidylinositol-4-phosphate binding / actinin binding / M band / regulation of small GTPase mediated signal transduction / I band / cardiac muscle cell development / structural constituent of muscle / ankyrin binding / sarcomere organization / NRAGE signals death through JNK / myofibril / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / striated muscle thin filament / skeletal muscle thin filament assembly / RHOA GTPase cycle / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / titin binding / phosphatidylinositol-4,5-bisphosphate binding / muscle contraction / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / sarcolemma / Z disc / actin filament binding / Platelet degranulation / G alpha (12/13) signalling events / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
類似検索 - 分子機能
Obscurin, SH3 domain / : / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / SOS1/NGEF-like PH domain ...Obscurin, SH3 domain / : / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / SOS1/NGEF-like PH domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-Type / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin V-set domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
引用ジャーナル: J.Mol.Biol. / 年: 2015
タイトル: The Crystal Structure of the Human Titin:Obscurin Complex Reveals a Conserved Yet Specific Muscle M-Band Zipper Module.
著者: Pernigo, S. / Fukuzawa, A. / Pandini, A. / Holt, M. / Kleinjung, J. / Gautel, M. / Steiner, R.A.
履歴
登録2014年6月10日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年12月17日Provider: repository / タイプ: Initial release
改定 1.12014年12月24日Group: Atomic model / Derived calculations / Non-polymer description
改定 1.22015年3月4日Group: Database references
改定 1.32019年10月30日Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _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_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
改定 1.42024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
0: Titin
1: Obscurin
2: Titin
3: Obscurin
4: Titin
5: Obscurin
6: Titin
7: Obscurin
8: Titin
9: Obscurin
A: Titin
B: Obscurin
C: Titin
D: Obscurin
E: Titin
F: Obscurin
G: Titin
H: Obscurin
I: Titin
J: Obscurin
K: Titin
L: Obscurin
M: Titin
N: Obscurin
O: Titin
P: Obscurin
Q: Titin
R: Obscurin
S: Titin
T: Obscurin
U: Titin
V: Obscurin
W: Titin
X: Obscurin
Y: Titin
Z: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)367,68545
ポリマ－367,37936
非ポリマー3079
水00
1
Y: Titin
Z: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16.4 kcal/mol
Surface area9630 Å2
手法PISA
2
M: Titin
N: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-16.2 kcal/mol
Surface area9620 Å2
手法PISA
3
E: Titin
F: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-16.4 kcal/mol
Surface area9620 Å2
手法PISA
4
8: Titin
9: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4.3 kcal/mol
Surface area9700 Å2
手法PISA
5
6: Titin
7: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4.2 kcal/mol
Surface area9730 Å2
手法PISA
6
0: Titin
1: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-16 kcal/mol
Surface area9660 Å2
手法PISA
7
I: Titin
J: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4.2 kcal/mol
Surface area9690 Å2
手法PISA
8
C: Titin
D: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4.1 kcal/mol
Surface area9690 Å2
手法PISA
9
4: Titin
5: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4.3 kcal/mol
Surface area9690 Å2
手法PISA
10
O: Titin
P: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4333
ポリマ－20,4102
非ポリマー231
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4.1 kcal/mol
Surface area9690 Å2
手法PISA
11
K: Titin
L: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4.2 kcal/mol
Surface area9680 Å2
手法PISA
12
U: Titin
V: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4.4 kcal/mol
Surface area9720 Å2
手法PISA
13
G: Titin
H: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area9680 Å2
手法PISA
14
Q: Titin
R: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16.7 kcal/mol
Surface area9650 Å2
手法PISA
15
W: Titin
X: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-16.2 kcal/mol
Surface area9670 Å2
手法PISA
16
2: Titin
3: Obscurin


分子量 (理論値)分子数
合計 (水以外)20,4102
ポリマ－20,4102
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4.2 kcal/mol
Surface area9720 Å2
手法PISA
17
A: Titin
B: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-15 kcal/mol
Surface area9610 Å2
手法PISA
18
S: Titin
T: Obscurin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4453
ポリマ－20,4102
非ポリマー351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-17.2 kcal/mol
Surface area9650 Å2
手法PISA
単位格子
Length a, b, c (Å)201.560, 201.560, 183.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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要素

#1: タンパク質
Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


分子量: 10479.673 Da / 分子数: 18 / 断片: FIRST IG DOMAIN, RESIDUES 26829-26925 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TTN / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): ROSETTA
参照: UniProt: Q8WZ42, UniProt: Q5VST9*PLUS, non-specific serine/threonine protein kinase
#2: タンパク質
Obscurin / Obscurin-RhoGEF / Obscurin-myosin light chain kinase / Obscurin-MLCK


分子量: 9930.262 Da / 分子数: 18 / 断片: M10 DOMAIN, RESIDUES 7-99 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: OBSCN, KIAA1556, KIAA1639 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): ROSETTA
参照: UniProt: Q5VST9, UniProt: Q8WZ42*PLUS, non-specific serine/threonine protein kinase
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Cl
#4: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
配列の詳細INITIAL GSS IS DERIVED FROM VECTOR AFTER TEV CLEAVAGE INITIAL GSS IS DERIVED FROM VECTOR AFTER TEV CLEAVAG

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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: 58.3 % / 解説: NONE
結晶化温度: 291 K / 手法: マイクロバッチ法 / pH: 3.6
詳細: 3.0 M SODIUM CHLORIDE 0.1 M TRI-SODIUM CITRATE PH 3.6 BATCH SETUP

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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: I24 / 波長: 0.9778
検出器タイプ: DECTRIS PILATUS / 検出器: PIXEL / 日付: 2010年2月12日 / 詳細: MIRRORS
放射モノクロメーター: SI(111) / 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: 0.9778 Å / 相対比: 1
反射解像度: 3.3→40 Å / Num. obs: 64369 / % possible obs: 98.9 % / Observed criterion σ(I): -1 / 冗長度: 3 % / Biso Wilson estimate: 48.94 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 4.3
反射 シェル解像度: 3.3→3.48 Å / 冗長度: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.0精密化
MOSFLMデータ削減
SCALAデータスケーリング
MOLREP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 2WP3

2wp3


解像度: 3.3→39.43 Å / Cor.coef. Fo:Fc: 0.9313 / Cor.coef. Fo:Fc free: 0.9107 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.424
Rfactor反射数%反射Selection details
Rfree0.2097 3285 5.1 %RANDOM
Rwork0.177 ---
obs0.1787 64358 98.83 %-
原子変位パラメータBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.9925 Å20 Å20 Å2
2---2.9925 Å20 Å2
3---5.985 Å2
Refine analyzeLuzzati coordinate error obs: 0.611 Å
精密化ステップサイクル: LAST / 解像度: 3.3→39.43 Å
タンパク質核酸リガンド溶媒全体
原子数25776 0 9 0 25785
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00826235HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135617HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8971SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes684HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3837HARMONIC5
X-RAY DIFFRACTIONt_it26235HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion21.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3547SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact27711SEMIHARMONIC4
LS精密化 シェル解像度: 3.3→3.39 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2859 237 5.05 %
Rwork0.2321 4455 -
all0.2348 4692 -
obs--98.83 %
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)
13.09650.41350.12137.76770.25820-0.06220.12550.31040.12050.02560.0122-0.3268-0.01330.03670.14350.1442-0.0593-0.09340.0471-0.126376.048398.798433.6939
20.40541.3034-4.69934.38540.89883.91240.0651-0.2722-0.00330.1853-0.1010.1195-0.0816-0.09770.0359-0.0373-0.079-0.0844-0.11730.00490.091266.169198.853734.8278
33.9082-0.81252.47915.4172-1.82696.0248-0.03760.21230.1655-0.25480.076-0.0913-0.2238-0.1624-0.0385-0.06640.0219-0.0321-0.1770.058-0.080775.707597.718828.9131
4-2.62121.214-0.64873.65821.13200.0312-0.02230.12090.0846-0.0284-0.008-0.1017-0.147-0.00280.00590.0438-0.02190.1125-0.0258-0.097178.756481.373940.5705
50.33571.09820.57581.15991.60130.5088-0.00750.0028-0.01230.00690.0014-0.1283-0.00260.05210.00610.00030.0081-0.06980.082-0.10820.097189.201574.346434.5276
6-0.53050.59590.46840.86490.70172.06250.04530.25620.011-0.3384-0.0416-0.0107-0.16340.3289-0.0037-0.0806-0.01080.0279-0.03790.0419-0.050682.109480.670338.3086
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911.65650.4477-0.69475.5741.90343.3056-0.10140.014-0.29510.06090.0474-0.01960.1668-0.18530.0540.0901-0.10580.12970.03560.0251-0.002567.86522.835624.1781
922.35860.36212.503-0.3681-0.87830.710.01740.2198-0.0312-0.1995-0.02060.03420.01220.05250.0032-0.1277-0.1418-0.00320.0933-0.0228-0.05660.017424.851422.3364
932.70571.71180.11974.4220.253.1485-0.0504-0.1561-0.00510.05610.073-0.03210.3698-0.2747-0.02260.03490.03110.1135-0.15850.0557-0.059268.190923.800729.3582
941.1355-0.3791-3.89842.23840.54222.36850.080.0944-0.0047-0.03-0.21110.18010.22180.02120.1311-0.1133-0.05670.01790.0726-0.0938-0.078974.176739.650217.0036
951.2763-1.16742.03620.2151.31783.69980.0622-0.0334-0.02140.005-0.0562-0.10030.03640.0029-0.0060.0120.03860.08720.0444-0.14140.045685.604541.793724.7739
965.1035-0.9704-1.90652.7416-0.18264.9779-0.0256-0.1008-0.05150.3020.1735-0.14080.26060.1185-0.1479-0.16910.0101-0.0368-0.056-0.0466-0.030378.018839.226319.9349
973.6009-1.0616-0.56675.47781.90890.3256-0.20940.0408-0.4045-0.02220.25540.09010.2818-0.2244-0.0460.1369-0.18230.14060.0371-0.0659-0.124767.82223.0528-53.8624
986.38222.74433.52294.6856-1.85212.7944-0.01940.14930.0412-0.0705-0.01750.04730.0335-0.06970.0368-0.0123-0.05620.003-0.0783-0.0277-0.179660.64327.1863-51.9887
995.21420.9661-0.27334.97380.72430-0.0907-0.0926-0.07320.09940.0951-0.22140.164-0.1746-0.00440.30130.05090.1846-0.20340.0775-0.10670.74521.8009-49.3108
1000.811-1.5945-2.60063.11272.42731.58170.1507-0.11180.0290.0199-0.28210.06950.4910.0380.1314-0.0643-0.02970.01330.1073-0.0557-0.008774.873439.3546-60.2308
101-3.2332.5953-2.90345.6988-0.72063.68030.03440.00050.0890.01330.1044-0.19760.04020.1024-0.1388-0.09210.16850.03950.1198-0.0809-0.091679.4145.9094-59.2702
1025.87630.1408-0.69812.20931.38671.80530.0096-0.2133-0.15260.0682-0.0164-0.33390.1920.04730.00680.01240.028-0.0411-0.0596-0.0089-0.070879.42637.1257-56.9332
1032.1263-1.29190.08913.51691.11032.7345-0.14890.12210.23910.01390.1330.0127-0.0707-0.17470.01580.29220.0367-0.1865-0.10450.0266-0.023675.228499.1567-44.3738
104-2.72940.5143-4.2067.10532.33192.11580.0391-0.1916-0.01350.1166-0.06560.1061-0.03-0.07610.02650.08080.0284-0.2482-0.14730.01810.216466.568398.7963-43.0872
1053.3617-1.841.38044.18480.89184.27980.02610.19890.1317-0.3197-0.0833-0.0312-0.2454-0.17790.05710.2888-0.0685-0.2059-0.29270.0988-0.15175.336998.0867-49.167
106-0.2373-0.62373.86943.5187-1.34192.14030.04410.08170.02160.0385-0.14540.1343-0.26130.05770.10130.09030.0281-0.03980.0698-0.041-0.165978.828281.8236-37.7506
1070.14420.52782.35440.5614-1.35651.84150.0193-0.0599-0.0473-0.03450.0309-0.10750.00630.0277-0.05030.0144-0.0001-0.12140.1706-0.09420.136188.674374.8616-43.5574
1081.69020.41863.46252.6597-0.90046.41420.00960.23170.0443-0.24970.03450.0462-0.4060.2064-0.0441-0.03440.0263-0.0393-0.1542-0.0153-0.107882.154281.4268-40.0073
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ 0|2 - 0|48 }
2X-RAY DIFFRACTION2{ 0|49 - 0|60 }
3X-RAY DIFFRACTION3{ 0|61 - 0|98 }
4X-RAY DIFFRACTION4{ 1|7 - 1|47 }
5X-RAY DIFFRACTION5{ 1|48 - 1|57 }
6X-RAY DIFFRACTION6{ 1|58 - 1|99 }
7X-RAY DIFFRACTION7{ 2|2 - 2|47 }
8X-RAY DIFFRACTION8{ 2|48 - 2|73 }
9X-RAY DIFFRACTION9{ 2|74 - 2|98 }
10X-RAY DIFFRACTION10{ 3|7 - 3|47 }
11X-RAY DIFFRACTION11{ 3|48 - 3|66 }
12X-RAY DIFFRACTION12{ 3|67 - 3|99 }
13X-RAY DIFFRACTION13{ 4|2 - 4|52 }
14X-RAY DIFFRACTION14{ 4|53 - 4|84 }
15X-RAY DIFFRACTION15{ 4|85 - 4|98 }
16X-RAY DIFFRACTION16{ 5|7 - 5|48 }
17X-RAY DIFFRACTION17{ 5|49 - 5|57 }
18X-RAY DIFFRACTION18{ 5|58 - 5|99 }
19X-RAY DIFFRACTION19{ 6|2 - 6|45 }
20X-RAY DIFFRACTION20{ 6|46 - 6|51 }
21X-RAY DIFFRACTION21{ 6|52 - 6|98 }
22X-RAY DIFFRACTION22{ 7|7 - 7|47 }
23X-RAY DIFFRACTION23{ 7|48 - 7|64 }
24X-RAY DIFFRACTION24{ 7|65 - 7|99 }
25X-RAY DIFFRACTION25{ 8|2 - 8|30 }
26X-RAY DIFFRACTION26{ 8|31 - 8|56 }
27X-RAY DIFFRACTION27{ 8|57 - 8|98 }
28X-RAY DIFFRACTION28{ 9|7 - 9|49 }
29X-RAY DIFFRACTION29{ 9|50 - 9|57 }
30X-RAY DIFFRACTION30{ 9|58 - 9|99 }
31X-RAY DIFFRACTION31{ A|2 - A|43 }
32X-RAY DIFFRACTION32{ A|44 - A|72 }
33X-RAY DIFFRACTION33{ A|73 - A|98 }
34X-RAY DIFFRACTION34{ B|7 - B|46 }
35X-RAY DIFFRACTION35{ B|47 - B|58 }
36X-RAY DIFFRACTION36{ B|59 - B|99 }
37X-RAY DIFFRACTION37{ C|2 - C|49 }
38X-RAY DIFFRACTION38{ C|50 - C|68 }
39X-RAY DIFFRACTION39{ C|69 - C|98 }
40X-RAY DIFFRACTION40{ D|7 - D|47 }
41X-RAY DIFFRACTION41{ D|48 - D|57 }
42X-RAY DIFFRACTION42{ D|58 - D|99 }
43X-RAY DIFFRACTION43{ E|2 - E|48 }
44X-RAY DIFFRACTION44{ E|49 - E|60 }
45X-RAY DIFFRACTION45{ E|61 - E|98 }
46X-RAY DIFFRACTION46{ F|7 - F|48 }
47X-RAY DIFFRACTION47{ F|49 - F|57 }
48X-RAY DIFFRACTION48{ F|58 - F|99 }
49X-RAY DIFFRACTION49{ G|2 - G|45 }
50X-RAY DIFFRACTION50{ G|46 - G|51 }
51X-RAY DIFFRACTION51{ G|52 - G|98 }
52X-RAY DIFFRACTION52{ H|7 - H|48 }
53X-RAY DIFFRACTION53{ H|49 - H|57 }
54X-RAY DIFFRACTION54{ H|58 - H|99 }
55X-RAY DIFFRACTION55{ I|2 - I|23 }
56X-RAY DIFFRACTION56{ I|24 - I|60 }
57X-RAY DIFFRACTION57{ I|61 - I|98 }
58X-RAY DIFFRACTION58{ J|7 - J|47 }
59X-RAY DIFFRACTION59{ J|48 - J|57 }
60X-RAY DIFFRACTION60{ J|58 - J|99 }
61X-RAY DIFFRACTION61{ K|2 - K|45 }
62X-RAY DIFFRACTION62{ K|46 - K|72 }
63X-RAY DIFFRACTION63{ K|73 - K|98 }
64X-RAY DIFFRACTION64{ L|7 - L|47 }
65X-RAY DIFFRACTION65{ L|48 - L|66 }
66X-RAY DIFFRACTION66{ L|67 - L|99 }
67X-RAY DIFFRACTION67{ M|2 - M|42 }
68X-RAY DIFFRACTION68{ M|43 - M|51 }
69X-RAY DIFFRACTION69{ M|52 - M|98 }
70X-RAY DIFFRACTION70{ N|7 - N|48 }
71X-RAY DIFFRACTION71{ N|49 - N|57 }
72X-RAY DIFFRACTION72{ N|58 - N|99 }
73X-RAY DIFFRACTION73{ O|2 - O|36 }
74X-RAY DIFFRACTION74{ O|37 - O|67 }
75X-RAY DIFFRACTION75{ O|68 - O|98 }
76X-RAY DIFFRACTION76{ P|7 - P|48 }
77X-RAY DIFFRACTION77{ P|49 - P|57 }
78X-RAY DIFFRACTION78{ P|58 - P|99 }
79X-RAY DIFFRACTION79{ Q|2 - Q|52 }
80X-RAY DIFFRACTION80{ Q|53 - Q|87 }
81X-RAY DIFFRACTION81{ Q|88 - Q|98 }
82X-RAY DIFFRACTION82{ R|7 - R|48 }
83X-RAY DIFFRACTION83{ R|49 - R|57 }
84X-RAY DIFFRACTION84{ R|58 - R|99 }
85X-RAY DIFFRACTION85{ S|2 - S|42 }
86X-RAY DIFFRACTION86{ S|43 - S|59 }
87X-RAY DIFFRACTION87{ S|60 - S|98 }
88X-RAY DIFFRACTION88{ T|7 - T|48 }
89X-RAY DIFFRACTION89{ T|49 - T|57 }
90X-RAY DIFFRACTION90{ T|58 - T|99 }
91X-RAY DIFFRACTION91{ U|2 - U|49 }
92X-RAY DIFFRACTION92{ U|50 - U|61 }
93X-RAY DIFFRACTION93{ U|62 - U|98 }
94X-RAY DIFFRACTION94{ V|7 - V|45 }
95X-RAY DIFFRACTION95{ V|46 - V|57 }
96X-RAY DIFFRACTION96{ V|58 - V|99 }
97X-RAY DIFFRACTION97{ W|2 - W|49 }
98X-RAY DIFFRACTION98{ W|50 - W|71 }
99X-RAY DIFFRACTION99{ W|72 - W|98 }
100X-RAY DIFFRACTION100{ X|7 - X|48 }
101X-RAY DIFFRACTION101{ X|49 - X|66 }
102X-RAY DIFFRACTION102{ X|67 - X|99 }
103X-RAY DIFFRACTION103{ Y|2 - Y|49 }
104X-RAY DIFFRACTION104{ Y|50 - Y|60 }
105X-RAY DIFFRACTION105{ Y|61 - Y|98 }
106X-RAY DIFFRACTION106{ Z|7 - Z|47 }
107X-RAY DIFFRACTION107{ Z|48 - Z|58 }
108X-RAY DIFFRACTION108{ Z|59 - Z|99 }

+
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://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