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- PDB-5h9e: Crystal structure of E. coli Cascade bound to a PAM-containing ds... -

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基本情報

登録情報
データベース: PDB / ID: 5h9e
タイトルCrystal structure of E. coli Cascade bound to a PAM-containing dsDNA target (32-nt spacer) at 3.20 angstrom resolution.
要素
  • (CRISPR system Cascade subunit ...) x 5
  • (DNA (47-MER) ...) x 2
  • crRNA (61-MER)
キーワードImmune System/RNA / CRISPR Cascade / Immune System-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 / 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 Cse2 / 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
DNA / DNA (> 10) / 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: 3.21 Å
データ登録者Hayes, R.P. / Xiao, Y. / Ding, F. / van Erp, P.B.G. / Rajashankar, K. / Bailey, S. / Wiedenheft, B. / Ke, A.
引用ジャーナル: Nature / 年: 2016
タイトル: Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.
著者: Hayes, R.P. / Xiao, Y. / Ding, F. / van Erp, P.B. / Rajashankar, K. / Bailey, S. / Wiedenheft, B. / Ke, A.
履歴
登録2015年12月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月17日Provider: repository / タイプ: Initial release
改定 1.12016年2月24日Group: Database references
改定 1.22016年3月9日Group: Database references
改定 1.32023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: CRISPR system Cascade subunit CasA
B: CRISPR system Cascade subunit CasB
C: CRISPR system Cascade subunit CasB
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 CasC
I: CRISPR system Cascade subunit CasC
J: CRISPR system Cascade subunit CasD
L: crRNA (61-MER)
M: DNA (47-MER) Non-target
N: DNA (47-MER) Target
K: CRISPR system Cascade subunit CasE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)434,99615
ポリマ－434,93114
非ポリマー651
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area62890 Å2
ΔGint-275 kcal/mol
Surface area125820 Å2
手法PISA
単位格子
Length a, b, c (Å)92.807, 149.825, 404.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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要素

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CRISPR system Cascade subunit ... , 5種, 11分子 ABCDEFGHIJK

#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: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (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
#2: タンパク質 CRISPR system Cascade subunit CasB


分子量: 21207.279 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (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
#3: タンパク質
CRISPR system Cascade subunit CasC


分子量: 40071.402 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (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
#4: タンパク質 CRISPR system Cascade subunit CasD


分子量: 25239.803 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (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
#8: タンパク質 CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease


分子量: 22324.002 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (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

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DNA (47-MER) ... , 2種, 2分子 MN

#6: DNA鎖 DNA (47-MER) Non-target


分子量: 14447.288 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)
#7: DNA鎖 DNA (47-MER) Target


分子量: 14434.274 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)

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RNA鎖 / 非ポリマー , 2種, 2分子 L

#5: RNA鎖 crRNA (61-MER)


分子量: 19677.646 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 発現宿主: Escherichia coli (大腸菌)
#9: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 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

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試料調製

結晶マシュー密度: 3.27 Å3/Da / 溶媒含有率: 62.35 %
結晶化温度: 291.95 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2 / 詳細: 1.6 M Na/K Phosphate

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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: APS / ビームライン: 24-ID-C / 波長: 0.979 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2015年8月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.979 Å / 相対比: 1
反射解像度: 3.2→50.085 Å / Num. obs: 90280 / % possible obs: 96.8 % / 冗長度: 3.6 % / Rmerge(I) obs: 0.265 / Net I/σ(I): 5.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.4_1496精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5H9F

5h9f


解像度: 3.21→50.085 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 23.38 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.247 1997 2.22 %
Rwork0.209 --
obs0.21 90154 97.2 %
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: 3.21→50.085 Å
タンパク質核酸リガンド溶媒全体
原子数24709 2507 1 0 27217
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00527955
X-RAY DIFFRACTIONf_angle_d0.9538390
X-RAY DIFFRACTIONf_dihedral_angle_d16.59710389
X-RAY DIFFRACTIONf_chiral_restr0.0344401
X-RAY DIFFRACTIONf_plane_restr0.0044569
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2137-3.29410.34981270.28215612X-RAY DIFFRACTION88
3.2941-3.38310.32781410.27226209X-RAY DIFFRACTION97
3.3831-3.48260.29021380.25226168X-RAY DIFFRACTION96
3.4826-3.5950.25951440.23416325X-RAY DIFFRACTION99
3.595-3.72350.29211430.22356351X-RAY DIFFRACTION99
3.7235-3.87250.2861450.22156379X-RAY DIFFRACTION99
3.8725-4.04870.24981450.20996377X-RAY DIFFRACTION99
4.0487-4.2620.21981420.19356311X-RAY DIFFRACTION98
4.262-4.52890.23321430.17966285X-RAY DIFFRACTION97
4.5289-4.87830.20571450.17216387X-RAY DIFFRACTION98
4.8783-5.36870.21481450.1836410X-RAY DIFFRACTION99
5.3687-6.14440.2411450.19866392X-RAY DIFFRACTION98
6.1444-7.73670.24611450.21166375X-RAY DIFFRACTION96
7.7367-50.09070.2141490.20036576X-RAY DIFFRACTION96
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)
12.7544-1.0264-0.43023.56470.97431.97880.14410.7183-0.1291-0.8588-0.2959-0.3130.12950.3340.16020.84360.09540.13860.65970.03480.458712.54521.7508-134.034
21.717-1.10710.27263.5891-0.15162.13390.18930.3588-0.0734-0.6928-0.2355-0.06660.2109-0.00560.04630.59240.0578-0.01190.4879-0.03530.39492.4954-2.4338-126.6491
36.5810.1271-3.25071.7441-0.60021.2009-0.1030.0501-0.08950.01640.03820.00920.038-0.01010.05110.34660.0187-0.08750.378-0.0630.402-4.82831.5695-96.0704
42.0455-1.0996-2.85548.613-0.76963.65520.66410.10430.7458-0.2063-0.1576-0.6747-1.09850.8015-0.45871.282-0.31720.12290.8545-0.10150.8192-3.396646.3767-48.2276
51.3633-0.1798-0.40050.0649-0.30373.29720.0951-0.32820.35810.2459-0.81360.1218-0.50660.09920.51791.6674-0.37690.06160.8076-0.17320.6563-8.482651.3086-34.9748
66.9754-1.1153-3.32234.8412-3.72175.45410.63590.10270.31880.5911-0.06140.4433-0.2580.0314-0.5581.43670.04510.08740.6416-0.1310.5869-20.27348.4372-39.4934
74.57810.0311-1.05044.79740.76863.30050.45780.40390.3521-0.9452-0.1922-0.3476-1.61570.3761-0.21841.4736-0.09310.17870.62720.00840.6418-11.355346.8811-46.2848
81.9997-0.9345-8.67436.0626-3.16398.186-0.31850.60230.28680.0731-0.4024-0.463-0.64521.15190.68311.1599-0.13490.01660.94950.10.38660.409730.6646-49.5713
96.038-2.6465.48474.2403-3.14275.1509-0.32440.66420.2162-0.0769-0.1814-0.51190.05710.31070.36710.47580.0062-0.14920.5659-0.02980.5245-5.588426.1111-43.1058
102.0367-1.66162.73666.14350.09838.4243-0.5691-0.21870.02480.9932-0.02110.51420.00870.01780.64340.7556-0.08590.05680.6035-0.11210.4367-16.108823.9481-39.5611
112.0042-1.83370.77532.00312.46736.3731-0.06560.54690.42840.1335-0.23120.7312-0.0108-0.17010.27490.67730.00630.00770.6505-0.17810.5299-25.329133.0667-45.4434
126.525-3.02340.41162.4794-0.82142.90380.15540.37980.55410.3967-0.10810.3774-0.67250.17-0.10020.8576-0.163-0.05540.444-0.01140.4725-15.49234.1722-38.3765
133.8837-1.19910.96033.8661-1.41750.59820.5656-0.35070.2648-0.22880.2133-0.4852-0.60921.5848-0.55130.705-0.1501-0.05170.7089-0.12480.4551-2.909333.0843-42.0083
142.02544.64531.69436.48321.05042.28510.3519-0.0133-0.0938-1.23110.12710.26220.1806-0.0557-0.36330.9841-0.15370.15830.6208-0.0150.7556-11.189936.4271-52.1892
155.4129-5.44942.29195.6364-1.84529.7783-0.0391-0.07850.5823-0.22130.0998-0.6294-0.46550.29830.06950.5461-0.1242-0.09490.4679-0.02250.5335-10.691322.3683-49.3761
167.5144-1.881-3.59065.0025-0.57248.14870.3277-0.4961-0.36170.2676-0.0779-0.21860.08691.2237-0.17630.43070.0396-0.11240.5587-0.05060.3772-13.92173.5323-54.33
177.69711.0652.72328.39737.9541.9823-0.345-0.41151.0252-0.8274-0.5678-0.0717-0.2336-0.5810.79190.57230.03410.07670.4588-0.00890.4848-21.433416.4209-57.3139
185.06040.142-0.69754.14410.24585.71910.2518-0.00150.3026-0.0506-0.2315-0.3822-0.13960.9453-0.03680.32340.01130.00830.4728-0.0360.3549-11.499812.136-58.0859
197.3151-3.2086-3.10792.04635.04424.1021-0.5248-0.0377-0.780.33190.15080.27960.810.78450.32310.76720.1443-0.05840.60450.09110.4897-15.384-5.9998-64.5981
202.87951.047-1.68715.8874-1.7286.3242-0.390.2322-0.1691-0.2588-0.2542-0.1303-0.09440.29380.58710.3737-0.0166-0.16710.36620.05550.5895-24.5066-4.5278-73.2105
212.8391-2.4152-2.72426.9602-0.59764.35890.23710.35890.4012-0.31210.48270.1342-0.7526-0.4927-0.56410.41850.0277-0.06480.53380.0650.5031-25.6659.0007-77.1576
223.3241-2.9787-0.62866.56610.54522.73010.3222-0.18810.0599-0.7387-0.1160.00170.23480.2881-0.14380.37680.00560.01780.44690.00320.263-23.92033.2674-67.2229
239.7218-1.63981.04897.4004-5.30342.01910.00750.34570.3246-0.39510.5783-0.8596-0.07311.0162-0.44440.4256-0.052-0.0460.4788-0.09250.4991-11.24824.9288-69.706
242.05817.0725-0.26732.033-0.06437.9377-0.01510.2187-0.25720.50670.0699-0.7378-0.76640.63820.02120.394-0.0022-0.05180.37330.03160.506-18.51181.1961-80.4248
250.6881-0.7177-0.14521.4531-0.17140.7113-0.1885-0.0296-0.071-0.01770.1452-0.1884-0.79280.14060.06661.6011-0.08760.06680.6017-0.09250.5621-24.059458.1146-12.6979
261.2142-0.78170.04862.21520.56041.6046-0.2144-0.10960.3663-0.03170.3467-0.6178-0.54030.8503-0.0521.2825-0.3923-0.09871.0144-0.13250.93724.984550.5871-9.7689
271.8085-0.23320.31484.19920.85962.8028-0.0145-0.61730.31351.02020.2343-0.9429-0.13530.8683-0.2881.351-0.1562-0.24461.2348-0.1660.89226.36737.0897-2.1413
281.7688-0.55560.60772.03270.40761.4861-0.1974-0.07680.11140.4810.1501-0.057-0.54220.13240.07851.4355-0.12710.06610.6308-0.06250.5061-22.020151.3-4.4285
290.6793-0.2879-0.10273.29171.35950.62360.1887-0.7354-0.09230.95150.25430.5411-0.8262-0.6516-0.26911.83750.14690.30760.6815-0.06820.6051-38.697451.72421.4139
305.45541.23381.52432.01514.00868.16730.222-0.068-0.0123-0.18990.25110.02980.1597-0.022-0.20482.09720.19290.37360.6763-0.33170.4324-34.271256.469610.8632
310.6828-1.2865-0.2532.7838-0.20541.27710.0921-0.25320.3090.07380.4612-0.6032-0.38250.6551-0.49212.488-0.2507-0.18970.269-0.61910.2248-23.476753.788211.9488
321.93150.27830.7661.60420.62271.1425-0.1342-0.2470.39940.2128-0.01380.0461-0.1938-0.07190.1510.97760.03480.13140.4466-0.05640.4613-31.312534.4101-18.0955
332.8558-0.0717-0.93212.7185-1.3542.6973-0.1502-0.2367-0.29250.39910.1134-0.09360.40350.29520.02840.8613-0.0074-0.01170.4941-0.02270.4002-17.16467.4013-11.4169
341.2475-0.4201-0.0830.69330.07361.45920.0433-0.19940.16330.39060.06490.1344-0.5770.0003-0.07571.039-0.07580.07680.5272-0.06920.3782-29.523934.079-15.2625
351.5615-0.15430.3840.4418-0.5591.51750.0569-0.26380.12481.00750.11660.5784-0.5247-0.7849-0.11711.13050.05490.31340.6306-0.05110.67-49.67833.8088-14.3777
360.8358-0.1370.01632.969-0.26521.86060.0156-0.2403-0.22860.69130.01070.29250.1363-0.1541-0.01510.5362-0.01820.09070.47420.02220.4789-42.04845.9928-36.871
372.079-0.02660.8471.46370.31531.72140.043-0.1698-0.28350.148-0.08520.44250.1294-0.34170.06270.5561-0.0160.19270.44330.03420.3936-46.78457.6-38.844
382.62370.7641.55011.13550.80632.10730.1130.04710.12190.28320.03640.3211-0.415-0.1781-0.12510.79970.00290.21680.4988-0.02730.636-47.806123.9793-32.1343
394.7392.13662.25772.38460.27873.1254-0.201-0.02110.66210.3923-0.00150.6829-0.4736-0.5640.21980.60460.16720.1340.53220.01520.5783-53.598635.0393-45.1812
402.1718-0.13880.95142.12520.46913.089-0.123-0.56090.72720.564-0.30551.0561-0.7575-1.00210.26390.75050.11760.19910.8311-0.08260.828-64.838427.6207-36.8905
411.06060.18290.54541.38010.30.93480.0459-0.02050.00790.13030.01290.40330.1287-0.0876-0.05640.30390.0604-0.01610.45740.0450.464-49.844813.5364-66.4426
422.23490.52790.07522.74010.08713.99930.203-0.2034-0.2829-0.1977-0.05040.29330.6549-0.1705-0.18840.3206-0.0275-0.11740.4505-0.02580.7524-59.9711-6.8057-83.7386
431.1996-0.03561.07470.8287-0.03491.98310.0115-0.02710.10070.0969-0.01760.268-0.1572-0.24670.04410.32240.03120.05230.39870.01680.459-50.00919.5848-66.4916
444.4071-1.04214.30832.5986-5.24262.0178-0.25490.06180.45220.346-0.11450.8391-1.6017-0.08610.2760.57940.0611-0.06480.3647-0.03290.7043-48.363141.2973-69.3843
453.39371.2424-1.50971.7320.40962.1529-0.2299-0.09520.5226-0.1055-0.01431.1447-0.3758-0.34650.19140.53540.11020.03860.58420.02660.8005-62.773135.5337-69.6488
461.57970.6765-0.24611.9689-0.6821.2610.03590.04750.0452-0.21530.00890.24580.1647-0.07190.01420.27790.0441-0.0860.3493-0.00650.3874-36.001727.048-88.2234
471.8861-2.4487-0.6986.44560.7341.9447-0.5080.445-0.4671-0.15310.562.1643-0.0072-0.7919-0.04740.6285-0.1193-0.22210.72130.08810.7203-52.258915.1577-109.7702
482.0526-0.97720.43872.8517-2.17142.8630.00710.3384-0.3752-1.1380.44610.74190.5138-0.563-0.4080.6491-0.0667-0.26570.64140.02850.7188-45.025618.8419-117.853
491.83041.27063.36312.41562.72316.3529-0.06940.3549-0.2833-0.55220.1874-0.1552-0.07070.504-0.10190.3822-0.0425-0.15740.4950.08210.5873-34.213727.0166-103.8354
501.16411.0181-0.48981.3461-0.73461.6053-0.05290.05190.08490.14650.01010.0919-0.3181-0.00860.01930.25870.1009-0.06120.3514-0.06820.4968-39.483725.8831-86.4105
511.77771.4436-1.23446.9237-3.44695.814-0.0706-0.05340.3041-0.02280.22240.6241-0.1788-0.2161-0.1130.23980.0866-0.02980.4161-0.00640.4356-41.55631.5725-84.0098
522.07590.4731-0.37861.1254-3.0178.5469-0.10860.15450.0684-0.0340.0950.1192-0.2842-0.25760.05850.3388-0.07950.05330.3021-0.03450.5383-25.786538.8981-83.4796
532.00317.59161.8832.0555-9.20691.96090.68-0.24870.6830.5534-0.2360.1904-0.76420.5025-0.42750.63880.12920.05920.4137-0.00150.501-26.793145.7112-82.9998
541.7661-1.732-0.59961.62640.69512.6058-0.4275-0.56610.69260.13070.2050.2059-0.717-0.16230.02410.39790.046-0.01040.4732-0.0050.5788-39.830448.5675-90.9121
551.046-1.34630.87521.6463-0.94333.56230.27180.12620.82450.1739-0.3423-0.21610.12960.3580.14290.43110.0085-0.09620.3063-0.10770.5498-3.31242.8547-99.855
561.5472-0.378-0.6780.3544-0.24221.0473-0.16570.15180.5094-0.02970.098-0.46830.10780.0373-0.03480.226-0.0522-0.01390.62690.06670.3011-19.757626.8946-96.9099
572.0126-8.4499-8.53092.0059.43492.00660.01890.1814-0.1420.32360.281-0.34840.06340.077-0.1210.3648-0.0794-0.1190.48410.03550.4401-18.043116.4607-100.6772
580.8131-1.2475-0.18145.9392-5.46528.15220.1217-0.3146-0.22340.4069-0.16850.82490.429-0.77050.13340.2250.0372-0.12030.3069-0.05270.4669-7.232722.4924-95.3751
590.86931.077-1.53592.237-0.90924.5197-0.24150.3090.1956-0.40180.0430.1186-0.0587-0.30590.17840.238-0.0318-0.00910.36890.05640.4435-13.680733.7025-104.3897
606.15570.7769-0.83529.6222-2.15242.04530.00620.97070.8607-1.49260.13370.7325-0.6714-0.9085-0.17910.8347-0.0261-0.04310.65210.1770.7189-11.369450.2677-124.5237
615.633-1.6922-2.09239.67872.0388.93880.06340.04640.1319-0.6620.0202-0.9507-0.28711.1364-0.22860.5882-0.02760.03890.7690.21211.07735.063446.5907-136.5598
621.6903-0.81051.80611.62890.45833.31240.30140.06320.2645-0.1620.30660.2313-0.0706-0.2736-0.51151.19680.04310.28130.70990.24840.9476-4.297645.4755-141.4675
631.48990.0563-1.04391.6403-0.34455.43410.00120.51850.1945-0.666-0.0830.0781-0.3864-0.15590.12050.5670.0305-0.09660.49390.09650.5425-6.70936.4681-125.7939
642.37480.8057-0.4621.4157-0.21260.84480.0922-0.15050.24710.0137-0.0090.0424-0.16180.0604-0.0730.33820.0461-0.07470.322-0.04080.3766-13.034834.9377-96.9591
659.0886-4.26220.80415.86360.35543.1807-0.1388-0.56650.9033-0.13350.049-0.235-0.15490.25850.13980.3814-0.0432-0.04680.4092-0.06050.5975-4.920850.481-92.71
662.0049-5.707-3.04884.50412.2577.48330.0665-0.31280.34580.34070.0421-1.91730.18731.6058-0.11040.4009-0.13490.01270.7620.06870.976128.376630.6807-103.3291
671.34252.6461-1.82866.7142-0.97527.0552-0.1248-0.30570.3096-0.0399-0.30930.0414-0.11070.11680.3480.25210.0131-0.04650.3893-0.03460.471913.460730.4132-99.2072
681.61081.62570.82986.21662.37973.3389-0.0129-0.20380.1410.0445-0.3216-0.10240.07070.18610.46770.3885-0.0245-0.02470.31560.0380.5783.19921.483-106.4253
697.53370.8816-2.72218.83910.26167.2439-0.47520.06540.3664-0.976-0.14010.20320.1471-0.12410.53340.65860.0331-0.0930.32940.00350.3583-2.720716.0508-116.5197
704.91621.9234.60391.69671.734.3261-0.25890.16660.1801-0.4476-0.1509-0.0052-0.1039-0.2570.3960.32630.1464-0.03440.28730.01840.64556.562517.1318-104.6036
712.0004-7.6378-9.36982.00051.99971.99990.1750.6557-0.9201-0.4614-0.12390.38940.74650.2954-0.06520.06910.14590.06750.1302-0.16310.602210.731121.9562-107.5588
722.4007-3.18150.01954.18630.03552.01620.13910.39450.5957-0.3940.09050.4263-0.13140.511-0.26870.2369-0.0014-0.02230.41260.07520.513512.208929.846-111.646
732.00613.94524.54496.69972.22682.06250.01821.01130.6255-0.768-0.64520.2462-0.66240.4090.49460.61830.0258-0.06070.8140.13170.52939.170836.3302-120.5048
746.9201-3.25285.8842.0079-7.81512.0074-0.00240.72310.4942-0.7531-0.5933-1.31280.35360.72440.54260.57010.07440.01190.6640.08680.535818.10331.3035-120.6428
751.8013-0.3358-0.53192.3029-0.53864.3133-0.0205-0.1820.0215-0.07890.0970.46480.30730.2722-0.11470.27440.007-0.00530.5260.070.599514.217123.3622-97.9993
769.47411.64164.53349.50582.58912.00910.2003-2.11810.75862.28810.43320.66131.1199-0.7185-0.51750.799-0.02210.09320.6234-0.17460.49865.404419.2778-85.5287
772.0529-8.36917.72318.4904-7.77427.6217-0.5669-0.76410.3655-0.19020.09750.516-0.1467-0.15440.37470.3014-0.0586-0.09540.32060.05010.5906-9.902520.3065-107.1054
786.78150.85380.26863.5943-2.36082.3319-0.03271.5504-0.1179-0.9925-0.2050.39281.0294-0.48150.18120.890.0629-0.27320.7552-0.11050.4335-13.656925.3788-126.5766
792.0463-0.22781.75421.32710.27821.49140.21890.4257-0.058-0.1751-0.1009-0.469-0.20650.2379-0.14620.32210.07850.03190.46120.0830.4748.996925.0389-108.0778
803.8751-2.40242.92335.93510.81466.77880.10890.53460.81180.049-0.1913-0.6468-0.49220.79760.0840.4854-0.131-0.03880.47490.06780.771314.628340.6435-108.4223
811.80720.77830.48962.1278-0.03162.78830.06750.27980.23330.06760.0366-0.18150.12180.3218-0.09730.33670.0086-0.08160.47150.04050.55189.249732.8173-102.1976
823.56112.8188-0.58495.00161.36995.54340.3252-0.74820.380.1232-0.0679-0.58580.03691.062-0.35560.3766-0.0766-0.15880.6664-0.00970.653626.869824.8009-97.2151
831.09940.77080.07793.1863-0.43462.8608-0.4557-0.18290.19670.0740.0865-0.5540.04160.70720.280.38410.1808-0.11810.70360.07090.693320.727320.9342-98.9161
846.6681-2.66313.91025.2169-2.03237.88040.07870.11090.1295-0.1273-0.1641-0.9550.10090.44660.0940.4047-0.0648-0.05430.4840.05460.605718.768514.3292-110.3485
850.30980.13650.20330.07860.08890.12710.14260.53340.6531-0.4616-0.2699-0.4278-0.89020.430.17120.52580.10480.02880.64320.64630.31259.292924.3316-124.8036
867.2428-1.45836.93653.3415-1.23592.02970.34180.44260.527-0.0434-0.3676-0.68940.50960.0086-0.10720.33980.00610.07210.5168-0.01710.581317.607515.6409-109.2967
873.5149-1.6298-1.08731.99981.39271.96290.02350.28050.111-0.08610.1579-0.01340.05950.4495-0.10330.3647-0.0057-0.07310.4490.15160.61962.649927.6816-115.279
888.196.989-5.38717.6439-4.67253.55540.15411.0767-0.0124-0.1197-0.03140.0657-0.1358-0.0299-0.03680.3750.0122-0.1630.47960.1180.3476-14.972326.1313-111.1802
890.01350.0738-0.09540.8907-0.23710.33980.0663-0.04070.04730.3073-0.00430.11620.06250.071-0.03050.37560.00520.02850.4057-0.03270.3867-34.173716.9669-56.3687
900.9516-0.127-0.10970.2185-0.80133.0963-0.03530.02870.73-0.4815-0.0654-0.669-1.09070.2081-0.05681.735-0.33810.27970.6784-0.25980.7877-12.319755.8819-17.5539
911.23831.44380.8721.65441.01240.62080.2876-0.08240.0983-0.33940.17510.6509-0.26320.0618-0.3212.6904-0.99190.70470.7389-0.48251.6008-7.589573.3079-22.9644
920.02470.01460.01670.01430.01780.0166-0.99670.0213-0.2383-0.68481.1064-0.1499-0.93870.4502-0.0393.6603-0.68390.69171.3308-0.15011.4594-11.174693.1066-33.9445
932.2574-1.6902-0.0181.4406-0.56961.74090.0216-0.52090.9322-0.2910.0133-1.3735-0.41780.4464-0.27453.5966-0.50390.40920.9384-0.28651.506-14.242193.5604-28.7596
945.64492.7670.67496.9545-3.32698.9080.97891.53351.9348-0.753-0.35382.0489-1.7727-0.5825-0.63031.44890.3174-0.06211.07420.15291.3659-24.386511.3822-133.6922
952.5444-0.164-2.26333.8159-5.67332.0220.32330.79940.5864-1.44820.6919-0.035-0.9451-0.3214-0.91231.3901-0.1135-0.05690.82890.10311.0112-13.2644-6.7283-102.3786
962.00073.3914-1.31951.313-1.06241.63660.30310.3593-0.1658-0.2329-0.0507-0.01280.2655-0.1848-0.19622.25180.1518-0.11931.9534-0.26261.3346-5.58022.8059-79.0614
977.8502-5.35631.65097.10052.68015.8233-0.21060.24991.01140.1572-0.6894-0.2705-1.16490.17340.7851.8287-0.58670.09580.8416-0.16190.579-5.823953.3766-26.6373
980.36670.24510.13630.3685-0.39640.56370.0787-0.02990.1170.1489-0.02260.04760.11190.0025-0.02280.40730.10680.0010.3644-0.05330.4113-26.54299.7537-68.176
990.04240.1704-0.1011.0045-0.63380.372-0.15372.82391.5859-2.0964-0.84672.2391-1.1259-3.5780.80981.79180.6937-0.64342.06160.09921.2052-23.478812.4238-139.9653
1001.2017-0.55030.77890.2609-0.37830.50040.29970.86380.154-0.57890.305-0.15290.2394-0.0763-0.57452.5102-0.0577-0.13421.1983-0.09830.9077-31.927876.0071-45.0168
1011.36360.5115-1.89462.7133-0.97042.6509-0.30050.74640.3151-0.5902-0.43930.0473-0.42110.2110.62942.4125-0.44240.48571.2247-0.1590.917-25.972780.606-47.864
1022.08341.3424-0.2981.98510.77795.49050.21910.4262-0.4767-1.30280.49211.34850.71980.3302-0.59882.88080.1338-0.00720.78170.06421.1941-34.224678.8447-42.6229
1031.0563-0.4182-0.11572.14442.13393.7085-0.49050.1332-0.1848-1.7785-0.3241.4103-1.3934-0.21480.33372.8423-0.10610.08250.59740.14020.0041-30.510280.1542-27.3279
1041.5551-2.1510.85477.30510.45331.0004-0.24260.09720.0225-0.11440.05440.2036-0.4637-0.21090.08922.86740.0494-0.15770.684-0.2321-0.2579-28.678980.0645-18.9066
1050.32310.40380.41490.9544-0.23810.9767-0.32140.03810.8481-1.14990.3979-0.628-1.21750.7778-0.19973.1661-0.06160.01030.4006-0.54790.2778-27.18480.5054-28.25
1067.2697-2.4058-2.13631.18821.57692.7693-0.4512-0.2028-1.432-1.07760.01940.1368-0.410.55460.40392.6374-0.0635-0.1830.7306-0.10280.7459-30.648380.0001-30.3816
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 130 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 131 THROUGH 375 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 376 THROUGH 495 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 3 THROUGH 16 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 17 THROUGH 26 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 27 THROUGH 37 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 38 THROUGH 75 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 76 THROUGH 86 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 87 THROUGH 94 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 95 THROUGH 106 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 107 THROUGH 111 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 112 THROUGH 124 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 125 THROUGH 129 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 130 THROUGH 142 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 143 THROUGH 159 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 3 THROUGH 26 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 27 THROUGH 37 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 38 THROUGH 67 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 68 THROUGH 86 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 87 THROUGH 98 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 99 THROUGH 111 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 112 THROUGH 129 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 130 THROUGH 141 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 142 THROUGH 156 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 2 THROUGH 50 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 51 THROUGH 115 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 116 THROUGH 155 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 156 THROUGH 304 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 305 THROUGH 334 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 335 THROUGH 349 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 350 THROUGH 361 )
32X-RAY DIFFRACTION32CHAIN 'E' AND (RESID 2 THROUGH 57 )
33X-RAY DIFFRACTION33CHAIN 'E' AND (RESID 58 THROUGH 170 )
34X-RAY DIFFRACTION34CHAIN 'E' AND (RESID 171 THROUGH 279 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 280 THROUGH 361 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 2 THROUGH 115 )
37X-RAY DIFFRACTION37CHAIN 'F' AND (RESID 116 THROUGH 260 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 261 THROUGH 285 )
39X-RAY DIFFRACTION39CHAIN 'F' AND (RESID 286 THROUGH 322 )
40X-RAY DIFFRACTION40CHAIN 'F' AND (RESID 323 THROUGH 362 )
41X-RAY DIFFRACTION41CHAIN 'G' AND (RESID 2 THROUGH 79 )
42X-RAY DIFFRACTION42CHAIN 'G' AND (RESID 80 THROUGH 146 )
43X-RAY DIFFRACTION43CHAIN 'G' AND (RESID 147 THROUGH 304 )
44X-RAY DIFFRACTION44CHAIN 'G' AND (RESID 305 THROUGH 322 )
45X-RAY DIFFRACTION45CHAIN 'G' AND (RESID 323 THROUGH 362 )
46X-RAY DIFFRACTION46CHAIN 'H' AND (RESID 2 THROUGH 57 )
47X-RAY DIFFRACTION47CHAIN 'H' AND (RESID 58 THROUGH 84 )
48X-RAY DIFFRACTION48CHAIN 'H' AND (RESID 85 THROUGH 170 )
49X-RAY DIFFRACTION49CHAIN 'H' AND (RESID 171 THROUGH 190 )
50X-RAY DIFFRACTION50CHAIN 'H' AND (RESID 191 THROUGH 260 )
51X-RAY DIFFRACTION51CHAIN 'H' AND (RESID 261 THROUGH 284 )
52X-RAY DIFFRACTION52CHAIN 'H' AND (RESID 285 THROUGH 304 )
53X-RAY DIFFRACTION53CHAIN 'H' AND (RESID 305 THROUGH 322 )
54X-RAY DIFFRACTION54CHAIN 'H' AND (RESID 323 THROUGH 361 )
55X-RAY DIFFRACTION55CHAIN 'I' AND (RESID 2 THROUGH 11 )
56X-RAY DIFFRACTION56CHAIN 'I' AND (RESID 12 THROUGH 21 )
57X-RAY DIFFRACTION57CHAIN 'I' AND (RESID 22 THROUGH 26 )
58X-RAY DIFFRACTION58CHAIN 'I' AND (RESID 27 THROUGH 31 )
59X-RAY DIFFRACTION59CHAIN 'I' AND (RESID 32 THROUGH 57 )
60X-RAY DIFFRACTION60CHAIN 'I' AND (RESID 58 THROUGH 71 )
61X-RAY DIFFRACTION61CHAIN 'I' AND (RESID 72 THROUGH 84 )
62X-RAY DIFFRACTION62CHAIN 'I' AND (RESID 85 THROUGH 97 )
63X-RAY DIFFRACTION63CHAIN 'I' AND (RESID 107 THROUGH 195 )
64X-RAY DIFFRACTION64CHAIN 'I' AND (RESID 196 THROUGH 319 )
65X-RAY DIFFRACTION65CHAIN 'I' AND (RESID 320 THROUGH 361 )
66X-RAY DIFFRACTION66CHAIN 'J' AND (RESID 1 THROUGH 5 )
67X-RAY DIFFRACTION67CHAIN 'J' AND (RESID 6 THROUGH 10 )
68X-RAY DIFFRACTION68CHAIN 'J' AND (RESID 11 THROUGH 20 )
69X-RAY DIFFRACTION69CHAIN 'J' AND (RESID 21 THROUGH 25 )
70X-RAY DIFFRACTION70CHAIN 'J' AND (RESID 26 THROUGH 30 )
71X-RAY DIFFRACTION71CHAIN 'J' AND (RESID 31 THROUGH 32 )
72X-RAY DIFFRACTION72CHAIN 'J' AND (RESID 33 THROUGH 43 )
73X-RAY DIFFRACTION73CHAIN 'J' AND (RESID 44 THROUGH 50 )
74X-RAY DIFFRACTION74CHAIN 'J' AND (RESID 51 THROUGH 60 )
75X-RAY DIFFRACTION75CHAIN 'J' AND (RESID 61 THROUGH 72 )
76X-RAY DIFFRACTION76CHAIN 'J' AND (RESID 73 THROUGH 79 )
77X-RAY DIFFRACTION77CHAIN 'J' AND (RESID 80 THROUGH 89 )
78X-RAY DIFFRACTION78CHAIN 'J' AND (RESID 90 THROUGH 102 )
79X-RAY DIFFRACTION79CHAIN 'J' AND (RESID 103 THROUGH 129 )
80X-RAY DIFFRACTION80CHAIN 'J' AND (RESID 130 THROUGH 143 )
81X-RAY DIFFRACTION81CHAIN 'J' AND (RESID 144 THROUGH 163 )
82X-RAY DIFFRACTION82CHAIN 'J' AND (RESID 164 THROUGH 173 )
83X-RAY DIFFRACTION83CHAIN 'J' AND (RESID 174 THROUGH 187 )
84X-RAY DIFFRACTION84CHAIN 'J' AND (RESID 188 THROUGH 201 )
85X-RAY DIFFRACTION85CHAIN 'J' AND (RESID 202 THROUGH 206 )
86X-RAY DIFFRACTION86CHAIN 'J' AND (RESID 207 THROUGH 219 )
87X-RAY DIFFRACTION87CHAIN 'L' AND (RESID 1 THROUGH 5 )
88X-RAY DIFFRACTION88CHAIN 'L' AND (RESID 6 THROUGH 10 )
89X-RAY DIFFRACTION89CHAIN 'L' AND (RESID 11 THROUGH 35 )
90X-RAY DIFFRACTION90CHAIN 'L' AND (RESID 36 THROUGH 40 )
91X-RAY DIFFRACTION91CHAIN 'L' AND (RESID 41 THROUGH 43 )
92X-RAY DIFFRACTION92CHAIN 'L' AND (RESID 44 THROUGH 53 )
93X-RAY DIFFRACTION93CHAIN 'L' AND (RESID 54 THROUGH 60 )
94X-RAY DIFFRACTION94CHAIN 'M' AND (RESID 11 THROUGH 18 )
95X-RAY DIFFRACTION95CHAIN 'M' AND (RESID 19 THROUGH 28 )
96X-RAY DIFFRACTION96CHAIN 'M' AND (RESID 29 THROUGH 29 )
97X-RAY DIFFRACTION97CHAIN 'N' AND (RESID 1 THROUGH 5 )
98X-RAY DIFFRACTION98CHAIN 'N' AND (RESID 6 THROUGH 34 )
99X-RAY DIFFRACTION99CHAIN 'N' AND (RESID 35 THROUGH 40 )
100X-RAY DIFFRACTION100CHAIN 'K' AND (RESID 1 THROUGH 15 )
101X-RAY DIFFRACTION101CHAIN 'K' AND (RESID 16 THROUGH 24 )
102X-RAY DIFFRACTION102CHAIN 'K' AND (RESID 25 THROUGH 63 )
103X-RAY DIFFRACTION103CHAIN 'K' AND (RESID 64 THROUGH 129 )
104X-RAY DIFFRACTION104CHAIN 'K' AND (RESID 130 THROUGH 142 )
105X-RAY DIFFRACTION105CHAIN 'K' AND (RESID 143 THROUGH 181 )
106X-RAY DIFFRACTION106CHAIN 'K' AND (RESID 182 THROUGH 199 )

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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

他の情報も見る