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- PDB-4u7u: Crystal structure of RNA-guided immune Cascade complex from E.coli -

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基本情報

登録情報
データベース: PDB / ID: 4u7u
タイトルCrystal structure of RNA-guided immune Cascade complex from E.coli
要素
  • (CRISPR system Cascade subunit ...) x 5
  • crRNA
キーワードRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
機能・相同性
機能・相同性情報


CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding ...CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding / RNA binding / zinc ion binding
類似検索 - 分子機能
CRISPR-associated protein Cse2 / Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) ...CRISPR-associated protein Cse2 / Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / Peroxidase; domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
: / RNA / RNA (> 10) / CRISPR system Cascade subunit CasB / CRISPR system Cascade subunit CasE / CRISPR system Cascade subunit CasD / CRISPR system Cascade subunit CasC / CRISPR system Cascade subunit CasA
類似検索 - 構成要素
生物種Escherichia coli K12 (大腸菌)
Escherichia coli str. K-12 substr. MG1655 (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.003 Å
データ登録者Zhao, H. / Sheng, G. / Wang, J. / Wang, M. / Bunkoczi, G. / Gong, W. / Wei, Z. / Wang, Y.
資金援助 中国, 1件
組織認可番号国
中国
引用ジャーナル: Nature / 年: 2014
タイトル: Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli
著者: Zhao, H. / Sheng, G. / Wang, J. / Wang, M. / Bunkoczi, G. / Gong, W. / Wei, Z. / Wang, Y.
履歴
登録2014年7月31日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02014年8月27日Provider: repository / タイプ: Initial release
改定 1.12014年11月12日Group: Database references
改定 1.22019年12月4日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
カテゴリ: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / software / struct_conn / struct_conn_type / struct_ref
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.tilt / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _software.pdbx_ordinal / _struct_ref.pdbx_seq_one_letter_code
改定 1.32024年3月20日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _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: CRISPR system Cascade subunit CasA
B: CRISPR system Cascade subunit CasB
C: CRISPR system Cascade subunit CasB
D: CRISPR system Cascade subunit CasE
E: CRISPR system Cascade subunit CasC
F: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasC
I: CRISPR system Cascade subunit CasC
J: CRISPR system Cascade subunit CasC
K: CRISPR system Cascade subunit CasD
L: crRNA
M: CRISPR system Cascade subunit CasA
N: CRISPR system Cascade subunit CasB
O: CRISPR system Cascade subunit CasB
P: CRISPR system Cascade subunit CasE
Q: CRISPR system Cascade subunit CasC
R: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasC
U: CRISPR system Cascade subunit CasC
V: CRISPR system Cascade subunit CasC
W: CRISPR system Cascade subunit CasD
X: crRNA


分子量 (理論値)分子数
合計 (水以外)802,61224
ポリマ－802,61224
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area108980 Å2
ΔGint-550 kcal/mol
Surface area259260 Å2
2
A: CRISPR system Cascade subunit CasA
B: CRISPR system Cascade subunit CasB
C: CRISPR system Cascade subunit CasB
D: CRISPR system Cascade subunit CasE
E: CRISPR system Cascade subunit CasC
F: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasC
I: CRISPR system Cascade subunit CasC
J: CRISPR system Cascade subunit CasC
K: CRISPR system Cascade subunit CasD
L: crRNA


分子量 (理論値)分子数
合計 (水以外)401,30612
ポリマ－401,30612
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area53550 Å2
ΔGint-269 kcal/mol
Surface area130410 Å2
手法PISA
3
M: CRISPR system Cascade subunit CasA
N: CRISPR system Cascade subunit CasB
O: CRISPR system Cascade subunit CasB
P: CRISPR system Cascade subunit CasE
Q: CRISPR system Cascade subunit CasC
R: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasC
U: CRISPR system Cascade subunit CasC
V: CRISPR system Cascade subunit CasC
W: CRISPR system Cascade subunit CasD
X: crRNA


分子量 (理論値)分子数
合計 (水以外)401,30612
ポリマ－401,30612
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area53480 Å2
ΔGint-277 kcal/mol
Surface area130800 Å2
手法PISA
単位格子
Length a, b, c (Å)111.412, 118.143, 225.873
Angle α, β, γ (deg.)92.230, 93.550, 106.060
Int Tables number1
Space group name H-MP1
詳細biological unit is the same as asym.

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要素

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CRISPR system Cascade subunit ... , 5種, 22分子 AMBCNODPEFGHIJQRSTUVKW

#1: タンパク質 CRISPR system Cascade subunit CasA / CRISPR type I-E/Ecoli-associated protein CasA/Cse1 / CRISPR-associated protein CasA/Cse1


分子量: 55964.957 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K12 (大腸菌) / 遺伝子: casA, cse1, ygcL, b2760, JW2730 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q46901
#2: タンパク質
CRISPR system Cascade subunit CasB


分子量: 18728.525 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K12 (大腸菌) / 遺伝子: casB, cse2, ygcK, b2759, JW2729 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P76632
#3: タンパク質 CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease


分子量: 22581.293 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K12 (大腸菌) / 遺伝子: casE, cas6e, ygcH, b2756, JW2726 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q46897, 加水分解酵素; エステル加水分解酵素
#4: タンパク質
CRISPR system Cascade subunit CasC


分子量: 40071.402 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K12 (大腸菌) / 遺伝子: casC, cas4, cse4, ygcJ, b2758, JW2728 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46899
#5: タンパク質 CRISPR system Cascade subunit CasD


分子量: 25239.803 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K12 (大腸菌) / 遺伝子: casD, cas5, ygcI, b2757, JW5844 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46898

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RNA鎖 , 1種, 2分子 LX

#6: RNA鎖 crRNA


分子量: 19634.629 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Escherichia coli str. K-12 substr. MG1655 (大腸菌)
参照: GenBank: 882596

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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: 3.55 Å3/Da / 溶媒含有率: 65.32 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 11%-13% PEG4000, 100mM Tris-HCl, 200mM NaAc, 100mM Glycine, 50mM LiAc

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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: Photon Factory / ビームライン: BL-1A / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2013年5月17日 / 詳細: Mono-chromator and mirrors
放射モノクロメーター: Cryo-cooled channel-cut 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: 1.1 Å / 相対比: 1
反射解像度: 3→50 Å / Num. obs: 216153 / % possible obs: 98.8 % / 冗長度: 3.1 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.105 / Χ2: 0.88 / Net I/av σ(I): 9.889 / Net I/σ(I): 8.3 / Num. measured all: 680117
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.1130.625214420.88798.3
3.11-3.233.30.483215300.89398.5
3.23-3.383.30.334216050.92798.6
3.38-3.563.20.241216060.97798.6
3.56-3.783.20.168215751.03198.6
3.78-4.0730.12215921.01798.8
4.07-4.4830.084216570.9399
4.48-5.133.20.067216820.84999
5.13-6.463.20.061217190.72599.2
6.46-503.10.039217450.56799.4

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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
HKL-2000data processing
HKL-2000データスケーリング
RESOLVE位相決定
Cootモデル構築
PDB_EXTRACT3.14データ抽出
PHASER位相決定
PHASERモデル構築
HKLデータ削減
HKLデータスケーリング
PHENIX(phenix.refine: 1.8.4_1496)精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.003→43.797 Å / FOM work R set: 0.8826 / SU ML: 0.24 / 交差検証法: NONE / σ(F): 1.96 / 位相誤差: 22.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2185 9789 5.01 %
Rwork0.1795 185443 -
obs0.1815 195232 88.77 %
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
原子変位パラメータBiso max: 165.3 Å2 / Biso mean: 57.04 Å2 / Biso min: 20.55 Å2
精密化ステップサイクル: final / 解像度: 3.003→43.797 Å
タンパク質核酸リガンド溶媒全体
原子数51959 2596 0 0 54555
残基数----6823
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01255807
X-RAY DIFFRACTIONf_angle_d1.11176081
X-RAY DIFFRACTIONf_chiral_restr0.0558640
X-RAY DIFFRACTIONf_plane_restr0.0059464
X-RAY DIFFRACTIONf_dihedral_angle_d15.00620873
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0034-3.03760.38741360.2882568270437
3.0376-3.07330.31242020.28383235343747
3.0733-3.11070.29881830.27333660384352
3.1107-3.15010.35982010.2724201440260
3.1501-3.19160.3312420.26864729497168
3.1916-3.23530.29262630.2595100536374
3.2353-3.28150.29832950.25335688598380
3.2815-3.33040.31363340.24375906624087
3.3304-3.38250.28933490.24466365671491
3.3825-3.43790.28243480.24366458680694
3.4379-3.49710.2673530.23556750710396
3.4971-3.56070.26683820.21976758714097
3.5607-3.62920.26663530.21266859721298
3.6292-3.70320.23513780.20356854723298
3.7032-3.78370.25083710.19596802717399
3.7837-3.87160.2263610.19316872723399
3.8716-3.96840.20833460.18796940728699
3.9684-4.07560.20983920.18276868726099
4.0756-4.19550.20173580.16866855721399
4.1955-4.33080.21473780.16396911728999
4.3308-4.48540.19913320.15496907723999
4.4854-4.66480.18653810.14466827720899
4.6648-4.87680.17393600.14226946730699
4.8768-5.13360.19233590.14856940729999
5.1336-5.45470.20643640.15616848721299
5.4547-5.87490.20223270.16196983731099
5.8749-6.46450.18633490.15856923727299
6.4645-7.3960.19733950.15796933732899
7.396-9.30350.14583400.12376932727299
9.3035-43.80210.16383570.13836825718298
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)
11.87740.04120.22590.9468-0.13841.1012-0.10510.43870.6145-0.27220.0744-0.0818-0.74380.27750.04221.4333-0.06360.18940.60150.1850.9919.189654.7606-55.6207
21.77770.36580.28480.9173-0.21441.28050.1296-0.07010.15850.026-0.0937-0.3104-0.4650.33320.02161.1996-0.08730.16380.59030.04440.822328.057943.2605-40.0291
31.82670.99620.14571.8879-1.22841.60180.1238-0.05480.29880.0598-0.2007-0.3186-0.37240.3605-0.02650.7680.03730.11320.4112-0.10610.588321.996526.9157-23.2966
42.9410.6153-0.5454.6004-0.82083.95340.0027-0.63820.21850.44620.2117-0.3187-0.24391.0462-0.04830.5645-0.069-0.03020.5871-0.11530.442618.57713.094215.4629
53.1724-0.3316-0.53633.7917-0.0595.1039-0.11610.15280.149-0.12470.34030.0816-0.05230.1525-0.06380.5413-0.065-0.02710.4446-0.06510.33177.6352.883415.2052
62.8413-0.6533-1.15251.88170.26714.51060.2528-0.13780.62790.0389-0.098-0.4971-0.530.7569-0.12390.529-0.12310.00760.4967-0.06060.476220.80076.82323.8949
72.09930.0543-0.2622.0745-0.62435.03210.2195-0.0831-0.0089-0.3622-0.09630.2410.0158-0.0986-0.04240.51640.0440.06170.3411-0.06050.423912.5543-1.1193-5.8186
82.8063-0.14380.15052.872-0.28885.86020.3705-0.16850.3629-0.1513-0.386-0.0076-0.68230.4849-0.14220.5411-0.05610.08340.4145-0.07870.455319.08698.8155-4.7185
93.51580.2692-0.24933.1775-0.48672.9318-0.0360.42220.0681-0.04320.16770.9882-0.0992-0.9741-0.09330.4989-0.00750.07860.79620.10440.8987-25.44893.110627.3966
104.32523.4273-0.6226.8974-1.10892.45680.2601-0.69410.6330.92520.09650.6335-0.5811-0.2986-0.11470.66760.08850.17730.3679-0.0510.6193-13.5919.702636.1554
110.15810.5931-0.17893.5876-1.08760.3235-0.3646-0.34470.88110.044-0.0541-0.0506-0.89010.2484-0.15580.8169-0.07120.06910.4765-0.15280.8757-4.468219.139629.6452
124.8803-0.25790.30463.2441-0.87372.9202-0.06770.0572-0.3257-0.3237-0.10620.1570.0481-0.0203-0.04870.5498-0.05160.06120.4476-0.02590.3906-3.558-2.522626.1144
133.9330.51280.32924.59680.48043.7224-0.2156-0.1547-0.4067-0.00210.13830.57550.30340.0081-0.05120.4815-0.02620.1460.3804-0.02070.4977-10.8279-1.31730.3789
144.9413-0.6457-0.59272.5768-0.0232.2393-0.03560.48940.3347-0.11260.00770.2709-0.1669-0.1431-0.0080.4798-0.0077-0.01530.4292-0.00830.4218-5.06656.27522.4899
151.4239-0.49480.06462.728-0.03032.48720.13521.26130.0567-1.3014-0.00490.36470.4333-0.1671-0.02240.96870.0138-0.13621.242-0.13250.6936-42.8021-23.662522.5129
162.0161-0.49990.12892.7264-0.04951.84540.22910.09190.225-0.1677-0.2940.96170.036-0.3172-0.01550.3772-0.08430.00460.7103-0.10180.8283-47.1617-18.159841.7305
170.94070.44210.07760.8856-0.7022.3543-0.10260.35010.0368-0.51770.11490.02930.4188-0.0028-0.05510.80770.1489-0.05070.3445-0.01330.4066-3.5986-3.4371-48.416
180.5736-0.0447-0.07481.9561-0.17671.5667-0.09940.14280.1809-0.129-0.1338-0.1361-0.12150.11490.02720.55180.05560.02260.3285-0.01240.38092.0174-4.4035-30.3981
190.90730.3540.50011.2582-0.46642.23020.05410.01880.1087-0.31380.05850.36180.1306-0.4849-0.12340.61710.108-0.06690.4128-0.00830.4101-15.4581-2.4175-29.686
203.573-2.47841.00816.4741-1.62992.5947-0.2099-0.38030.18810.24090.27710.6855-0.0989-0.8126-0.19170.46680.10280.0080.5787-0.00210.5395-22.74015.0288-17.2117
211.82280.2179-0.10543.286-0.38172.62720.0874-0.11760.0618-0.17780.10860.83440.3068-1.0068-0.20090.6187-0.0309-0.10850.66480.09710.6507-28.6424-5.3054-28.2785
221.24730.0934-0.57411.47080.22951.62380.00730.2172-0.2292-0.6475-0.0402-0.4720.30730.2556-0.05490.90620.16550.12380.3219-0.05830.484715.5901-27.3774-28.2133
230.9764-0.48480.14061.29190.08221.19770.10180.0458-0.1052-0.4005-0.0842-0.1995-0.26480.0993-0.0170.5550.020.09560.2723-0.0430.415110.3362-21.1138-12.4713
241.01280.3746-0.20911.07740.30532.18350.03490.1177-0.141-0.42110.03440.10730.4203-0.3371-0.00290.65160.038-0.02180.3086-0.05570.3676-3.7727-27.3827-17.6552
252.6975-1.33523.452.3368-2.53848.9034-0.0566-0.1759-0.1969-0.51660.27590.55710.4577-1.2652-0.16610.6038-0.0581-0.10630.4773-0.02760.4225-18.2162-21.0156-13.9353
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1122.77521.5899-1.29763.8267-0.40592.59790.1412-0.76130.29430.66090.0969-0.0666-0.54240.0113-0.17910.6327-0.02150.12620.7176-0.08890.519-25.729156.2697128.191
1131.177-0.32290.13562.3199-0.2551.57630.3002-0.0093-0.1131-0.0142-0.27540.01410.08-0.2475-0.03930.3583-0.1245-0.01830.71190.07270.2573-35.08520.3884121.8536
1141.449-0.10730.61871.0724-0.15811.23090.2075-0.1227-0.2067-0.0555-0.05370.36370.3918-0.3498-0.09290.3634-0.1393-0.05420.71060.08520.4425-45.68516.0296113.1056
1152.5656-0.53510.18831.6719-0.01021.55060.0990.2226-0.8524-0.21420.00620.32070.5078-0.2527-0.13810.5734-0.1715-0.1620.92890.06880.6331-58.808314.082496.2847
1161.8971-0.48721.15421.7211-0.57591.3824-0.051-0.00150.3495-0.3299-0.30010.26080.0664-0.4968-0.16640.4686-0.1934-0.14191.0170.15280.6469-67.125825.884296.8724
1171.8752-0.10920.83391.1831-0.10751.34440.12360.12510.0947-0.28620.10210.47820.0071-0.1786-0.11470.3934-0.1318-0.08310.86050.10870.5176-54.149227.4067107.3745
1181.3214-0.1061-0.0542.3065-0.16730.98460.11120.0388-0.2438-0.042-0.1485-0.39460.54840.1236-0.06520.5994-0.0288-0.09540.71050.1120.3802-22.94664.0703120.4608
1191.366-0.52820.3291.4043-0.24831.2929-0.0269-0.35130.02940.26480.12120.2267-0.0381-0.2416-0.07520.3764-0.08680.02490.76640.04690.3657-41.480725.4744125.9762
1201.7389-0.93920.0996.9082-1.46731.45350.2467-0.75660.34630.89660.1528-0.1304-0.3559-0.14030.12990.4885-0.00960.07770.931-0.03690.3293-31.675535.0092134.7715
1211.6727-0.1007-0.4763.608-1.23622.08990.1357-0.50910.3430.6335-0.02310.54470.2082-0.2175-0.08680.5297-0.06090.13411.03340.0640.4836-46.0331.4122137.4756
1222.0564-0.0645-0.00031.79830.17241.33370.03710.5864-0.7545-0.35850.02890.32120.8222-0.2183-0.09011.0769-0.2079-0.14610.9184-0.01620.6545-35.5921-13.9137117.6824
1232.07430.03170.08542.14920.20741.5793-0.03430.7379-0.4796-0.83380.09750.0310.8323-0.2669-0.10511.0068-0.2609-0.11080.92620.05270.5315-38.7312-6.4314118.464
1243.16030.0389-0.4021.1571-0.67420.4430.1152-0.46810.4823-0.02360.2109-0.54-0.00180.2348-0.01290.7161-0.0339-0.14180.851-0.02290.6706-10.969.5586146.3775
1251.99420.3299-0.09352.1455-0.38491.48260.0335-0.1415-0.18320.30770.17820.28960.4794-0.4286-0.12090.751-0.2029-0.04070.74420.13660.394-36.6752-2.1685137.4863
1262.3633-0.1414-1.23223.4383-0.45770.9589-0.108-0.61620.24090.67320.33640.3650.393-0.4385-0.18050.6851-0.12290.04310.99150.12060.4302-38.7518.4012146.2227
1272.620.12120.21273.57270.6362.7099-0.0394-0.6315-0.06970.7097-0.14520.45050.5351-0.5425-0.14550.8994-0.23940.06791.03890.20330.6914-45.9208-2.5973146.951
1281.38570.4971-0.39351.1756-0.03551.41110.05270.05510.01110.1601-0.08-0.1085-0.1440.10060.0210.14090.0062-0.02570.2952-0.01990.375825.542237.403264.009
1292.1434-0.1257-0.04172.07740.35472.00790.02070.21310.2089-0.3934-0.1146-0.7708-0.05710.7999-0.10850.2487-0.04210.0260.8030.07030.914455.221539.615949.0686
1301.34380.34660.08012.73720.59711.19370.1404-0.00680.20360.1231-0.17680.5402-0.2634-0.24780.13460.2343-0.00420.01930.4163-0.01960.353710.734552.063768.6908
1311.4342-0.7055-0.53821.5034-0.12991.1292-0.0391-0.1658-0.13770.0966-0.0332-0.27740.20770.29550.02040.2031-0.0318-0.04790.38010.01010.435830.162230.283167.5135
1321.4730.09530.22762.50090.67472.51580.1659-0.1857-0.71220.0419-0.10970.11490.4449-0.04630.07650.2789-0.0165-0.0920.3710.04060.48222.860218.397170.3745
1332.8694-0.1138-0.3823.89110.72433.67250.1025-0.5051-1.08290.3094-0.1285-0.23330.43920.16290.03810.3377-0.0047-0.11240.53890.08790.610532.886920.892577.7226
1341.13580.28630.04672.3602-0.36181.6004-0.11370.1698-0.2018-0.23690.0062-0.12220.12420.1560.05280.23750.04180.02090.3729-0.08470.415127.864525.438742.8778
1352.7750.80640.95052.52290.2881.4478-0.34210.7059-0.5078-0.17720.2302-0.24470.12370.35520.03830.32810.03440.06150.4619-0.10180.528931.091719.32437.5526
1362.52092.23630.0075.04480.06041.9576-0.00120.2786-0.12010.23930.18390.37130.3278-0.20750.05580.2143-0.0185-0.04830.3269-0.02990.43813.808131.634653.1497
1373.33170.47530.83091.9013-0.27970.9412-0.005-0.00520.6748-0.13350.0074-0.6333-0.73550.6923-0.07330.3286-0.08450.04290.45590.11450.654740.383251.375947.2555
1380.66630.5720.12982.29770.22450.9353-0.1028-0.0261-0.1279-0.15740.03240.00020.06620.15780.07040.23890.0318-0.02920.3884-0.04510.371522.736530.639146.5291
1390.17190.06370.57080.37441.14424.288-0.07790.3603-0.2806-0.2385-0.037-0.16180.51990.68760.05910.5120.1030.05610.5378-0.10160.70636.012611.296140.9022
1401.3882-0.10650.22171.9215-0.13161.9127-0.09520.0954-0.2577-0.1894-0.0845-0.25240.50890.26050.03840.31980.0180.05920.3887-0.06510.471726.435116.797447.889
1413.76550.4514-1.26943.9995-2.37626.54-0.1242-0.0378-0.18310.01610.12030.44110.2238-0.2774-0.07720.3755-0.09170.01030.333-0.19250.497114.607514.969242.2321
1422.46081.45980.11616.0921-0.0791.8402-0.23950.2551-0.0143-0.63590.50680.03710.6237-0.37260.07630.4529-0.08050.01810.4865-0.07360.447416.61318.464129.0967
1431.28790.74910.18162.81510.11641.9629-0.10710.4-0.2349-0.35680.1013-0.26540.17650.3070.05920.33520.03040.02030.4243-0.07350.449627.000327.346432.3426
1441.18710.3881-0.3510.50620.33081.59160.125-0.09780.015-0.18530.1105-0.1555-0.13030.2024-0.13880.1342-0.0387-0.00340.26740.02080.411626.040546.345457.5924
1451.173-0.99970.63881.77890.10650.77710.18280.6840.6621-0.25830.09710.3314-0.6048-0.2464-0.43440.5182-0.04910.03040.4510.04460.576-5.936364.350784.2432
1461.39290.0533-0.8817-0.0361-0.13431.0556-0.17360.37590.3592-0.50950.47730.41150.0583-0.5607-0.36170.46460.058-0.01590.80560.05760.4815-32.384444.16197.9294
1470.30460.0014-0.2311.6185-0.06181.30780.26870.2187-0.2742-0.3544-0.1056-0.1790.97230.10130.13260.7379-0.0344-0.10630.78580.05030.5412-21.9508-3.3531119.6174
1480.9557-0.27481.82260.0829-0.48913.52540.3836-0.3866-0.47020.1467-0.1419-0.83830.41430.7360.36261.11640.5405-0.02931.74230.11881.186916.8834-10.8702131.5554
1492.04750.142-0.26530.13310.49862.11820.1843-0.0271-0.90190.0227-0.0364-0.79830.70890.91210.3981.32690.3298-0.22431.36520.04641.198712.5342-14.3848138.0534
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 283 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 374 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 375 through 495 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 25 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 51 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 94 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 124 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 125 through 159 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 4 through 67 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 77 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 78 through 86 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 87 through 111 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 112 through 129 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 130 through 160 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid -1 through 75 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 76 through 199 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 155 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 156 through 221 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 222 through 304 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 305 through 323 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 324 through 363 )E0
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 155 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 156 through 221 )F0
24X-RAY DIFFRACTION24chain 'F' and (resid 222 through 304 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 305 through 323 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 324 through 363 )F0
27X-RAY DIFFRACTION27chain 'G' and (resid 1 through 79 )G0
28X-RAY DIFFRACTION28chain 'G' and (resid 80 through 145 )G0
29X-RAY DIFFRACTION29chain 'G' and (resid 146 through 184 )G0
30X-RAY DIFFRACTION30chain 'G' and (resid 185 through 221 )G0
31X-RAY DIFFRACTION31chain 'G' and (resid 222 through 304 )G0
32X-RAY DIFFRACTION32chain 'G' and (resid 305 through 323 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 324 through 362 )G0
34X-RAY DIFFRACTION34chain 'H' and (resid 1 through 145 )H0
35X-RAY DIFFRACTION35chain 'H' and (resid 146 through 184 )H0
36X-RAY DIFFRACTION36chain 'H' and (resid 185 through 221 )H0
37X-RAY DIFFRACTION37chain 'H' and (resid 222 through 304 )H0
38X-RAY DIFFRACTION38chain 'H' and (resid 305 through 323 )H0
39X-RAY DIFFRACTION39chain 'H' and (resid 324 through 363 )H0
40X-RAY DIFFRACTION40chain 'I' and (resid 1 through 27 )I0
41X-RAY DIFFRACTION41chain 'I' and (resid 28 through 57 )I0
42X-RAY DIFFRACTION42chain 'I' and (resid 58 through 79 )I0
43X-RAY DIFFRACTION43chain 'I' and (resid 80 through 115 )I0
44X-RAY DIFFRACTION44chain 'I' and (resid 116 through 145 )I0
45X-RAY DIFFRACTION45chain 'I' and (resid 146 through 184 )I0
46X-RAY DIFFRACTION46chain 'I' and (resid 185 through 221 )I0
47X-RAY DIFFRACTION47chain 'I' and (resid 222 through 260 )I0
48X-RAY DIFFRACTION48chain 'I' and (resid 261 through 284 )I0
49X-RAY DIFFRACTION49chain 'I' and (resid 285 through 304 )I0
50X-RAY DIFFRACTION50chain 'I' and (resid 305 through 323 )I0
51X-RAY DIFFRACTION51chain 'I' and (resid 324 through 363 )I0
52X-RAY DIFFRACTION52chain 'J' and (resid 1 through 195 )J0
53X-RAY DIFFRACTION53chain 'J' and (resid 196 through 221 )J0
54X-RAY DIFFRACTION54chain 'J' and (resid 222 through 304 )J0
55X-RAY DIFFRACTION55chain 'J' and (resid 305 through 333 )J0
56X-RAY DIFFRACTION56chain 'J' and (resid 334 through 362 )J0
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 20 )K0
58X-RAY DIFFRACTION58chain 'K' and (resid 21 through 32 )K0
59X-RAY DIFFRACTION59chain 'K' and (resid 33 through 68 )K0
60X-RAY DIFFRACTION60chain 'K' and (resid 69 through 89 )K0
61X-RAY DIFFRACTION61chain 'K' and (resid 90 through 102 )K0
62X-RAY DIFFRACTION62chain 'K' and (resid 103 through 122 )K0
63X-RAY DIFFRACTION63chain 'K' and (resid 123 through 218 )K0
64X-RAY DIFFRACTION64chain 'L' and (resid 1 through 35 )L0
65X-RAY DIFFRACTION65chain 'L' and (resid 36 through 61 )L0
66X-RAY DIFFRACTION66chain 'M' and (resid 1 through 208 )M0
67X-RAY DIFFRACTION67chain 'M' and (resid 209 through 374 )M0
68X-RAY DIFFRACTION68chain 'M' and (resid 375 through 495 )M0
69X-RAY DIFFRACTION69chain 'N' and (resid 4 through 15 )N0
70X-RAY DIFFRACTION70chain 'N' and (resid 16 through 25 )N0
71X-RAY DIFFRACTION71chain 'N' and (resid 26 through 37 )N0
72X-RAY DIFFRACTION72chain 'N' and (resid 38 through 67 )N0
73X-RAY DIFFRACTION73chain 'N' and (resid 68 through 86 )N0
74X-RAY DIFFRACTION74chain 'N' and (resid 87 through 106 )N0
75X-RAY DIFFRACTION75chain 'N' and (resid 107 through 124 )N0
76X-RAY DIFFRACTION76chain 'N' and (resid 125 through 141 )N0
77X-RAY DIFFRACTION77chain 'N' and (resid 142 through 159 )N0
78X-RAY DIFFRACTION78chain 'O' and (resid 4 through 25 )O0
79X-RAY DIFFRACTION79chain 'O' and (resid 26 through 37 )O0
80X-RAY DIFFRACTION80chain 'O' and (resid 38 through 51 )O0
81X-RAY DIFFRACTION81chain 'O' and (resid 52 through 77 )O0
82X-RAY DIFFRACTION82chain 'O' and (resid 78 through 86 )O0
83X-RAY DIFFRACTION83chain 'O' and (resid 87 through 124 )O0
84X-RAY DIFFRACTION84chain 'O' and (resid 125 through 141 )O0
85X-RAY DIFFRACTION85chain 'O' and (resid 142 through 159 )O0
86X-RAY DIFFRACTION86chain 'P' and (resid -1 through 15 )P0
87X-RAY DIFFRACTION87chain 'P' and (resid 16 through 65 )P0
88X-RAY DIFFRACTION88chain 'P' and (resid 66 through 110 )P0
89X-RAY DIFFRACTION89chain 'P' and (resid 111 through 143 )P0
90X-RAY DIFFRACTION90chain 'P' and (resid 144 through 160 )P0
91X-RAY DIFFRACTION91chain 'P' and (resid 161 through 199 )P0
92X-RAY DIFFRACTION92chain 'Q' and (resid 1 through 57 )Q0
93X-RAY DIFFRACTION93chain 'Q' and (resid 58 through 79 )Q0
94X-RAY DIFFRACTION94chain 'Q' and (resid 80 through 146 )Q0
95X-RAY DIFFRACTION95chain 'Q' and (resid 147 through 184 )Q0
96X-RAY DIFFRACTION96chain 'Q' and (resid 185 through 221 )Q0
97X-RAY DIFFRACTION97chain 'Q' and (resid 222 through 284 )Q0
98X-RAY DIFFRACTION98chain 'Q' and (resid 285 through 304 )Q0
99X-RAY DIFFRACTION99chain 'Q' and (resid 305 through 322 )Q0
100X-RAY DIFFRACTION100chain 'Q' and (resid 323 through 344 )Q0
101X-RAY DIFFRACTION101chain 'Q' and (resid 345 through 363 )Q0
102X-RAY DIFFRACTION102chain 'R' and (resid 1 through 146 )R0
103X-RAY DIFFRACTION103chain 'R' and (resid 147 through 195 )R0
104X-RAY DIFFRACTION104chain 'R' and (resid 196 through 221 )R0
105X-RAY DIFFRACTION105chain 'R' and (resid 222 through 284 )R0
106X-RAY DIFFRACTION106chain 'R' and (resid 285 through 344 )R0
107X-RAY DIFFRACTION107chain 'R' and (resid 345 through 363 )R0
108X-RAY DIFFRACTION108chain 'S' and (resid 1 through 184 )S0
109X-RAY DIFFRACTION109chain 'S' and (resid 185 through 239 )S0
110X-RAY DIFFRACTION110chain 'S' and (resid 240 through 304 )S0
111X-RAY DIFFRACTION111chain 'S' and (resid 305 through 323 )S0
112X-RAY DIFFRACTION112chain 'S' and (resid 324 through 362 )S0
113X-RAY DIFFRACTION113chain 'T' and (resid 1 through 27 )T0
114X-RAY DIFFRACTION114chain 'T' and (resid 28 through 79 )T0
115X-RAY DIFFRACTION115chain 'T' and (resid 80 through 115 )T0
116X-RAY DIFFRACTION116chain 'T' and (resid 116 through 145 )T0
117X-RAY DIFFRACTION117chain 'T' and (resid 146 through 184 )T0
118X-RAY DIFFRACTION118chain 'T' and (resid 185 through 221 )T0
119X-RAY DIFFRACTION119chain 'T' and (resid 222 through 304 )T0
120X-RAY DIFFRACTION120chain 'T' and (resid 305 through 323 )T0
121X-RAY DIFFRACTION121chain 'T' and (resid 324 through 362 )T0
122X-RAY DIFFRACTION122chain 'U' and (resid 1 through 155 )U0
123X-RAY DIFFRACTION123chain 'U' and (resid 156 through 189 )U0
124X-RAY DIFFRACTION124chain 'U' and (resid 190 through 221 )U0
125X-RAY DIFFRACTION125chain 'U' and (resid 222 through 304 )U0
126X-RAY DIFFRACTION126chain 'U' and (resid 305 through 337 )U0
127X-RAY DIFFRACTION127chain 'U' and (resid 338 through 362 )U0
128X-RAY DIFFRACTION128chain 'V' and (resid 1 through 57 )V0
129X-RAY DIFFRACTION129chain 'V' and (resid 58 through 184 )V0
130X-RAY DIFFRACTION130chain 'V' and (resid 185 through 221 )V0
131X-RAY DIFFRACTION131chain 'V' and (resid 222 through 304 )V0
132X-RAY DIFFRACTION132chain 'V' and (resid 305 through 333 )V0
133X-RAY DIFFRACTION133chain 'V' and (resid 334 through 362 )V0
134X-RAY DIFFRACTION134chain 'W' and (resid 1 through 50 )W0
135X-RAY DIFFRACTION135chain 'W' and (resid 51 through 68 )W0
136X-RAY DIFFRACTION136chain 'W' and (resid 69 through 89 )W0
137X-RAY DIFFRACTION137chain 'W' and (resid 90 through 102 )W0
138X-RAY DIFFRACTION138chain 'W' and (resid 103 through 122 )W0
139X-RAY DIFFRACTION139chain 'W' and (resid 123 through 138 )W0
140X-RAY DIFFRACTION140chain 'W' and (resid 139 through 173 )W0
141X-RAY DIFFRACTION141chain 'W' and (resid 174 through 183 )W0
142X-RAY DIFFRACTION142chain 'W' and (resid 184 through 196 )W0
143X-RAY DIFFRACTION143chain 'W' and (resid 197 through 218 )W0
144X-RAY DIFFRACTION144chain 'X' and (resid 1 through 15 )X0
145X-RAY DIFFRACTION145chain 'X' and (resid 16 through 20 )X0
146X-RAY DIFFRACTION146chain 'X' and (resid 21 through 30 )X0
147X-RAY DIFFRACTION147chain 'X' and (resid 31 through 45 )X0
148X-RAY DIFFRACTION148chain 'X' and (resid 46 through 51 )X0
149X-RAY DIFFRACTION149chain 'X' and (resid 52 through 61 )X0

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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

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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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