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- PDB-4md9: Crystal Structure of symmetric CK2 holoenzyme with mutated alpha ... -

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基本情報

登録情報
データベース: PDB / ID: 4md9
タイトルCrystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336)
要素
  • Casein kinase II subunit alpha
  • Casein kinase II subunit beta
キーワードTRANSFERASE / protein serine/threonine kinase
機能・相同性
機能・相同性情報


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / protein-macromolecule adaptor activity / peptidyl-serine phosphorylation / positive regulation of cell growth / protein-containing complex assembly / secretory granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin binding / positive regulation of cell population proliferation / Neutrophil degranulation / chromatin / apoptotic process / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Casein kinase II subunit beta / Casein kinase II subunit alpha
類似検索 - 構成要素
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: 3.5 Å
データ登録者Lolli, G. / Ranchio, A. / Battistutta, R.
引用ジャーナル: Acs Chem.Biol. / 年: 2014
タイトル: Active Form of the Protein Kinase CK2 alpha 2 beta 2 Holoenzyme Is a Strong Complex with Symmetric Architecture.
著者: Lolli, G. / Ranchio, A. / Battistutta, R.
履歴
登録2013年8月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年11月20日Provider: repository / タイプ: Initial release
改定 1.12014年3月5日Group: Database references
改定 1.22023年9月20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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

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集合体

登録構造単位
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
G: Casein kinase II subunit alpha
H: Casein kinase II subunit alpha
I: Casein kinase II subunit beta
J: Casein kinase II subunit beta
K: Casein kinase II subunit alpha
L: Casein kinase II subunit alpha
M: Casein kinase II subunit alpha
N: Casein kinase II subunit beta
O: Casein kinase II subunit beta
P: Casein kinase II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)521,36524
ポリマ－520,84116
非ポリマー5238
水00
1
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,3416
ポリマ－130,2104
非ポリマー1312
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-62 kcal/mol
Surface area49980 Å2
手法PISA
2
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
H: Casein kinase II subunit alpha
K: Casein kinase II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,3416
ポリマ－130,2104
非ポリマー1312
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-61 kcal/mol
Surface area49650 Å2
手法PISA
3
G: Casein kinase II subunit alpha
N: Casein kinase II subunit beta
O: Casein kinase II subunit beta
P: Casein kinase II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,3416
ポリマ－130,2104
非ポリマー1312
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-64 kcal/mol
Surface area50010 Å2
手法PISA
4
I: Casein kinase II subunit beta
J: Casein kinase II subunit beta
L: Casein kinase II subunit alpha
M: Casein kinase II subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,3416
ポリマ－130,2104
非ポリマー1312
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-61 kcal/mol
Surface area49930 Å2
手法PISA
単位格子
Length a, b, c (Å)283.924, 115.707, 208.223
Angle α, β, γ (deg.)90.00, 119.22, 90.00
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
11A
21B
31C
41D
51I
61J
71N
81O
12E
22F
32G
42H
52K
62L
72M
82P

NCSドメイン領域:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPROAA8 - 588 - 58
211SERSERPROPROBB8 - 588 - 58
311SERSERPROPROCC8 - 588 - 58
411SERSERPROPRODD8 - 588 - 58
511SERSERPROPROII8 - 588 - 58
611SERSERPROPROJJ8 - 588 - 58
711SERSERPROPRONN8 - 588 - 58
811SERSERPROPROOO8 - 588 - 58
121GLNGLNTYRTYRAA68 - 18868 - 188
221GLNGLNTYRTYRBB68 - 18868 - 188
321GLNGLNTYRTYRCC68 - 18868 - 188
421GLNGLNTYRTYRDD68 - 18868 - 188
521GLNGLNTYRTYRII68 - 18868 - 188
621GLNGLNTYRTYRJJ68 - 18868 - 188
721GLNGLNTYRTYRNN68 - 18868 - 188
821GLNGLNTYRTYROO68 - 18868 - 188
112PROPROLEULEUEE4 - 414 - 41
212PROPROLEULEUFF4 - 414 - 41
312PROPROLEULEUGG4 - 414 - 41
412PROPROLEULEUHH4 - 414 - 41
512PROPROLEULEUKK4 - 414 - 41
612PROPROLEULEULL4 - 414 - 41
712PROPROLEULEUMM4 - 414 - 41
812PROPROLEULEUPP4 - 414 - 41
122TYRTYRLYSLYSEE50 - 7150 - 71
222TYRTYRLYSLYSFF50 - 7150 - 71
322TYRTYRLYSLYSGG50 - 7150 - 71
422TYRTYRLYSLYSHH50 - 7150 - 71
522TYRTYRLYSLYSKK50 - 7150 - 71
622TYRTYRLYSLYSLL50 - 7150 - 71
722TYRTYRLYSLYSMM50 - 7150 - 71
822TYRTYRLYSLYSPP50 - 7150 - 71
132VALVALLYSLYSEE73 - 10273 - 102
232VALVALLYSLYSFF73 - 10273 - 102
332VALVALLYSLYSGG73 - 10273 - 102
432VALVALLYSLYSHH73 - 10273 - 102
532VALVALLYSLYSKK73 - 10273 - 102
632VALVALLYSLYSLL73 - 10273 - 102
732VALVALLYSLYSMM73 - 10273 - 102
832VALVALLYSLYSPP73 - 10273 - 102
142THRTHRPHEPHEEE108 - 113108 - 113
242THRTHRPHEPHEFF108 - 113108 - 113
342THRTHRPHEPHEGG108 - 113108 - 113
442THRTHRPHEPHEHH108 - 113108 - 113
542THRTHRPHEPHEKK108 - 113108 - 113
642THRTHRPHEPHELL108 - 113108 - 113
742THRTHRPHEPHEMM108 - 113108 - 113
842THRTHRPHEPHEPP108 - 113108 - 113
152THRTHRILEILEEE127 - 263127 - 263
252THRTHRILEILEFF127 - 263127 - 263
352THRTHRILEILEGG127 - 263127 - 263
452THRTHRILEILEHH127 - 263127 - 263
552THRTHRILEILEKK127 - 263127 - 263
652THRTHRILEILELL127 - 263127 - 263
752THRTHRILEILEMM127 - 263127 - 263
852THRTHRILEILEPP127 - 263127 - 263
162GLYGLYHISHISEE274 - 286274 - 286
262GLYGLYHISHISFF274 - 286274 - 286
362GLYGLYHISHISGG274 - 286274 - 286
462GLYGLYHISHISHH274 - 286274 - 286
562GLYGLYHISHISKK274 - 286274 - 286
662GLYGLYHISHISLL274 - 286274 - 286
762GLYGLYHISHISMM274 - 286274 - 286
862GLYGLYHISHISPP274 - 286274 - 286
172GLNGLNVALVALEE290 - 327290 - 327
272GLNGLNVALVALFF290 - 327290 - 327
372GLNGLNVALVALGG290 - 327290 - 327
472GLNGLNVALVALHH290 - 327290 - 327
572GLNGLNVALVALKK290 - 327290 - 327
672GLNGLNVALVALLL290 - 327290 - 327
772GLNGLNVALVALMM290 - 327290 - 327
872GLNGLNVALVALPP290 - 327290 - 327

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Casein kinase II subunit beta / CK2 subunit beta / CK II beta / Phosvitin / Protein G5a


分子量: 24969.412 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CSNK2B, CK2N, G5A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P67870
#2: タンパク質
Casein kinase II subunit alpha / CK2 subunit alpha / CK II alpha


分子量: 40135.758 Da / 分子数: 8 / Fragment: kinase domain (UNP residues 1-336) / Mutation: F121E / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CSNK2A1, CK2A1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21
参照: UniProt: P68400, non-specific serine/threonine protein kinase
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn

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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: 2.87 Å3/Da / 溶媒含有率: 57.08 %
結晶化温度: 277 K / 手法: 蒸気拡散法 / pH: 6.5
詳細: 20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K

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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: ESRF / ビームライン: ID23-2 / 波長: 0.873 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2011年4月9日
放射モノクロメーター: horizontally diffracting 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: 0.873 Å / 相対比: 1
反射解像度: 3.5→181.725 Å / Num. all: 74256 / Num. obs: 74256 / % possible obs: 99.7 % / 冗長度: 3.3 % / Rsym value: 0.172 / Net I/σ(I): 6.6
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.5-3.693.20.6211.20.621199.9
3.69-3.913.20.4291.80.4291100
3.91-4.183.30.2962.60.296199.9
4.18-4.523.40.1983.90.198199.9
4.52-4.953.40.1644.70.164199.9
4.95-5.533.40.15650.156199.8
5.53-6.393.40.1465.20.146199.8
6.39-7.833.30.1057.10.105199.6
7.83-11.073.30.05510.20.055199.1
11.07-48.3063.20.03912.50.039197.2

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
SCALA3.3.20データスケーリング
PHASER位相決定
REFMAC精密化
PDB_EXTRACT3.11データ抽出
XSCALEデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 4DGL AND 4KWP

4dgl

4kwp


解像度: 3.5→181.725 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 55.068 / SU ML: 0.379 / SU R Cruickshank DPI: 0.1441 / 交差検証法: THROUGHOUT / ESU R Free: 0.138 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor反射数%反射Selection details
Rfree0.25897 3736 5 %RANDOM
Rwork0.22888 ---
obs0.23038 70519 99.37 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 90.224 Å2
Baniso -1Baniso -2Baniso -3
1--24.26 Å2-0 Å26.04 Å2
2--16.99 Å20 Å2
3---7.26 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→181.725 Å
タンパク質核酸リガンド溶媒全体
原子数35065 0 8 0 35073
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0236042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.94848781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47654180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22423.4951943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95156194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.98815272
X-RAY DIFFRACTIONr_chiral_restr0.0830.25005
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
11A688MEDIUM POSITIONAL0.230.5
12B688MEDIUM POSITIONAL0.210.5
13C688MEDIUM POSITIONAL0.190.5
14D688MEDIUM POSITIONAL0.180.5
15I688MEDIUM POSITIONAL0.20.5
16J688MEDIUM POSITIONAL0.20.5
17N688MEDIUM POSITIONAL0.210.5
18O688MEDIUM POSITIONAL0.210.5
11A722LOOSE POSITIONAL0.535
12B722LOOSE POSITIONAL0.55
13C722LOOSE POSITIONAL0.495
14D722LOOSE POSITIONAL0.55
15I722LOOSE POSITIONAL0.55
16J722LOOSE POSITIONAL0.475
17N722LOOSE POSITIONAL0.495
18O722LOOSE POSITIONAL0.535
11A688MEDIUM THERMAL5.432
12B688MEDIUM THERMAL4.992
13C688MEDIUM THERMAL5.042
14D688MEDIUM THERMAL5.212
15I688MEDIUM THERMAL5.632
16J688MEDIUM THERMAL6.512
17N688MEDIUM THERMAL5.392
18O688MEDIUM THERMAL10.12
11A722LOOSE THERMAL6.210
12B722LOOSE THERMAL6.5110
13C722LOOSE THERMAL6.5310
14D722LOOSE THERMAL6.8510
15I722LOOSE THERMAL7.2710
16J722LOOSE THERMAL7.2710
17N722LOOSE THERMAL6.8710
18O722LOOSE THERMAL10.6210
21E1136MEDIUM POSITIONAL0.20.5
22F1136MEDIUM POSITIONAL0.230.5
23G1136MEDIUM POSITIONAL0.210.5
24H1136MEDIUM POSITIONAL0.260.5
25K1136MEDIUM POSITIONAL0.260.5
26L1136MEDIUM POSITIONAL0.220.5
27M1136MEDIUM POSITIONAL0.220.5
28P1136MEDIUM POSITIONAL0.240.5
21E1276LOOSE POSITIONAL0.475
22F1276LOOSE POSITIONAL0.435
23G1276LOOSE POSITIONAL0.455
24H1276LOOSE POSITIONAL0.485
25K1276LOOSE POSITIONAL0.465
26L1276LOOSE POSITIONAL0.485
27M1276LOOSE POSITIONAL0.495
28P1276LOOSE POSITIONAL0.55
21E1136MEDIUM THERMAL5.862
22F1136MEDIUM THERMAL5.152
23G1136MEDIUM THERMAL5.442
24H1136MEDIUM THERMAL5.342
25K1136MEDIUM THERMAL5.72
26L1136MEDIUM THERMAL5.552
27M1136MEDIUM THERMAL6.262
28P1136MEDIUM THERMAL5.472
21E1276LOOSE THERMAL6.7410
22F1276LOOSE THERMAL6.9310
23G1276LOOSE THERMAL6.7110
24H1276LOOSE THERMAL7.2310
25K1276LOOSE THERMAL6.8610
26L1276LOOSE THERMAL7.410
27M1276LOOSE THERMAL7.5910
28P1276LOOSE THERMAL7.1810
LS精密化 シェル解像度: 3.498→3.588 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.313 255 -
Rwork0.291 5045 -
obs--96.86 %
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)
10.3320.3061-1.07490.5403-2.04867.85570.0777-0.31180.08680.06960.02750.0289-0.3701-0.2045-0.10520.3507-0.07640.09390.6659-0.03170.5992-98.5945-3.0472-43.0705
23.7626-0.3398-2.27376.8875-5.08557.54780.07350.0352-0.1440.20950.03610.3920.6204-0.8147-0.10960.3745-0.1883-0.01720.6649-0.03520.6605-113.0738-10.2149-45.2348
32.18240.4201-0.731.0140.42781.5569-0.0229-0.3490.0399-0.1046-0.00850.0750.0702-0.04250.03140.11320.0312-0.01460.2673-0.00120.5204-89.994-2.6874-56.6607
46.158716.591-0.857745.45190.404111.6862-0.5177-0.0543-0.112-1.5623-0.1304-0.05160.94190.47280.64810.25610.2244-0.05050.40210.04380.7936-62.4603-14.5564-74.3491
57.083-7.28834.339741.5587-13.80175.22650.9106-0.2956-0.2493-0.457-0.67170.29270.48610.1523-0.23890.40620.21480.0321.0301-0.19310.4724-53.0189-10.272-38.0542
60.5659-0.3596-0.36751.40782.12834.538-0.0352-0.25430.10610.36710.2354-0.07370.0960.7695-0.20010.304-0.08990.02710.5590.0380.6039-46.5133-5.2569-45.7151
72.6555-0.20591.07680.8554-0.34831.57460.1451-0.2323-0.12140.01730.01350.01750.1837-0.058-0.15860.06730.0370.04640.26260.02420.4691-64.4602-8.0542-56.3421
85.11495.5365-0.245720.289210.54948.6220.2018-0.05580.4019-0.6894-0.44520.6744-1.0124-0.22790.24340.33380.1046-0.12610.56930.04590.4769-90.90526.6998-73.6608
97.85280.0623-4.78013.9985.18089.7315-0.66390.06540.2324-0.45130.20330.505-0.17930.33690.46060.28760.22910.12760.47190.15040.571810.899430.1466-49.2774
100.2035-0.7854-1.37916.96664.030811.69250.06190.0237-0.0264-0.60920.07710.44390.01670.9759-0.1390.25710.18830.0010.79080.03580.62325.267822.5982-46.2996
113.70190.0738-0.74671.25640.15261.74360.20210.22990.0576-0.2753-0.16240.07040.06540.0399-0.03970.1159-0.0277-0.00520.31770.04730.46073.537728.3305-35.0237
120.81770.3995-0.1551.75484.384612.87810.35330.0577-0.2750.78840.2031-0.29871.72290.173-0.55640.5604-0.07850.12060.730.02960.7219-25.470215.9845-18.0861
134.3461-1.0765-0.35551.4716-0.47460.70570.26350.22260.3559-0.21620.06760.08410.1846-0.4411-0.33110.1958-0.0462-0.00650.53420.0420.5558-40.21527.6966-45.0018
143.7536-0.20061.04890.32960.55321.5104-0.03740.03360.03290.003-0.05660.0065-0.04890.01960.0940.0689-0.13760.06350.3092-0.02210.4907-23.109623.7624-34.5191
150.6949-2.6882-2.867115.33598.602113.3809-0.06150.05780.15571.44920.0028-1.4679-0.4933-0.71390.05870.37270.0216-0.16450.6746-0.08860.81444.892134.9167-16.7314
162.6894-0.8826-0.46080.63430.03440.83480.193-0.03890.5068-0.0195-0.0345-0.278-0.460.3816-0.15850.3358-0.07210.04630.47930.00180.5824-29.3747-0.7814-75.5945
175.6472-0.5704-1.01511.6411-0.34441.9767-0.1715-0.05220.27240.17120.1403-0.01490.01420.11180.03110.16430.0040.05520.3081-0.02380.4488-41.412-5.6104-74.9567
180.71260.03360.82593.40991.42781.57890.13640.0024-0.24390.8355-0.2340.48010.4824-0.07260.09750.26240.07290.07920.5132-0.00340.6452-44.3422-12.276-76.7972
193.5261-0.1760.99033.1903-0.25023.95310.2697-0.0589-0.05540.1104-0.21890.02120.1470.2947-0.05080.10690.06-0.00180.4039-0.03250.4786-27.3792-16.5789-76.325
201.5920.1075-0.04022.6189-0.80380.69840.2031-0.1191-0.35360.3083-0.1387-0.22750.32340.1232-0.06440.48040.0524-0.06380.64440.0250.6521-19.0578-28.5673-72.6429
212.8263-0.8486-0.51491.81640.15920.17720.01650.0608-0.37460.1957-0.0840.24340.1795-0.07140.06750.4611-0.01850.07540.5574-0.07010.6492-127.2682-7.0013-82.0951
223.8022-0.66041.9742.4658-1.19391.34330.0921-0.2506-0.13750.19-0.07440.00370.0081-0.122-0.01770.23840.02370.0910.4684-0.04460.5033-109.4942-2.8919-77.1705
232.22431.0173-0.88950.4908-0.42040.37520.0164-0.1933-0.08380.12380.0041-0.1129-0.1119-0.0038-0.02050.89210.2205-0.21780.8789-0.02690.7528-108.933613.7878-79.0861
241.5805-0.2559-0.64271.3910.68712.2034-0.0128-0.08340.01680.3168-0.04880.16210.0648-0.19980.06160.23250.05310.06230.4930.00030.4886-129.126813.3714-73.1857
252.05320.4668-0.59162.1721-1.89225.304-0.12850.34650.2288-0.22390.13090.2284-0.1426-0.3052-0.00240.19610.103-0.02890.568-0.05070.5308-130.14723.8194-82.489
260.83690.7391-0.21262.8722-0.0530.304-0.24510.09050.46050.14720.14740.374-0.1535-0.01130.09760.52530.0061-0.16370.5131-0.01190.6923-61.8453-27.3132-12.2913
274.0108-0.7966-2.02582.27880.02872.39-0.32680.47930.2586-0.27680.065-0.2070.0023-0.27660.26180.2051-0.0661-0.01810.40210.05480.467-40.6371-32.9857-15.1321
282.87735.9461-3.196312.48-6.67313.5748-0.01850.170.2007-0.0740.36480.81420.0354-0.1998-0.34620.4672-0.0104-0.02160.5617-0.00730.8456-42.3919-50.2709-10.2106
291.85510.54230.80712.30380.66042.4906-0.0080.0011-0.1896-0.01450.05450.10520.0902-0.144-0.04650.05230.02390.07960.424-0.02330.461-62.7093-50.3654-14.7824
300.5075-0.64330.13331.4508-0.18440.0376-0.33330.17640.31390.45860.2382-0.0096-0.09990.00750.09510.5593-0.1355-0.00690.83270.00270.8348-60.286831.2525-12.242
316.37060.6301-0.99172.9602-0.24220.8982-0.3337-0.07630.2226-0.06480.15550.0325-0.16610.0360.17830.2531-0.14570.07840.4159-0.08930.3094-42.918824.4094-14.2993
320.52621.4986-0.283417.8282-2.82720.9441-0.2293-0.101-0.2573-0.4772-0.0443-0.21250.3457-0.0090.27370.3512-0.04250.04690.6752-0.00530.5426-42.57413.6864-14.2339
332.41090.74351.00772.6527-0.53.09880.0991-0.0602-0.1011-0.2375-0.05310.29390.22670.1367-0.0460.18160.0010.12340.4591-0.09670.4825-63.99118.5063-17.9593
346.7689-5.59890.18824.6637-0.19390.05110.1776-0.0756-0.2032-0.3584-0.04130.2230.17690.0066-0.13640.6738-0.1035-0.06260.6868-0.05850.6732-61.6725-63.445-40.8029
355.5054-0.03042.16556.58832.02213.1509-0.1251-0.20240.49690.30010.2861-0.4479-0.1833-0.3933-0.1610.0361-0.03270.03590.60420.00840.5613-47.278-57.3705-45.1902
361.79371.20091.73912.0210.81053.34020.1137-0.52310.0725-0.1478-0.26110.0475-0.0765-0.10620.14730.19230.03510.06120.4826-0.0190.5443-67.4507-61.7906-52.3592
370.7904-0.68831.04430.7311-1.18052.06070.08440.26270.20490.0119-0.0334-0.1374-0.17830.0171-0.0510.42150.090.00830.4558-0.02740.7572-91.2034-60.7033-68.1964
381.52340.26410.00391.2784-1.05890.915-0.1545-0.4287-0.45120.0760.2950.1065-0.1272-0.2864-0.14050.46870.04370.04160.72-0.03240.7975-113.1068-60.2303-42.7966
392.7031-0.121-0.96510.62430.14491.4716-0.0135-0.0790.1652-0.00870.00990.11790.0829-0.07040.00360.26680.1199-0.0790.4418-0.05250.5937-92.6206-59.4951-56.3034
400.9677-0.23591.00020.1017-0.11871.45740.0316-0.2252-0.082-0.08660.132-0.03770.04660.2487-0.16360.5888-0.00620.11380.62630.11990.713250.527520.1712-14.5769
413.8231-0.98011.00742.21080.70491.84820.1207-0.0187-0.119-0.0781-0.1607-0.08830.45850.03840.040.252-0.09940.07010.39190.02450.424623.855922.1152-16.8301
420.17360.03070.05011.87332.77444.1094-0.0979-0.18580.2832-0.7052-0.13770.1629-1.0486-0.16380.23560.4154-0.0716-0.15620.7806-0.00040.799224.676440.011-11.7503
432.1283-0.0031-0.13292.3566-0.40512.4514-0.095-0.04050.2426-0.07070.01780.0504-0.0170.21610.07720.1099-0.05290.03270.48280.04220.425140.264235.0203-15.5395
442.0901-1.2134-0.73412.29930.57935.08750.1602-0.1150.2713-0.1936-0.1259-0.1303-0.3830.267-0.03430.2091-0.1873-0.06130.45590.03440.580749.307346.2304-19.7881
450.71670.1152-0.4580.67260.08962.30860.0447-0.0286-0.20660.158-0.11610.14210.3573-0.35040.07140.29330.0447-0.01090.4009-0.07050.6268-129.7954-63.3337-76.9207
464.14040.83741.08893.5202-0.18693.27770.1772-0.1858-0.10850.4502-0.10810.0255-0.0799-0.0989-0.0690.20560.15130.00050.35440.01880.5598-117.3894-60.3551-73.682
470.03470.00360.00330.00210.0010.0029-0.1244-0.05430.0704-0.02270.09330.0142-0.03580.0090.03111.13610.2195-0.09510.84930.02010.8875-115.8386-42.588-78.8009
481.6135-0.3989-0.46612.34360.22711.75150.0562-0.03590.09510.1631-0.17690.0005-0.34370.00350.12060.34710.0997-0.02680.47780.01340.6012-136.4737-41.1049-74.9959
490.29690.08120.18750.2366-0.22261.0705-0.04140.17290.2830.08130.0121-0.0895-0.57950.11570.02930.4272-0.01230.08510.47630.00770.7994-37.0857-58.4798-78.0824
501.8201-0.4615-0.23073.19472.02033.28060.1216-0.08110.4343-0.0563-0.052-0.1134-0.41480.0384-0.06960.34180.09350.00410.44920.00580.6065-49.8806-61.1994-74.6952
512.5278-1.999-1.92411.62531.46211.6647-0.34320.14270.09550.44810.0573-0.22640.3012-0.47830.28590.45460.0184-0.16250.8991-0.15420.8714-51.2083-78.9676-78.0058
521.4507-0.3958-0.62121.4563-0.48721.56520.0584-0.07380.08450.21160.0133-0.0757-0.2774-0.0241-0.07170.2146-0.008-0.00850.4153-0.02140.5352-31.0876-77.5738-71.5393
534.5670.94870.75050.84381.65223.7281-0.00660.1948-0.2348-0.01480.0575-0.13370.06850.2773-0.05090.23870.10690.04410.46440.01370.5931-30.0408-87.5548-82.0159
543.03650.83281.76452.9426-0.02828.28690.1836-0.0836-0.0691-0.1292-0.0077-0.18210.00940.4609-0.17590.2935-0.00590.24650.53480.08150.482919.7062-34.6977-44.3178
554.7197-1.543-4.40651.10411.70174.2393-0.1566-0.20950.1003-0.06390.5046-0.69130.14240.4616-0.3480.71410.14120.00690.8475-0.21510.952728.1193-40.188-52.2686
562.1160.22080.2990.6813-0.6980.91380.16930.15890.2154-0.0204-0.1661-0.0247-0.02430.1257-0.00330.4108-0.08140.11550.41740.02840.6315.5099-32.2691-35.1662
570.60692.45331.335212.26878.94148.69570.03720.2292-0.25071.01150.8319-0.85841.13240.2133-0.86910.3105-0.08780.19710.56360.02160.7925-23.8461-43.1057-17.7491
581.0575-0.72060.62490.5318-0.43451.21230.05010.1378-0.0109-0.0989-0.00270.1189-0.2286-0.3072-0.04740.58530.1037-0.06460.8064-0.05250.6199-36.4818-35.8343-43.813
596.42390.02025.2724.7671-2.10895.27730.019-0.29940.3609-0.3163-0.4296-0.35650.1441-0.09390.41070.78340.12270.01920.9005-0.0540.8389-45.0725-31.2547-51.5094
602.0773-0.06460.58480.9967-0.07910.93890.00190.26540.064-0.01550.00020.0725-0.4163-0.0356-0.00210.3553-0.01630.12480.4845-0.03460.5706-17.7884-35.6522-32.554
613.14330.75-0.07971.15840.54790.54620.1206-0.0719-0.48850.2801-0.1503-0.23980.42250.030.02980.532-0.11070.04950.5130.10340.561138.645-36.5558-12.5279
623.9388-0.52752.2751.9722-0.25591.33880.17150.10810.0839-0.0451-0.2116-0.0239-0.01190.14150.04010.4385-0.32880.13560.5129-0.00850.544225.9497-34.1967-15.3844
632.43680.28750.277812.19411.50650.2406-0.0054-0.26820.2683-1.7118-0.1337-0.2702-0.2087-0.1490.13910.6878-0.25390.15730.7309-0.12720.652423.7985-17.5112-10.5094
641.04480.80780.24463.2792-0.61562.73690.15760.21960.133-0.01-0.2391-0.05430.0552-0.10960.08160.2417-0.10140.02970.43210.07330.537443.4815-16.1441-16.8994
652.9655-1.6346-0.45771.46680.53174.43370.1608-0.28950.57220.3893-0.0781-0.5391-0.30540.0751-0.08280.4989-0.2154-0.05270.52190.03310.66444.707-7.5341-5.7584
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 26
2X-RAY DIFFRACTION2A27 - 65
3X-RAY DIFFRACTION3A66 - 189
4X-RAY DIFFRACTION4A190 - 207
5X-RAY DIFFRACTION5B6 - 15
6X-RAY DIFFRACTION6B16 - 58
7X-RAY DIFFRACTION7B66 - 189
8X-RAY DIFFRACTION8B190 - 207
9X-RAY DIFFRACTION9C6 - 26
10X-RAY DIFFRACTION10C27 - 61
11X-RAY DIFFRACTION11C66 - 186
12X-RAY DIFFRACTION12C187 - 207
13X-RAY DIFFRACTION13D6 - 58
14X-RAY DIFFRACTION14D65 - 189
15X-RAY DIFFRACTION15D190 - 207
16X-RAY DIFFRACTION16E2 - 44
17X-RAY DIFFRACTION17E45 - 96
18X-RAY DIFFRACTION18E97 - 129
19X-RAY DIFFRACTION19E130 - 226
20X-RAY DIFFRACTION20E227 - 330
21X-RAY DIFFRACTION21F4 - 38
22X-RAY DIFFRACTION22F39 - 108
23X-RAY DIFFRACTION23F109 - 129
24X-RAY DIFFRACTION24F130 - 280
25X-RAY DIFFRACTION25F281 - 330
26X-RAY DIFFRACTION26G2 - 35
27X-RAY DIFFRACTION27G36 - 109
28X-RAY DIFFRACTION28G110 - 129
29X-RAY DIFFRACTION29G130 - 330
30X-RAY DIFFRACTION30H3 - 38
31X-RAY DIFFRACTION31H39 - 103
32X-RAY DIFFRACTION32H104 - 129
33X-RAY DIFFRACTION33H130 - 330
34X-RAY DIFFRACTION34I7 - 26
35X-RAY DIFFRACTION35I27 - 60
36X-RAY DIFFRACTION36I66 - 170
37X-RAY DIFFRACTION37I171 - 207
38X-RAY DIFFRACTION38J7 - 58
39X-RAY DIFFRACTION39J66 - 207
40X-RAY DIFFRACTION40K3 - 24
41X-RAY DIFFRACTION41K25 - 108
42X-RAY DIFFRACTION42K109 - 129
43X-RAY DIFFRACTION43K130 - 226
44X-RAY DIFFRACTION44K227 - 330
45X-RAY DIFFRACTION45L3 - 44
46X-RAY DIFFRACTION46L45 - 109
47X-RAY DIFFRACTION47L110 - 129
48X-RAY DIFFRACTION48L130 - 330
49X-RAY DIFFRACTION49M2 - 44
50X-RAY DIFFRACTION50M45 - 109
51X-RAY DIFFRACTION51M110 - 129
52X-RAY DIFFRACTION52M130 - 280
53X-RAY DIFFRACTION53M281 - 332
54X-RAY DIFFRACTION54N7 - 45
55X-RAY DIFFRACTION55N46 - 61
56X-RAY DIFFRACTION56N66 - 186
57X-RAY DIFFRACTION57N187 - 207
58X-RAY DIFFRACTION58O7 - 45
59X-RAY DIFFRACTION59O46 - 61
60X-RAY DIFFRACTION60O65 - 207
61X-RAY DIFFRACTION61P3 - 44
62X-RAY DIFFRACTION62P45 - 108
63X-RAY DIFFRACTION63P109 - 129
64X-RAY DIFFRACTION64P130 - 280
65X-RAY DIFFRACTION65P281 - 330

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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

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