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- PDB-5cd4: The Type IE CRISPR Cascade complex from E. coli, with two assembl... -

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基本情報

登録情報
データベース: PDB / ID: 5cd4
タイトルThe Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back
要素
  • (CRISPR system Cascade subunit ...) x 5
  • crRNA
キーワードHYDROLASE/RNA / CRISPR / Cascade / RNA Surveillance / Adaptive Immunity / HYDROLASE-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 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD ...CRISPR-associated protein Cse2 / Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / 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 (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Jackson, R.N. / Golden, S.M. / Carter, J. / Wiedenheft, B.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108888 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM108436 米国
引用ジャーナル: Nucleic Acids Res. / 年: 2015
タイトル: Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.
著者: van Erp, P.B. / Jackson, R.N. / Carter, J. / Golden, S.M. / Bailey, S. / Wiedenheft, B.
履歴
登録2015年7月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年8月26日Provider: repository / タイプ: Initial release
改定 1.12015年10月28日Group: Database references
改定 1.22016年6月1日Group: Data collection
改定 1.32017年9月20日Group: Author supporting evidence / Derived calculations / カテゴリ: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.42019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年9月27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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
改定 1.62024年12月25日Group: Advisory / Derived calculations / Structure summary
カテゴリ: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement

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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 CasE
B: CRISPR system Cascade subunit CasC
C: CRISPR system Cascade subunit CasC
D: CRISPR system Cascade subunit CasC
E: CRISPR system Cascade subunit CasC
F: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasD
I: CRISPR system Cascade subunit CasA
J: CRISPR system Cascade subunit CasB
K: CRISPR system Cascade subunit CasB
L: crRNA
M: CRISPR system Cascade subunit CasE
N: CRISPR system Cascade subunit CasC
O: CRISPR system Cascade subunit CasC
P: CRISPR system Cascade subunit CasC
Q: CRISPR system Cascade subunit CasC
R: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasD
U: CRISPR system Cascade subunit CasA
V: CRISPR system Cascade subunit CasB
W: CRISPR system Cascade subunit CasB
X: crRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)804,32526
ポリマ－804,19424
非ポリマー1312
水00
1
A: CRISPR system Cascade subunit CasE
B: CRISPR system Cascade subunit CasC
C: CRISPR system Cascade subunit CasC
D: CRISPR system Cascade subunit CasC
E: CRISPR system Cascade subunit CasC
F: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasD
I: CRISPR system Cascade subunit CasA
J: CRISPR system Cascade subunit CasB
K: CRISPR system Cascade subunit CasB
L: crRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)402,16213
ポリマ－402,09712
非ポリマー651
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area55210 Å2
ΔGint-327 kcal/mol
Surface area128550 Å2
手法PISA
2
M: CRISPR system Cascade subunit CasE
N: CRISPR system Cascade subunit CasC
O: CRISPR system Cascade subunit CasC
P: CRISPR system Cascade subunit CasC
Q: CRISPR system Cascade subunit CasC
R: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasD
U: CRISPR system Cascade subunit CasA
V: CRISPR system Cascade subunit CasB
W: CRISPR system Cascade subunit CasB
X: crRNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)402,16213
ポリマ－402,09712
非ポリマー651
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area53600 Å2
ΔGint-297 kcal/mol
Surface area127700 Å2
手法PISA
単位格子
Length a, b, c (Å)105.990, 244.800, 426.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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

#1: タンパク質 CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease


分子量: 22324.002 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 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
#2: 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 (大腸菌) / 株: K12 / 遺伝子: casC, cas4, cse4, ygcJ, b2758, JW2728 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46899
#3: 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 (大腸菌) / 株: K12 / 遺伝子: casD, cas5, ygcI, b2757, JW5844 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46898
#4: 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 (大腸菌) / 株: K12 / 遺伝子: casA, cse1, ygcL, b2760, JW2730 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46901
#5: タンパク質
CRISPR system Cascade subunit CasB


分子量: 19231.049 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casB, cse2, ygcK, b2759, JW2729 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P76632

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RNA鎖 / 非ポリマー , 2種, 4分子 LX

#6: RNA鎖 crRNA


分子量: 19677.646 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K-12 / 発現宿主: Escherichia coli (大腸菌)
#7: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.44 Å3/Da / 溶媒含有率: 64.27 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1 M HEPES pH 7.0, 0-0.1 M KCl, and 8-14 percent (w/v) PEG 8000. The crystal used in this study grew in the presence of an 11-nt ssDNA containing a 5-CTT-3 PAM and nine nucleotides ...詳細: 0.1 M HEPES pH 7.0, 0-0.1 M KCl, and 8-14 percent (w/v) PEG 8000. The crystal used in this study grew in the presence of an 11-nt ssDNA containing a 5-CTT-3 PAM and nine nucleotides complementary to the crRNA-guide sequence in a 2:1 oligonucleotide:protein ratio. However, the target DNA is not observed in the electron
PH範囲: 6.5-7.5

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データ収集

回折平均測定温度: 80 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1 Å
検出器タイプ: MAR scanner 300 mm plate / 検出器: IMAGE PLATE / 日付: 2014年3月22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: 1 Å / 相対比: 1
反射解像度: 3.2→49.74 Å / Num. obs: 183649 / % possible obs: 100 % / Observed criterion σ(I): 2 / 冗長度: 7.3 % / Net I/σ(I): 8
反射 シェル解像度: 3.2→3.25 Å / 冗長度: 6.9 % / Mean I/σ(I) obs: 2 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10pre_2089: ???)精密化
XDSデータ削減
Aimless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: 1VY8

1vy8
PDB 未公開エントリ


解像度: 3.2→49.735 Å / SU ML: 0.44 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 24.47 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2496 2000 1.09 %
Rwork0.2122 --
obs0.2127 183492 99.98 %
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
精密化ステップサイクル: LAST / 解像度: 3.2→49.735 Å
タンパク質核酸リガンド溶媒全体
原子数50706 2600 2 0 53308
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00454557
X-RAY DIFFRACTIONf_angle_d0.7474581
X-RAY DIFFRACTIONf_dihedral_angle_d11.45932412
X-RAY DIFFRACTIONf_chiral_restr0.0348588
X-RAY DIFFRACTIONf_plane_restr0.0039271
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.32691410.303312803X-RAY DIFFRACTION100
3.28-3.36870.33061420.28212843X-RAY DIFFRACTION100
3.3687-3.46780.29231410.270112818X-RAY DIFFRACTION100
3.4678-3.57970.33511410.255412835X-RAY DIFFRACTION100
3.5797-3.70760.28271420.236412873X-RAY DIFFRACTION100
3.7076-3.8560.28611420.230412883X-RAY DIFFRACTION100
3.856-4.03140.30161410.215212868X-RAY DIFFRACTION100
4.0314-4.24380.22991430.198412943X-RAY DIFFRACTION100
4.2438-4.50960.22131430.184912895X-RAY DIFFRACTION100
4.5096-4.85750.22741420.173412953X-RAY DIFFRACTION100
4.8575-5.34580.19721430.180213004X-RAY DIFFRACTION100
5.3458-6.11810.23231440.203613056X-RAY DIFFRACTION100
6.1181-7.70360.22591460.212813152X-RAY DIFFRACTION100
7.7036-49.7410.1941490.175213566X-RAY DIFFRACTION100
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)
12.1270.51961.20130.44341.06713.64110.75070.518-0.828-0.7445-0.0396-0.08420.7437-0.2728-0.46911.0667-0.02560.01330.5619-0.03151.3689-83.4375.5641-95.3854
21.3685-0.7454-0.13893.8155-0.60652.5797-0.1790.1488-0.8363-0.02640.13080.7840.7763-0.3524-0.02150.7367-0.074-0.07310.4830.01720.9879-88.936583.7691-89.7468
32.20630.2718-0.44052.5126-0.60485.05160.28470.24510.4804-0.160.21510.0776-0.6043-0.6692-0.23170.46960.0623-0.13440.41030.09340.5037-81.6989100.5849-100.1403
48.1134-1.1527-2.46622.96950.62964.9551-0.1330.2365-0.7183-0.46220.01950.62170.6984-0.32950.1230.5763-0.0579-0.15060.35890.04650.5549-86.736391.2205-93.7158
52.38460.54450.17650.4922-0.79922.0066-0.04720.15450.22270.20510.0860.0854-0.2626-0.11070.02670.54650.17030.04990.30830.02220.4373-72.2703107.1939-71.641
65.9836-0.9372-2.48025.87770.78735.1513-0.39390.89560.2898-0.9008-0.3852-0.3073-1.56140.5310.23620.9642-0.29470.07480.7608-0.00810.6517-50.0368120.5472-79.3449
71.88510.10180.1042.31540.55923.1083-0.25990.5181-0.0294-0.46040.342-0.9765-1.16151.6916-0.15720.9451-0.35720.07971.0107-0.16731.3101-39.5313120.8016-72.4709
80.82271.1691.38413.44640.95365.0605-0.15420.20620.38920.62820.5512-0.8297-0.73030.9109-0.27530.7367-0.0673-0.08690.4683-0.07920.7287-51.6374115.7781-63.6722
93.56871.23460.83542.51171.3582.9146-0.2709-0.161-0.51580.12630.20430.38540.4065-0.9860.02180.6018-0.09610.02550.58530.21540.6806-90.03494.2018-76.2328
106.55211.54772.54461.57610.42192.7181-0.3256-0.15930.76160.3479-0.01250.1663-0.790.05780.38240.75450.17630.00080.3976-0.03360.4947-67.764117.2829-60.5549
112.03470.47271.35082.72711.70656.3289-0.52090.06010.8575-0.3561-0.23420.4857-0.321-0.78620.41870.64340.2639-0.08010.5720.09960.7223-81.0464115.1429-68.5904
121.56180.6096-0.25824.58720.24412.6054-0.049-0.64050.10850.40210.17770.5065-0.4697-0.7758-0.00630.55590.31120.09610.63580.03180.5543-83.9183105.1206-56.9805
136.08811.7328-0.24393.4982-0.00683.3056-0.2073-0.39050.58830.18360.10140.632-0.5803-0.64280.10340.97920.42090.14360.73120.09370.7304-81.6866120.1434-54.8798
141.81760.54950.4832.00720.00752.26660.1435-0.15840.25250.43170.0412-0.4102-0.35370.4182-0.18220.650.1227-0.03020.4967-0.0650.4338-49.111594.2139-45.5827
151.3575-0.23380.66661.2693-0.57612.357-0.1293-0.20640.19430.47540.0869-0.1823-0.23680.2935-0.01470.57110.1486-0.05540.4297-0.080.3488-55.950890.6102-45.8055
161.42930.2786-0.82911.187-1.66514.46830.0459-0.24860.28440.49750.33160.4962-0.20220.2879-0.15830.55120.19170.09160.3204-0.05960.3725-68.954795.4567-52.5152
170.64650.88940.24123.1298-1.41674.2262-0.313-0.35510.570.30220.18330.07510.1573-0.8528-0.15880.40220.13560.10660.4990.03710.3966-78.294878.9005-50.6679
182.01490.52751.62063.56662.2052.3080.1741-0.56070.26810.343-0.30660.63160.1207-0.80560.29730.75290.29780.31720.7081-0.00940.5251-79.118490.2616-37.7226
191.95240.310.07232.34340.22.21680.0431-0.68220.00270.79680.0209-0.3428-0.18240.2229-0.08410.45690.0832-0.04240.5632-0.0070.3551-50.235561.5324-37.6177
201.7311-0.03050.441.7143-0.3680.5084-0.2763-0.7385-0.27691.0059-0.0386-0.33910.31080.48370.15120.84570.2411-0.07080.91910.19310.496-47.673147.627-26.5452
211.61842.0613-0.28824.22310.06420.3358-0.10170.26230.3291-0.12590.26850.2236-0.14430.360.05150.27710.1318-0.0010.4595-0.00230.2434-58.078772.3026-59.8869
222.18120.44910.10163.77911.47882.9887-0.1241-0.00210.5802-0.44060.2591-0.7952-0.82070.2989-0.15210.76360.2537-0.01790.4126-0.05620.6277-48.00489.7966-56.7727
231.4578-0.4109-0.02273.7156-0.96471.4291-0.1837-0.3893-0.28560.6496-0.0834-0.1515-0.1903-0.27910.11910.35590.11250.10720.56970.06090.3264-65.439353.7538-38.2438
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1091.5979-0.2412-1.7424.1133-2.3817.6697-0.32750.4683-0.4786-0.5972-0.08970.0872-0.05770.20920.08780.5003-0.2133-0.01130.84840.08790.521-7.6787-16.3595-77.9895
1100.73410.22420.22081.4265-1.10651.5817-0.03960.176-0.01130.0605-0.08030.02970.5275-0.45750.32750.32950.0239-0.00880.46380.20460.4656-13.2515-20.1007-43.3275
1111.0958-0.11550.11342.28560.9362.7368-0.20680.23770.14940.2004-0.12240.26550.0957-0.26460.30530.26590.0271-0.02720.41290.2170.372-10.5927-13.6072-42.8765
1121.7961-0.46510.08452.7382.68364.071-0.16370.40510.0875-0.08610.0777-0.34060.04030.5973-0.02690.33440.0950.0360.65110.26790.45690.788-21.8547-50.2276
1131.86730.40850.03476.48433.99985.2444-0.2957-0.0825-0.60580.8090.5188-0.50891.33371.1287-0.24620.60680.17940.04870.50850.07740.6159-6.4618-36.7444-38.8948
1146.6154.36512.66727.98892.89712.3589-0.02490.0069-0.80570.3604-0.0678-1.1870.760.9829-0.03140.52520.2840.03940.80760.19120.76887.721-34.6686-47.5863
1151.07030.5280.34331.25230.3082.29160.07090.28340.0906-0.0619-0.16410.19530.19640.09720.06170.58480.06230.07960.29490.13920.4305-25.2151-40.07-54.7198
1161.22740.04230.9621.22830.25862.2670.28410.5699-0.7685-0.65810.27550.07990.99280.619-0.26451.56640.20840.03110.7547-0.11630.775-24.2222-63.8532-84.212
1171.80050.50440.86851.92730.02983.4988-0.10590.79460.2575-0.85040.0490.01720.16330.5278-0.0021.38640.09970.01250.63630.03260.5722-27.9861-53.4018-86.4221
1181.55720.79120.61162.81391.06363.6887-0.00820.3613-0.1772-0.50680.43670.47290.61910.3890.01380.86210.0340.21290.48690.05030.4377-30.6582-50.1556-72.5055
1194.26752.5908-2.06593.5095-1.31273.5910.2306-0.13350.56130.8092-0.11820.8738-0.41320.2673-0.41580.36440.0861-0.11430.37950.14610.3482-22.4736-20.5603-50.1977
1200.5051-0.1351-0.28183.54070.29241.5146-0.06870.1698-0.0054-0.04050.19140.44020.38930.22810.35860.56770.01580.22950.27580.40780.3548-25.222-42.2809-55.1913
1210.71810.09050.29362.82030.08810.9234-0.3329-0.0112-0.07340.07440.22760.13250.50870.36210.010.67610.13870.13840.46880.1310.4555-17.4105-48.2334-55.9038
1222.49812.2009-0.10485.31082.64133.10060.3178-0.00210.12631.0495-0.70880.21240.73920.08990.14790.55240.08470.08790.36630.20790.4375-29.6292-46.3984-40.5739
1232.8799-0.1067-1.09883.9417-1.09942.1622-0.1417-0.3422-0.63840.5384-0.0515-0.05880.6026-0.0102-0.07131.00890.17120.0080.32290.18020.6968-23.9718-53.6397-39.0372
1242.82280.7211.71265.74050.79783.51150.0858-0.3519-0.2260.36580.1009-0.48380.9643-0.077-0.16771.02770.36140.11340.57650.14170.772-14.2413-59.6578-46.6476
1251.5616-0.02740.37625.8916-3.24754.1112-0.1837-0.06560.07920.0371-0.11760.46010.7224-0.29190.23210.9114-0.04920.1960.38320.14160.6056-47.9055-54.2351-52.5038
1262.7957-0.36260.3864.5599-2.30664.5237-0.17780.3049-0.1673-0.5322-0.2070.28750.7329-0.08570.41090.7757-0.03150.02440.34690.12210.5896-45.0147-50.7271-63.7979
1274.2608-1.5869-5.03330.741.44927.2027-0.17720.5995-0.4890.04720.40380.28451.0883-0.4815-0.11380.913-0.10730.01290.4314-0.07470.936-51.3561-59.0536-60.6932
1287.462.7809-4.48153.7432-3.96964.71540.1963-1.0095-0.1950.7073-0.43690.3995-0.72170.2226-0.29340.8549-0.0310.15650.2680.06680.6941-41.4272-38.6065-47.7673
1292.48421.0755-1.46445.74680.74381.2488-0.33151.01430.4733-1.48690.3366-0.1878-0.4933-0.09990.05250.81450.00590.03030.68740.1350.641-30.566-37.9695-79.4498
1302.83443.2937-2.05324.4043-2.59112.2218-0.08650.1301-0.1292-0.31390.06720.46380.3866-0.12140.1590.65380.0410.07180.29270.05210.5323-44.2009-45.3588-56.1902
1316.9813.9736-0.90674.39030.00280.24730.232-0.2108-0.9395-0.4105-0.05150.32171.0388-0.1596-0.10031.232-0.06560.17680.38490.08150.843-48.7193-68.2185-58.4433
1324.70530.30642.84286.0295-3.85154.4267-0.04590.401-0.32670.0902-0.4611-0.00130.46930.26440.3040.64890.05680.22270.25420.09080.7491-36.5076-54.275-56.325
1333.54860.3118-0.01594.30490.03882.83310.0847-0.4485-0.22250.30220.17580.99030.5495-0.4825-0.32581.0307-0.18850.17370.48330.04761.0267-57.6516-57.2914-46.7265
1341.88810.33130.07213.61640.05682.2501-0.02380.1119-0.059-0.17670.00280.54990.01450.0405-0.13160.6789-0.0847-0.03610.40950.02481.1294-53.9355-49.4587-68.3511
1353.02860.53820.91475.09791.95876.98150.1544-0.2241-0.16880.4109-0.31071.12770.6474-0.42280.17540.7947-0.19030.11780.55040.08321.314-60.9501-49.4004-53.5186
1361.9244-0.344-0.29351.450.58352.91850.05190.0887-0.147-0.5081-0.08780.6954-0.026-0.54370.16640.7755-0.1403-0.23780.55130.07440.8875-64.4619-31.8377-79.04
1372.41790.40691.59191.0260.68212.2778-0.1125-0.05650.0397-0.0753-0.10730.44470.2388-0.23220.14820.4161-0.02390.02950.35940.12940.6123-49.2528-20.8652-45.279
1381.4148-0.03930.21720.3334-0.95962.76480.0674-0.1884-0.69830.69450.1382-0.17551.16740.0787-0.43031.81510.3608-0.1430.64610.13930.8633-5.9542-53.87538.5441
1391.93951.20791.91160.79671.09362.0871-0.35290.1658-0.19380.78170.3976-0.39780.58460.8715-0.06871.21710.7265-0.19131.4115-0.04250.89953.5664-43.48046.2156
1401.12311.89521.56446.47647.2828.7564-0.8231-0.4652-0.9170.43370.6809-0.45910.14150.51490.071.72060.6692-0.07971.3396-0.18490.69720.5537-54.8462-0.161
1413.98261.1770.08743.3634-0.06870.0050.00170.3769-0.4906-0.53210.0046-0.47930.2655-0.03870.01481.38310.2401-0.31310.80650.01330.7005-5.1969-46.53370.1793
1425.85361.0868-0.87962.2509-1.40973.19130.1097-0.2398-0.39250.18720.26770.52730.5068-0.5298-0.62221.7147-0.07430.02180.5730.25360.722-18.228-49.002310.5595
1437.2999-1.35280.01874.3665-1.25785.6085-0.36410.1150.11621.0090.4460.09520.02190.2283-0.21941.3199-0.0667-0.21890.42040.08620.5521-13.9824-35.45097.8716
1449.0302-2.44061.35558.118-0.79518.52670.36150.0467-0.4860.01990.30410.2450.282-0.8657-0.50191.0524-0.0035-0.14310.58380.11430.3761-19.5516-38.22580.6486
1457.966-1.45971.10474.6227-1.58657.57230.11610.10520.45060.8426-0.2161-0.1006-0.4536-0.4175-0.05881.0238-0.09180.02590.47090.07190.3389-29.8055-22.6951-3.3378
1462.267-1.94561.68041.6949-1.74024.75750.2473-0.1113-0.32390.172-0.10340.52160.356-0.7682-0.10910.65220.06370.05270.38460.02420.4902-35.6023-17.4181-13.8481
1471.47571.15480.28311.5571-0.58563.5502-0.10750.0423-0.11640.03770.0383-0.2375-0.1174-0.07170.06250.49740.1410.01770.33960.11570.3969-32.0369-15.3439-23.0509
1480.8578-0.55710.70560.3625-0.47890.8782-0.3129-0.0012-0.0172-0.49890.15630.53430.57820.4-0.02960.58940.01910.11710.33770.0530.461-34.0724-42.6558-65.8062
1490.52210.5820.72983.19141.87241.834-0.13480.0520.04-0.3485-0.14070.2278-0.234-0.20460.20820.36990.0236-0.06850.47770.23560.4153-14.7422-8.4403-48.0132
1500.0004-0.19020.00960.1878-0.0309-0.0026-0.2795-0.04950.45180.18240.37960.3541-0.097-0.7743-0.12211.05360.0864-0.25710.40360.14150.6534-14.4119-7.236.4592
1511.77430.9963-0.06270.65970.21652.9602-0.31740.3346-0.2732-0.2159-0.20960.3586-0.10080.4940.17441.28720.3265-0.11630.583-0.0690.6727-2.1933-43.588830.7166
1522.4234-0.80280.57911.8261-0.16282.21120.51970.6219-0.28770.0477-0.4013-0.04720.51170.4295-0.15971.69270.570.03350.78580.13390.635414.7043-65.154316.3229
1531.2613-0.14-0.3220.2280.49551.14110.12550.5977-0.3779-0.017-0.11950.0999-0.0087-0.17350.06821.62620.61370.06561.1780.23871.154526.3272-72.032318.4194
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 97 )
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 199 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 57 )
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 184 )
9X-RAY DIFFRACTION9chain 'B' and (resid 185 through 221 )
10X-RAY DIFFRACTION10chain 'B' and (resid 222 through 260 )
11X-RAY DIFFRACTION11chain 'B' and (resid 261 through 284 )
12X-RAY DIFFRACTION12chain 'B' and (resid 285 through 337 )
13X-RAY DIFFRACTION13chain 'B' and (resid 338 through 362 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 129 )
15X-RAY DIFFRACTION15chain 'C' and (resid 130 through 260 )
16X-RAY DIFFRACTION16chain 'C' and (resid 261 through 284 )
17X-RAY DIFFRACTION17chain 'C' and (resid 285 through 323 )
18X-RAY DIFFRACTION18chain 'C' and (resid 324 through 363 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 115 )
20X-RAY DIFFRACTION20chain 'D' and (resid 116 through 184 )
21X-RAY DIFFRACTION21chain 'D' and (resid 185 through 201 )
22X-RAY DIFFRACTION22chain 'D' and (resid 202 through 221 )
23X-RAY DIFFRACTION23chain 'D' and (resid 222 through 260 )
24X-RAY DIFFRACTION24chain 'D' and (resid 261 through 293 )
25X-RAY DIFFRACTION25chain 'D' and (resid 294 through 322 )
26X-RAY DIFFRACTION26chain 'D' and (resid 323 through 362 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 145 )
28X-RAY DIFFRACTION28chain 'E' and (resid 146 through 184 )
29X-RAY DIFFRACTION29chain 'E' and (resid 185 through 238 )
30X-RAY DIFFRACTION30chain 'E' and (resid 239 through 260 )
31X-RAY DIFFRACTION31chain 'E' and (resid 261 through 323 )
32X-RAY DIFFRACTION32chain 'E' and (resid 324 through 363 )
33X-RAY DIFFRACTION33chain 'F' and (resid 1 through 57 )
34X-RAY DIFFRACTION34chain 'F' and (resid 58 through 79 )
35X-RAY DIFFRACTION35chain 'F' and (resid 80 through 163 )
36X-RAY DIFFRACTION36chain 'F' and (resid 164 through 184 )
37X-RAY DIFFRACTION37chain 'F' and (resid 185 through 221 )
38X-RAY DIFFRACTION38chain 'F' and (resid 222 through 304 )
39X-RAY DIFFRACTION39chain 'F' and (resid 305 through 323 )
40X-RAY DIFFRACTION40chain 'F' and (resid 324 through 363 )
41X-RAY DIFFRACTION41chain 'G' and (resid 2 through 57 )
42X-RAY DIFFRACTION42chain 'G' and (resid 58 through 155 )
43X-RAY DIFFRACTION43chain 'G' and (resid 156 through 195 )
44X-RAY DIFFRACTION44chain 'G' and (resid 196 through 221 )
45X-RAY DIFFRACTION45chain 'G' and (resid 222 through 322 )
46X-RAY DIFFRACTION46chain 'G' and (resid 323 through 363 )
47X-RAY DIFFRACTION47chain 'H' and (resid 1 through 19 )
48X-RAY DIFFRACTION48chain 'H' and (resid 20 through 32 )
49X-RAY DIFFRACTION49chain 'H' and (resid 33 through 68 )
50X-RAY DIFFRACTION50chain 'H' and (resid 69 through 89 )
51X-RAY DIFFRACTION51chain 'H' and (resid 90 through 102 )
52X-RAY DIFFRACTION52chain 'H' and (resid 103 through 122 )
53X-RAY DIFFRACTION53chain 'H' and (resid 123 through 138 )
54X-RAY DIFFRACTION54chain 'H' and (resid 139 through 157 )
55X-RAY DIFFRACTION55chain 'H' and (resid 158 through 183 )
56X-RAY DIFFRACTION56chain 'H' and (resid 184 through 201 )
57X-RAY DIFFRACTION57chain 'H' and (resid 202 through 219 )
58X-RAY DIFFRACTION58chain 'I' and (resid 1 through 84 )
59X-RAY DIFFRACTION59chain 'I' and (resid 85 through 124 )
60X-RAY DIFFRACTION60chain 'I' and (resid 125 through 176 )
61X-RAY DIFFRACTION61chain 'I' and (resid 177 through 219 )
62X-RAY DIFFRACTION62chain 'I' and (resid 220 through 283 )
63X-RAY DIFFRACTION63chain 'I' and (resid 284 through 342 )
64X-RAY DIFFRACTION64chain 'I' and (resid 343 through 374 )
65X-RAY DIFFRACTION65chain 'I' and (resid 375 through 427 )
66X-RAY DIFFRACTION66chain 'I' and (resid 428 through 495 )
67X-RAY DIFFRACTION67chain 'J' and (resid 4 through 67 )
68X-RAY DIFFRACTION68chain 'J' and (resid 68 through 86 )
69X-RAY DIFFRACTION69chain 'J' and (resid 87 through 124 )
70X-RAY DIFFRACTION70chain 'J' and (resid 125 through 141 )
71X-RAY DIFFRACTION71chain 'J' and (resid 142 through 159 )
72X-RAY DIFFRACTION72chain 'K' and (resid 3 through 16 )
73X-RAY DIFFRACTION73chain 'K' and (resid 17 through 26 )
74X-RAY DIFFRACTION74chain 'K' and (resid 27 through 44 )
75X-RAY DIFFRACTION75chain 'K' and (resid 45 through 54 )
76X-RAY DIFFRACTION76chain 'K' and (resid 55 through 86 )
77X-RAY DIFFRACTION77chain 'K' and (resid 87 through 124 )
78X-RAY DIFFRACTION78chain 'K' and (resid 125 through 160 )
79X-RAY DIFFRACTION79chain 'L' and (resid 1 through 10 )
80X-RAY DIFFRACTION80chain 'L' and (resid 11 through 20 )
81X-RAY DIFFRACTION81chain 'L' and (resid 21 through 35 )
82X-RAY DIFFRACTION82chain 'L' and (resid 36 through 40 )
83X-RAY DIFFRACTION83chain 'L' and (resid 41 through 50 )
84X-RAY DIFFRACTION84chain 'L' and (resid 51 through 55 )
85X-RAY DIFFRACTION85chain 'L' and (resid 56 through 60 )
86X-RAY DIFFRACTION86chain 'M' and (resid 1 through 82 )
87X-RAY DIFFRACTION87chain 'M' and (resid 83 through 199 )
88X-RAY DIFFRACTION88chain 'N' and (resid 2 through 84 )
89X-RAY DIFFRACTION89chain 'N' and (resid 85 through 129 )
90X-RAY DIFFRACTION90chain 'N' and (resid 130 through 184 )
91X-RAY DIFFRACTION91chain 'N' and (resid 185 through 221 )
92X-RAY DIFFRACTION92chain 'N' and (resid 222 through 304 )
93X-RAY DIFFRACTION93chain 'N' and (resid 305 through 362 )
94X-RAY DIFFRACTION94chain 'O' and (resid 2 through 78 )
95X-RAY DIFFRACTION95chain 'O' and (resid 79 through 184 )
96X-RAY DIFFRACTION96chain 'O' and (resid 185 through 221 )
97X-RAY DIFFRACTION97chain 'O' and (resid 222 through 260 )
98X-RAY DIFFRACTION98chain 'O' and (resid 261 through 362 )
99X-RAY DIFFRACTION99chain 'P' and (resid 1 through 57 )
100X-RAY DIFFRACTION100chain 'P' and (resid 58 through 284 )
101X-RAY DIFFRACTION101chain 'P' and (resid 285 through 362 )
102X-RAY DIFFRACTION102chain 'Q' and (resid 1 through 57 )
103X-RAY DIFFRACTION103chain 'Q' and (resid 58 through 115 )
104X-RAY DIFFRACTION104chain 'Q' and (resid 116 through 145 )
105X-RAY DIFFRACTION105chain 'Q' and (resid 146 through 175 )
106X-RAY DIFFRACTION106chain 'Q' and (resid 176 through 322 )
107X-RAY DIFFRACTION107chain 'Q' and (resid 323 through 363 )
108X-RAY DIFFRACTION108chain 'R' and (resid 1 through 115 )
109X-RAY DIFFRACTION109chain 'R' and (resid 116 through 175 )
110X-RAY DIFFRACTION110chain 'R' and (resid 176 through 200 )
111X-RAY DIFFRACTION111chain 'R' and (resid 201 through 238 )
112X-RAY DIFFRACTION112chain 'R' and (resid 239 through 284 )
113X-RAY DIFFRACTION113chain 'R' and (resid 285 through 322 )
114X-RAY DIFFRACTION114chain 'R' and (resid 323 through 363 )
115X-RAY DIFFRACTION115chain 'S' and (resid 2 through 57 )
116X-RAY DIFFRACTION116chain 'S' and (resid 58 through 112 )
117X-RAY DIFFRACTION117chain 'S' and (resid 113 through 163 )
118X-RAY DIFFRACTION118chain 'S' and (resid 164 through 184 )
119X-RAY DIFFRACTION119chain 'S' and (resid 185 through 212 )
120X-RAY DIFFRACTION120chain 'S' and (resid 213 through 238 )
121X-RAY DIFFRACTION121chain 'S' and (resid 239 through 284 )
122X-RAY DIFFRACTION122chain 'S' and (resid 285 through 304 )
123X-RAY DIFFRACTION123chain 'S' and (resid 305 through 338 )
124X-RAY DIFFRACTION124chain 'S' and (resid 339 through 362 )
125X-RAY DIFFRACTION125chain 'T' and (resid 1 through 19 )
126X-RAY DIFFRACTION126chain 'T' and (resid 20 through 50 )
127X-RAY DIFFRACTION127chain 'T' and (resid 51 through 68 )
128X-RAY DIFFRACTION128chain 'T' and (resid 69 through 88 )
129X-RAY DIFFRACTION129chain 'T' and (resid 89 through 103 )
130X-RAY DIFFRACTION130chain 'T' and (resid 104 through 122 )
131X-RAY DIFFRACTION131chain 'T' and (resid 123 through 138 )
132X-RAY DIFFRACTION132chain 'T' and (resid 139 through 157 )
133X-RAY DIFFRACTION133chain 'T' and (resid 158 through 192 )
134X-RAY DIFFRACTION134chain 'T' and (resid 193 through 210 )
135X-RAY DIFFRACTION135chain 'T' and (resid 211 through 219 )
136X-RAY DIFFRACTION136chain 'U' and (resid 1 through 374 )
137X-RAY DIFFRACTION137chain 'U' and (resid 375 through 496 )
138X-RAY DIFFRACTION138chain 'V' and (resid 4 through 26 )
139X-RAY DIFFRACTION139chain 'V' and (resid 27 through 37 )
140X-RAY DIFFRACTION140chain 'V' and (resid 38 through 51 )
141X-RAY DIFFRACTION141chain 'V' and (resid 52 through 67 )
142X-RAY DIFFRACTION142chain 'V' and (resid 68 through 86 )
143X-RAY DIFFRACTION143chain 'V' and (resid 87 through 129 )
144X-RAY DIFFRACTION144chain 'V' and (resid 130 through 160 )
145X-RAY DIFFRACTION145chain 'W' and (resid 5 through 51 )
146X-RAY DIFFRACTION146chain 'W' and (resid 52 through 94 )
147X-RAY DIFFRACTION147chain 'W' and (resid 95 through 160 )
148X-RAY DIFFRACTION148chain 'X' and (resid 1 through 10 )
149X-RAY DIFFRACTION149chain 'X' and (resid 11 through 20 )
150X-RAY DIFFRACTION150chain 'X' and (resid 21 through 35 )
151X-RAY DIFFRACTION151chain 'X' and (resid 36 through 40 )
152X-RAY DIFFRACTION152chain 'X' and (resid 41 through 50 )
153X-RAY DIFFRACTION153chain 'X' and (resid 51 through 60 )

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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

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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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