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- PDB-4v9e: Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein... -

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基本情報

登録情報
データベース: PDB / ID: 4v9e
タイトルCrystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Hexamer Bound to Single-stranded RNA.
要素
  • 35-mer poly(U) RNA
  • Nucleocapsid proteinウイルス
キーワードVIRAL PROTEIN/RNA (ウイルス性) / nucleocapsid protein (ウイルス) / N protein / ribonucleoprotein (核タンパク質) / viral nucleoprotein / RNA binding (リボ核酸) / virus (ウイルス) / RNP / VIRAL PROTEIN-RNA complex (ウイルス性)
機能・相同性
機能・相同性情報


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding / identical protein binding
類似検索 - 分子機能
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
類似検索 - ドメイン・相同性
リボ核酸 / RNA (> 10) / 核タンパク質
類似検索 - 構成要素
生物種Rift Valley fever virus (リフトバレー熱ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Raymond, D.D. / Smith, J.L.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2012
タイトル: Phleboviruses encapsidate their genomes by sequestering RNA bases.
著者: Raymond, D.D. / Piper, M.E. / Gerrard, S.R. / Skiniotis, G. / Smith, J.L.
履歴
登録2012年9月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月9日Provider: repository / タイプ: Initial release
置き換え2014年12月10日ID: 4H6F, 4H6G
改定 1.12014年12月10日Group: Other
改定 1.22023年9月20日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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

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集合体

登録構造単位
AA: Nucleocapsid protein
AB: Nucleocapsid protein
AC: Nucleocapsid protein
AD: Nucleocapsid protein
AE: Nucleocapsid protein
AF: Nucleocapsid protein
AG: Nucleocapsid protein
AH: Nucleocapsid protein
AI: Nucleocapsid protein
AJ: Nucleocapsid protein
AK: Nucleocapsid protein
AL: Nucleocapsid protein
AM: Nucleocapsid protein
AN: Nucleocapsid protein
AO: Nucleocapsid protein
AP: Nucleocapsid protein
AQ: Nucleocapsid protein
AR: Nucleocapsid protein
Aa: 35-mer poly(U) RNA
Ag: 35-mer poly(U) RNA
Am: 35-mer poly(U) RNA
BA: Nucleocapsid protein
BB: Nucleocapsid protein
BC: Nucleocapsid protein
BD: Nucleocapsid protein
BE: Nucleocapsid protein
BF: Nucleocapsid protein
BG: Nucleocapsid protein
BH: Nucleocapsid protein
BI: Nucleocapsid protein
BJ: Nucleocapsid protein
BK: Nucleocapsid protein
BL: Nucleocapsid protein
BM: Nucleocapsid protein
BN: Nucleocapsid protein
BO: Nucleocapsid protein
BP: Nucleocapsid protein
BQ: Nucleocapsid protein
BR: Nucleocapsid protein
Ba: 35-mer poly(U) RNA
Bg: 35-mer poly(U) RNA
Bm: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)1,051,05842
ポリマ－1,051,05842
非ポリマー00
水0
1
AA: Nucleocapsid protein
AB: Nucleocapsid protein
AC: Nucleocapsid protein
AD: Nucleocapsid protein
AE: Nucleocapsid protein
AF: Nucleocapsid protein
Aa: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35600 Å2
ΔGint-320 kcal/mol
Surface area58340 Å2
手法PISA
2
AG: Nucleocapsid protein
AH: Nucleocapsid protein
AI: Nucleocapsid protein
AJ: Nucleocapsid protein
AK: Nucleocapsid protein
AL: Nucleocapsid protein
Ag: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35860 Å2
ΔGint-321 kcal/mol
Surface area57960 Å2
手法PISA
3
AM: Nucleocapsid protein
AN: Nucleocapsid protein
AO: Nucleocapsid protein
AP: Nucleocapsid protein
AQ: Nucleocapsid protein
AR: Nucleocapsid protein
Am: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area34960 Å2
ΔGint-318 kcal/mol
Surface area59370 Å2
手法PISA
4
BA: Nucleocapsid protein
BB: Nucleocapsid protein
BC: Nucleocapsid protein
BD: Nucleocapsid protein
BE: Nucleocapsid protein
BF: Nucleocapsid protein
Ba: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35590 Å2
ΔGint-326 kcal/mol
Surface area58080 Å2
手法PISA
5
BG: Nucleocapsid protein
BH: Nucleocapsid protein
BI: Nucleocapsid protein
BJ: Nucleocapsid protein
BK: Nucleocapsid protein
BL: Nucleocapsid protein
Bg: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35620 Å2
ΔGint-323 kcal/mol
Surface area58690 Å2
手法PISA
6
BM: Nucleocapsid protein
BN: Nucleocapsid protein
BO: Nucleocapsid protein
BP: Nucleocapsid protein
BQ: Nucleocapsid protein
BR: Nucleocapsid protein
Bm: 35-mer poly(U) RNA


分子量 (理論値)分子数
合計 (水以外)175,1767
ポリマ－175,1767
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area34720 Å2
ΔGint-319 kcal/mol
Surface area59490 Å2
手法PISA
単位格子
Length a, b, c (Å)91.660, 173.330, 172.900
Angle α, β, γ (deg.)119.950, 99.340, 90.120
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 ...
Nucleocapsid protein / ウイルス


分子量: 27366.547 Da / 分子数: 36 / 由来タイプ: 組換発現
由来: (組換発現) Rift Valley fever virus (リフトバレー熱ウイルス)
株: ZH-501 / 遺伝子: N / プラスミド: pSUMO / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Ai/prare2 / 参照: UniProt: D3K5I7
#2: RNA鎖
35-mer poly(U) RNA


分子量: 10977.009 Da / 分子数: 6 / Fragment: SEE REMARK 999 / 由来タイプ: 合成
配列の詳細EACH RNA CHAIN WAS ORIGINALLY MODELED AS SIX ISOLATED HEXAMERS.

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.23 Å3/Da / 溶媒含有率: 44.76 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 24% PEG3350, 350 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD
詳細: K-B pair of biomorph mirrors for vertical and horizontal focusing
放射モノクロメーター: double crystal 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: 1.0332 Å / 相対比: 1
反射解像度: 3.4→149.472 Å / Num. all: 117933 / Num. obs: 117933 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / 冗長度: 1.9 % / Rsym value: 0.19 / Net I/σ(I): 4
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.4-3.581.90.5131.331220167520.51392.3
3.58-3.81.90.3861.829799159930.38692.8
3.8-4.061.90.2862.328316150940.28693.3
4.06-4.391.90.1913.226831142590.19194.8
4.39-4.811.90.1614.325670133700.16196.1
4.81-5.381.90.1843.823533121080.18496.6
5.38-6.2120.164.420752106260.1696.6
6.21-7.620.1116.31764390200.11196.6
7.6-10.7520.0488.21361469420.04896.5
10.75-57.4171.90.053.5734337690.0595.6

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解析

ソフトウェア
名称バージョン分類NB
MOSFLMデータ削減
SCALA3.3.20データスケーリング
BUSTER-TNTBUSTER 2.10.0精密化
PDB_EXTRACT3.11データ抽出
Blu-IceEpicsデータ収集
PHASER位相決定
BUSTER2.10.0精密化
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3LYF

3lyf


解像度: 3.4→57.42 Å / Cor.coef. Fo:Fc: 0.7979 / Cor.coef. Fo:Fc free: 0.7723 / Occupancy max: 1 / Occupancy min: 1 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.617
Rfactor反射数%反射Selection details
Rfree0.2399 5935 5.03 %SHELL
Rwork0.2246 ---
obs0.2254 117932 94.72 %-
原子変位パラメータBiso max: 188.66 Å2 / Biso mean: 70.4665 Å2 / Biso min: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--19.8577 Å25.0466 Å2-4.8864 Å2
2--14.5611 Å2-5.0849 Å2
3---5.2966 Å2
Refine analyzeLuzzati coordinate error obs: 0.776 Å
精密化ステップサイクル: LAST / 解像度: 3.4→57.42 Å
タンパク質核酸リガンド溶媒全体
原子数33876 2160 0 0 36036
拘束条件
Refine-IDタイプ数Restraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d33768SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes1656HARMONIC2
X-RAY DIFFRACTIONt_gen_planes10296HARMONIC5
X-RAY DIFFRACTIONt_it73764HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion9720SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact81810SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d73764HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg100368HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion1.51
X-RAY DIFFRACTIONt_other_torsion2.88
LS精密化 シェル解像度: 3.4→3.49 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2674 1 0.01 %
Rwork0.2392 8436 -
all0.2392 8437 -
obs--94.72 %
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)
1-0.85050.30971.9358-0.112-0.43362.8860.0270.1616-0.0461-0.02110.0496-0.0095-0.06620.0185-0.07660.2040.02580.0384-0.18940.0656-0.0011-15.986157.347812.8134
25.0516-2.99131.87810.8068-0.17974.38410.0644-0.0303-0.0458-0.1717-0.0433-0.1336-0.03520.2502-0.0211-0.0925-0.00110.2035-0.31870.06060.379-6.258517.558918.8358
34.9774-0.26641.22437.55470.93784.50990.0795-0.0001-0.0268-0.07360.0013-0.0197-0.2811-0.1378-0.08080.19710.15290.1032-0.27680.1074-0.1816-27.72226.684420.8334
40.667-1.55751.03532.2207-0.5814-0.5753-0.02040.00820.1161-0.0310.00250.0783-0.01410.04160.01790.02910.0240.2592-0.08480.0252-0.0067-24.014680.083651.4933
52.00221.72233.74183.51410.04913.0440.0217-0.0191-0.06180.0521-0.0557-0.0936-0.12840.140.0340.2162-0.1330.3025-0.31060.04290.1443-6.698658.862822.0598
65.49580.20020.57184.3942-0.190112.40770.0289-0.0852-0.0568-0.1769-0.10110.236-0.1045-0.21630.07220.21980.17370.2459-0.48230.1942-0.183-28.849455.232228.3399
7-0.5005-1.03861.30221.4567-0.13050.1357-0.0172-0.04240.12380.0203-0.03220.0468-0.0318-0.04080.04940.1812-0.11460.0712-0.21830.0077-0.046-32.426157.068290.291
86.6947-1.733-2.15191.87781.18771.6102-0.0188-0.02290.14160.07910.0265-0.0441-0.00720.1093-0.0077-0.2131-0.10010.1412-0.1495-0.0240.3698-13.988373.757.3447
93.4245-1.902-0.53987.2813-0.07362.70810.0576-0.1990.1293-0.067-0.19950.06280.2911-0.00120.1419-0.00230.00450.0338-0.1836-0.0397-0.0215-35.101163.849456.6769
10-0.4546-2.24381.11351.9548-2.33241.0413-0.0248-0.20830.06110.03260.06240.01590.0915-0.0669-0.03760.161-0.0478-0.0676-0.1180.0549-0.1312-32.972612.174389.1481
113.69762.7782-1.98037.21511.8271-0.2876-0.0025-0.02770.01180.0427-0.0229-0.0580.07220.32310.02540.0894-0.2362-0.1023-0.0192-0.1004-0.0619-21.088750.11289.6357
124.4063-1.8244-1.0797.63073.21993.97860.10910.0576-0.237-0.2209-0.08540.0631-0.032-0.0797-0.0237-0.0585-0.1369-0.035-0.09270.0573-0.1743-39.638243.210877.4861
130.4411-1.4324-1.12721.5608-0.9922-0.04180.0107-0.0928-0.038-0.0360.00020.02280.0045-0.0314-0.01090.0824-0.0594-0.0383-0.03530.1077-0.0266-26.6959-11.373150.2904
143.40350.61072.68872.0081-1.18744.49510.0342-0.11170.00210.154-0.0124-0.2506-0.00230.0628-0.02180.00790.1344-0.18550.12010.0608-0.0456-20.717511.980284.2591
156.35291.5309-1.16762.3302-0.62134.56610.0378-0.00810.0138-0.0853-0.0186-0.02540.13910.0307-0.01920.0562-0.01180.0198-0.0955-0.0318-0.1292-38.954113.987269.8259
161.3330.79941.2507-1.32650.80982.27030.03140.1405-0.0929-0.0818-0.0368-0.02250.0081-0.00810.00540.12040.0182-0.0114-0.14540.0303-0.0027-16.550711.71612.8071
172.5921-1.3815-0.29755.7547-0.1647-0.56540.0459-0.1428-0.11470.01820.1106-0.2869-0.09560.0302-0.15650.07790.1195-0.0653-0.13030.08940.1501-14.7165-6.300148.1761
185.84765.55361.318210.5534-3.23284.9676-0.0210.12930.25660.152-0.1155-0.2507-0.1508-0.15480.1365-0.12810.14120.0422-0.10220.0308-0.1245-33.52975.852441.8414
190.4916-1.0503-1.4426-1.72671.29291.78040.03480.0489-0.1109-0.0871-0.0093-0.0256-0.0350.0035-0.02550.16090.08620.0386-0.2140.09930.09710.63312.048-86.4383
204.4052-0.48532.38386.19060.35143.02570.047-0.0897-0.09450.08340.0115-0.20250.03860.1049-0.0584-0.11930.17430.0132-0.21620.05130.3485.0081-3.819-48.1234
216.27142.75870.22284.26291.85377.51610.06150.0969-0.1254-0.0625-0.13280.0855-0.0833-0.02830.0713-0.24880.09940.0553-0.06040.09670.0804-14.72275.6204-56.2277
221.406-0.38150.21091.7722-0.9122-0.78610.00440.1547-0.0189-0.03260.0585-0.0066-0.0129-0.0386-0.06290.1028-0.0296-0.0207-0.03680.07030.02580.706756.8462-85.7722
232.8592-0.51811.76782.13342.95995.31160.0303-0.03830.0046-0.07410.0524-0.0997-0.04590.2075-0.0827-0.0337-0.03130.13790.0376-0.05590.066511.053618.775-81.8289
245.37491.11222.6246.91724.03986.9579-0.0053-0.10980.21260.10760.13020.2553-0.0171-0.0612-0.1249-0.15520.08690.211-0.21450.0342-0.0292-10.63126.1397-77.2052
25-0.1687-2.1690.58291.5922-1.2515-1.22-0.02560.06510.1269-0.05270.00140.1168-0.0040.01910.02420.1036-0.04780.0387-0.15380.160.0768-8.067580.6526-46.6619
266.2688-3.8338-0.61020.5998-1.69082.0023-0.01520.10330.1305-0.0074-0.0036-0.2281-0.08640.05640.0188-0.16740.06180.17850.0570.1380.175810.038457.1198-76.585
275.6049-2.75483.02494.45160.37847.76970.04250.21720.08520.14110.16560.0148-0.1143-0.0322-0.2081-0.3734-0.08770.10470.0170.080.0766-12.260355.4673-70.2348
280.7251-0.0067-1.36351.37451.13751.5832-0.0164-0.15340.11520.0235-0.01960.02260.0093-0.10.0360.0910.08310.1243-0.1703-0.03870.0576-15.194757.6422-9.4865
2910.0184-0.5229-3.77681.525-0.71983.8512-0.03250.01190.23760.03510.1223-0.2380.08780.101-0.0898-0.11670.07810.0542-0.11970.07370.13761.998975.0361-40.2475
307.4862-1.3191-0.38948.4126-1.14073.1911-0.0754-0.0355-0.1236-0.10510.07840.07010.2533-0.3519-0.0030.2661-0.0305-0.1646-0.2687-0.2137-0.2482-18.18463.7715-42.075
310.4574-2.91383.2281.09780.09211.6090.0238-0.06690.02120.04590.02650.0381-0.0354-0.0275-0.05040.13980.1956-0.0455-0.1042-0.01560.0733-14.494811.2263-8.7282
325.127-1.9539-0.03390.81590.94943.00640.064-0.0741-0.11030.0889-0.0507-0.09090.11640.1395-0.01330.18030.1153-0.0479-0.153-0.0318-0.0216-3.685851.1357-10.4604
334.8948-1.2597-2.07787.51190.28514.62350.014-0.04240.09790.0711-0.02160.0920.1996-0.08290.00770.2418-0.0991-0.062-0.2037-0.0829-0.2584-22.563842.6529-20.9767
34-0.52612.50141.49433.9052-0.3452-1.56980.0146-0.1193-0.2079-0.0479-0.01780.03720.0673-0.03140.00320.1211-0.0059-0.0713-0.19670.022-0.0129-6.4637-10.2064-46.6691
356.31440.4398-1.97810.2109-0.83114.0355-0.0155-0.03450.0258-0.0512-0.0935-0.36520.06760.14590.1090.1792-0.1091-0.13180.0313-0.0107-0.1762-2.323110.5429-13.3482
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383.94331.42490.85533.368-1.7217-1.12730.0363-0.0685-0.0124-0.006-0.07910.28380.0313-0.12620.0428-0.012-0.23120.19220.0407-0.10490.057-28.8743-91.8341-9.7534
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414.02113.9488-0.43321.1940.97530.00220.00990.05810.0269-0.0430.04810.0947-0.0446-0.1547-0.058-0.0303-0.30210.10640.040.01280.1856-36.3286-79.877427.7753
425.0405-2.5442-0.812511.38753.41185.345-0.0207-0.04790.27610.07560.0238-0.14050.12690.0157-0.00310.1114-0.15570.0623-0.2731-0.0369-0.3569-15.5914-69.140327.078
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454.2478-0.58621.65526.1418-1.76796.27910.06390.11310.1925-0.0772-0.0805-0.17440.0220.06360.0167-0.11650.13550.0944-0.1110.1664-0.0066-16.3339-39.105229.4973
460.7696-2.4867-1.87141.0113-1.2742-1.0774-0.00280.06690.0623-0.00370.0035-0.0394-0.02150.0732-0.00060.10070.15340.0271-0.1574-0.01610.0578-13.126-17.2984-28.4053
476.1895-1.94540.18333.4137-2.9367-1.78650.02830.0454-0.0521-0.1472-0.06840.2826-0.0573-0.09340.0401-0.03120.3071-0.054-0.0830.12630.0993-32.1269-12.32337.7739
484.3992-0.62590.30564.1094.582410.35160.0795-0.0607-0.05780.04370.00730.0121-0.12930.0063-0.0868-0.04620.1333-0.0348-0.31390.0433-0.0388-10.9393-22.09465.2798
490.09124.5983-0.60811.44340.86763.3185-0.00050.08140.0103-0.01190.0147-0.01650.02010.0403-0.01410.1838-0.0574-0.0477-0.13220.0301-0.0212-10.7041-61.0027-42.973
504.7175-3.35450.2467-0.98972.66694.26530.01960.04850.0218-0.19320.10810.18170.0261-0.2052-0.1277-0.0129-0.0215-0.1432-0.23690.01420.2567-24.3696-24.0382-29.7184
515.59790.8997-0.5165.46972.58515.64940.0025-0.0347-0.2076-0.17850.10740.14050.17980.1273-0.10990.0494-0.0892-0.0702-0.2603-0.016-0.043-5.3319-34.95-21.3312
520.3506-0.7522-1.02414.35550.22781.23570.01530.07080.0033-0.0066-0.0164-0.04150.04-0.01450.00110.2124-0.01320.0312-0.25550.02450.0245-16.8682-95.7661-13.1957
533.1812-2.64942.44741.6516-1.48353.4006-0.00310.0329-0.0346-0.1117-0.04610.22960.0872-0.19250.04910.0841-0.1396-0.0564-0.16520.25870.1208-23.168-63.2421-39.1281
545.072-0.7167-0.12959.013-4.16944.53810.0777-0.20270.06470.0638-0.0633-0.1107-0.0538-0.0928-0.01440.0163-0.12570.0091-0.2345-0.0689-0.1677-5.6263-64.9468-23.733
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563.2567-0.72421.1742.35340.41551.92210.05850.029-0.01060.1204-0.0610.1311-0.0041-0.22340.0025-0.08150.05060.1876-0.2670.10520.375217.067617.5151-26.2965
574.567-1.33483.58216.64361.38787.0680.1176-0.076-0.01410.1194-0.00870.0689-0.30830.2711-0.1089-0.1118-0.01250.2005-0.18490.01760.085738.499226.5926-28.2779
580.22591.0833-0.37490.93151.30550.818-0.0276-0.03080.09470.0179-0.0125-0.04520.0104-0.02950.04020.0186-0.06490.17520.018-0.04470.042534.516779.8715-58.845
593.268-1.13691.10991.7175-0.30674.27910.03670.0409-0.065-0.0873-0.05070.0908-0.1287-0.16480.0140.31110.21610.1876-0.34490.13930.008617.223458.8165-29.5573
603.1259-1.9128-0.66474.8504-0.843413.4613-0.0030.0962-0.09520.1921-0.0508-0.1122-0.13140.30280.05370.2698-0.07840.1465-0.3623-0.0839-0.223139.353355.2616-35.8238
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625.76370.6193-2.31914.9171.79042.9716-0.00990.03980.0526-0.0642-0.00010.070.0486-0.14910.01-0.10290.17610.165-0.22810.10260.310124.471773.4815-64.7906
636.19942.4473-0.52976.70952.60941.51890.05860.12780.01440.0313-0.1457-0.10740.14450.01610.0871-0.0140.0740.1737-0.09070.0473-0.031145.577563.5963-64.0872
641.120.1133-3.0390.76821.5691.2191-0.0110.20120.0296-0.02580.0598-0.01970.07930.0629-0.04870.09350.06470.0144-0.06620.0314-0.014143.781511.9481-96.6685
652.6384-0.1509-0.99153.27630.05053.3086-0.00980.0110.0275-0.0931-0.0202-0.03470.0488-0.29260.030.17370.2632-0.1128-0.02890.084-0.143431.649549.8468-97.1915
664.13711.4175-2.4416.48590.10824.61920.0958-0.0976-0.21560.13820.0914-0.1965-0.0180.0347-0.1872-0.0360.2136-0.0616-0.1820.11550.008350.217342.8562-84.9542
670.78010.0707-2.0381-0.31650.58190.0433-0.0003-0.0139-0.03420.00390.00320.03260.02120.004-0.00290.04850.14590.1235-0.02420.00750.012936.3158-86.8737-38.1118
681.8205-1.67521.15112.143-0.43754.02930.00780.10620.0417-0.0125-0.0056-0.2536-0.02180.1635-0.00220.01310.19590.1797-0.1350.15910.004740.0626-91.73132.3356
693.01860.3416-2.30935.5213-2.46218.4051-0.0297-0.0420.07660.02160.01880.0590.056-0.1180.01080.31370.10510.0771-0.42930.0486-0.121621.3643-82.1187-8.0514
702.482-1.504-0.68010.5669-0.60070.91570.00680.0774-0.0108-0.013-0.0270.0137-0.03410.0150.02020.04930.05320.0692-0.16130.08750.054639.5259-43.5263-52.5958
711.9599-1.7844-0.20190.3551-0.308-0.08250.0015-0.05310.00490.07020.074-0.0865-0.02080.1492-0.0755-0.06350.12770.16130.00610.03860.117347.3814-80.0964-35.1111
725.70041.6217-1.09679.0523-4.8193.88910.02050.01550.1552-0.07860.02810.1186-0.01230.0582-0.04860.17960.22480.1308-0.37090.0533-0.227126.6778-69.332-34.4901
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746.3742-1.64120.55410.16880.34620.69640.0352-0.03180.04050.0931-0.0927-0.2362-0.03010.11980.0575-0.12480.01670.27970.0728-0.02990.150949.4662-40.8637-44.277
753.84643.24190.12736.94042.03855.00420.1032-0.22960.14280.0157-0.04840.07530.023-0.0448-0.0548-0.0065-0.03110.1315-0.0975-0.0997-0.131627.2253-39.2546-36.9657
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774.987-0.62-0.6238-0.43940.7531.17490.0502-0.0787-0.13480.1744-0.0182-0.2482-0.02890.0362-0.032-0.031-0.2837-0.02480.0915-0.00850.081442.8735-12.37-15.2748
784.03670.1442-1.47414.3128-4.826410.03530.0623-0.0337-0.0448-0.00150.0221-0.0654-0.0643-0.0382-0.0844-0.00820.0458-0.0507-0.2836-0.0116-0.0421.7415-22.1032-12.7632
790.3289-0.77831.00311.02950.86443.81520.0077-0.0688-0.0130.00710.0150.00330.0048-0.0516-0.02270.16230.0174-0.1071-0.058-0.0397-0.052821.7357-60.958435.5166
805.73311.92871.53762.0812-1.79341.56240.02230.01990.05180.12060.1026-0.11290.03220.2674-0.1249-0.00870.077-0.1646-0.15480.08830.279935.2161-23.909722.1227
815.6668-1.4802-0.83925.2639-2.09056.32760.061-0.0687-0.29770.10730.1092-0.09960.07420.0913-0.17030.08060.09330.0091-0.33240.0706-0.021216.2167-34.926813.8322
820.3164-1.5186-0.93291.226-0.68921.31990.0067-0.08110.0034-0.00080.01440.03750.0266-0.023-0.02110.0912-0.02840.0789-0.11510.1020.062528.0355-95.77065.8477
832.94420.41153.07540.80123.13644.38040.0098-0.0321-0.06440.0634-0.0672-0.25920.04520.18070.05740.04550.1951-0.056-0.0249-0.14510.014534.1616-63.233631.6562
843.5896-0.4897-1.56158.16992.66657.10130.05790.05420.0139-0.04030.04370.0762-0.0806-0.0124-0.10160.18750.1180.0035-0.36730.0246-0.133416.6388-64.899916.2402
85-0.13261.33990.24030.0415-0.01350.94390.0209-0.0132-0.13060.0978-0.0120.031-0.05210.0109-0.00890.1251-0.09990.0591-0.1280.04230.01510.213412.295378.8286
863.44180.75814.46235.5142-0.72582.5020.0569-0.0427-0.08160.05450.01930.18670.0163-0.0914-0.0761-0.1053-0.0016-0.1122-0.2303-0.00260.33756.0015-3.635540.6462
874.1583-3.12481.4516.20962.52477.98660.1186-0.1904-0.1626-0.2172-0.15650.0513-0.12370.10980.038-0.1689-0.04160.1021-0.14090.0785-0.017325.58435.932548.7262
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890.5994-1.30082.45012.3657-1.27863.78180.0533-0.0122-0.0185-0.06230.05580.0964-0.0663-0.2522-0.1091-0.22030.06880.27150.09560.15840.1978-0.153519.098774.3177
904.4748-1.84821.99134.9038-4.93146.9028-0.08980.08560.3152-0.10190.2222-0.22070.0433-0.035-0.1325-0.2036-0.08050.1936-0.1182-0.05310.008421.447526.464869.7231
91-0.6967-0.02511.77932.03770.3050.3654-0.0079-0.05460.09990.0186-0.0332-0.06940.0047-0.02590.04110.0523-0.0661-0.0033-0.1764-0.05980.142618.590980.751839.2328
928.17242.0909-1.28892.54860.76080.75460.0119-0.04570.06680.0236-0.05750.1663-0.004-0.03380.0455-0.08830.11560.0577-0.0830.0110.11540.558757.392469.2496
934.0691.09220.96986.7031-0.67627.8386-0.0084-0.05870.2468-0.06520.1578-0.0578-0.00490.0478-0.1495-0.2640.07710.0685-0.0988-0.11420.026722.857655.739762.8149
940.54490.3605-1.42181.7241-1.14420.0087-0.01810.08490.1394-0.0644-0.04370.00520.01120.06650.06180.07050.06850.0623-0.1070.09560.06925.766757.66441.939
957.8321-0.218-1.37082.44390.6724.35050.01560.01770.02560.03820.05330.1398-0.01390.025-0.06880.028-0.04640.0262-0.0846-0.00040.03098.6175.092832.8768
964.30331.04610.80478.31212.0513.093-0.0923-0.03340.02490.0801-0.0253-0.10440.27680.18960.11750.22290.1608-0.0403-0.26810.149-0.169828.811263.835134.6426
972.28941.51060.33221.3974-1.01920.32590.02140.0202-0.0374-0.02770.0319-0.0359-0.03350.0561-0.05340.1516-0.06320.0041-0.06930.06940.077625.188111.36941.0994
984.7233-0.18091.267-1.55770.9562.98710.07240.0144-0.1104-0.0686-0.05390.06690.1314-0.0356-0.01850.1960.0015-0.0756-0.22950.05770.123414.266551.15793.0453
995.41131.3878-1.55795.4715-0.73174.20140.04090.08870.0266-0.05320.0337-0.10350.18170.0986-0.07470.31880.14170.0558-0.3930.1902-0.084433.169642.716513.5733
1000.2527-0.7064-0.51394.0958-0.8626-1.4040.02860.1298-0.12450.0339-0.0680.02290.02960.00140.03930.16480.08060.0128-0.29180.06820.11617.3855-10.014639.2326
1014.4745-1.7958-2.73521.37640.39294.07060.00970.00850.00730.0578-0.07330.20930.0169-0.19630.06360.13770.1679-0.0505-0.15630.18580.079213.046810.62955.9145
1028.9052-1.7898-3.81374.0890.42339.20490.0689-0.13120.07460.1054-0.1525-0.0726-0.136-0.00260.0836-0.00930.0379-0.1955-0.34370.0895-0.038731.083413.871220.1738
1033.0714.2045-1.4536-2.84082.33652.83370.03370.0707-0.0398-0.0424-0.0246-0.002-0.00120.014-0.00920.05220.0265-0.00670.118-0.06420.024737.6273-11.518-57.7069
1042.01220.02051.08751.76611.85233.83370.04150.15-0.0646-0.0774-0.07750.1420.0081-0.08470.036-0.0054-0.0524-0.21440.0696-0.04720.077431.515311.6139-91.8132
1056.1249-0.95520.24425.0819-2.1885.73290.0911-0.0873-0.07250.0673-0.0634-0.0120.064-0.1198-0.0276-0.04530.0097-0.0051-0.08260.1449-0.190549.716913.692-77.3683
1060.04241.29921.7001-0.93920.84572.45480.0058-0.11410.00050.0086-0.03480.0470.0221-0.00170.02910.10890.00560.0654-0.17380.14190.085427.284911.8612-20.2387
1073.4261-0.18690.13294.8795-0.1493-1.39330.04320.1318-0.05290.01770.05950.22-0.1166-0.0651-0.1027-0.0541-0.0502-0.1186-0.1828-0.01610.313425.6139-6.5594-55.6758
1086.2508-5.07730.918611.46361.19664.63170.0072-0.07310.0961-0.1892-0.14680.1905-0.1750.12960.1395-0.1735-0.08070.0664-0.10920.0819-0.062244.31165.6846-49.3483
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{AA|5 - 30}AA5 - 30
2X-RAY DIFFRACTION2{AA|35 - 112}AA35 - 112
3X-RAY DIFFRACTION3{AA|113 - 245}AA113 - 245
4X-RAY DIFFRACTION4{AB|5 - 30}AB5 - 30
5X-RAY DIFFRACTION5{AB|35 - 112}AB35 - 112
6X-RAY DIFFRACTION6{AB|113 - 245}AB113 - 245
7X-RAY DIFFRACTION7{AC|5 - 30}AC5 - 30
8X-RAY DIFFRACTION8{AC|35 - 111}AC35 - 111
9X-RAY DIFFRACTION9{AC|112 - 245}AC112 - 245
10X-RAY DIFFRACTION10{AD|5 - 30}AD5 - 30
11X-RAY DIFFRACTION11{AD|35 - 111}AD35 - 111
12X-RAY DIFFRACTION12{AD|112 - 245}AD112 - 245
13X-RAY DIFFRACTION13{AE|5 - 30}AE5 - 30
14X-RAY DIFFRACTION14{AE|35 - 112}AE35 - 112
15X-RAY DIFFRACTION15{AE|113 - 245}AE113 - 245
16X-RAY DIFFRACTION16{AF|5 - 30}AF5 - 30
17X-RAY DIFFRACTION17{AF|35 - 112}AF35 - 112
18X-RAY DIFFRACTION18{AF|113 - 245}AF113 - 245
19X-RAY DIFFRACTION19{AG|5 - 30}AG5 - 30
20X-RAY DIFFRACTION20{AG|35 - 111}AG35 - 111
21X-RAY DIFFRACTION21{AG|112 - 245}AG112 - 245
22X-RAY DIFFRACTION22{AH|5 - 30}AH5 - 30
23X-RAY DIFFRACTION23{AH|35 - 111}AH35 - 111
24X-RAY DIFFRACTION24{AH|112 - 245}AH112 - 245
25X-RAY DIFFRACTION25{AI|5 - 30}AI5 - 30
26X-RAY DIFFRACTION26{AI|35 - 112}AI35 - 112
27X-RAY DIFFRACTION27{AI|113 - 245}AI113 - 245
28X-RAY DIFFRACTION28{AJ|5 - 30}AJ5 - 30
29X-RAY DIFFRACTION29{AJ|35 - 112}AJ35 - 112
30X-RAY DIFFRACTION30{AJ|113 - 245}AJ113 - 245
31X-RAY DIFFRACTION31{AK|5 - 30}AK5 - 30
32X-RAY DIFFRACTION32{AK|35 - 112}AK35 - 112
33X-RAY DIFFRACTION33{AK|113 - 245}AK113 - 245
34X-RAY DIFFRACTION34{AL|5 - 30}AL5 - 30
35X-RAY DIFFRACTION35{AL|35 - 112}AL35 - 112
36X-RAY DIFFRACTION36{AL|113 - 245}AL113 - 245
37X-RAY DIFFRACTION37{AM|5 - 30}AM5 - 30
38X-RAY DIFFRACTION38{AM|35 - 112}AM35 - 112
39X-RAY DIFFRACTION39{AM|113 - 245}AM113 - 245
40X-RAY DIFFRACTION40{AN|5 - 30}AN5 - 30
41X-RAY DIFFRACTION41{AN|35 - 112}AN35 - 112
42X-RAY DIFFRACTION42{AN|113 - 245}AN113 - 245
43X-RAY DIFFRACTION43{AO|5 - 30}AO5 - 30
44X-RAY DIFFRACTION44{AO|35 - 112}AO35 - 112
45X-RAY DIFFRACTION45{AO|113 - 245}AO113 - 245
46X-RAY DIFFRACTION46{AP|5 - 30}AP5 - 30
47X-RAY DIFFRACTION47{AP|35 - 112}AP35 - 112
48X-RAY DIFFRACTION48{AP|113 - 245}AP113 - 245
49X-RAY DIFFRACTION49{AQ|5 - 30}AQ5 - 30
50X-RAY DIFFRACTION50{AQ|35 - 111}AQ35 - 111
51X-RAY DIFFRACTION51{AQ|112 - 245}AQ112 - 245
52X-RAY DIFFRACTION52{AR|5 - 30}AR5 - 30
53X-RAY DIFFRACTION53{AR|35 - 111}AR35 - 111
54X-RAY DIFFRACTION54{AR|112 - 245}AR112 - 245
55X-RAY DIFFRACTION55{BI|5 - 30}BI5 - 30
56X-RAY DIFFRACTION56{BI|35 - 112}BI35 - 112
57X-RAY DIFFRACTION57{BI|113 - 245}BI113 - 245
58X-RAY DIFFRACTION58{BJ|5 - 30}BJ5 - 30
59X-RAY DIFFRACTION59{BJ|35 - 112}BJ35 - 112
60X-RAY DIFFRACTION60{BJ|113 - 245}BJ113 - 245
61X-RAY DIFFRACTION61{BK|5 - 30}BK5 - 30
62X-RAY DIFFRACTION62{BK|35 - 111}BK35 - 111
63X-RAY DIFFRACTION63{BK|112 - 245}BK112 - 245
64X-RAY DIFFRACTION64{BL|5 - 30}BL5 - 30
65X-RAY DIFFRACTION65{BL|35 - 111}BL35 - 111
66X-RAY DIFFRACTION66{BL|112 - 245}BL112 - 245
67X-RAY DIFFRACTION67{BM|5 - 30}BM5 - 30
68X-RAY DIFFRACTION68{BM|35 - 112}BM35 - 112
69X-RAY DIFFRACTION69{BM|113 - 245}BM113 - 245
70X-RAY DIFFRACTION70{BN|5 - 30}BN5 - 30
71X-RAY DIFFRACTION71{BN|35 - 112}BN35 - 112
72X-RAY DIFFRACTION72{BN|113 - 245}BN113 - 245
73X-RAY DIFFRACTION73{BO|5 - 30}BO5 - 30
74X-RAY DIFFRACTION74{BO|35 - 112}BO35 - 112
75X-RAY DIFFRACTION75{BO|113 - 245}BO113 - 245
76X-RAY DIFFRACTION76{BP|5 - 30}BP5 - 30
77X-RAY DIFFRACTION77{BP|35 - 112}BP35 - 112
78X-RAY DIFFRACTION78{BP|113 - 245}BP113 - 245
79X-RAY DIFFRACTION79{BQ|5 - 30}BQ5 - 30
80X-RAY DIFFRACTION80{BQ|35 - 112}BQ35 - 112
81X-RAY DIFFRACTION81{BQ|113 - 245}BQ113 - 245
82X-RAY DIFFRACTION82{BR|5 - 30}BR5 - 30
83X-RAY DIFFRACTION83{BR|35 - 112}BR35 - 112
84X-RAY DIFFRACTION84{BR|113 - 245}BR113 - 245
85X-RAY DIFFRACTION85{BA|5 - 30}BA5 - 30
86X-RAY DIFFRACTION86{BA|35 - 112}BA35 - 112
87X-RAY DIFFRACTION87{BA|113 - 245}BA113 - 245
88X-RAY DIFFRACTION88{BB|5 - 30}BB5 - 30
89X-RAY DIFFRACTION89{BB|35 - 112}BB35 - 112
90X-RAY DIFFRACTION90{BB|113 - 245}BB113 - 245
91X-RAY DIFFRACTION91{BC|5 - 30}BC5 - 30
92X-RAY DIFFRACTION92{BC|35 - 112}BC35 - 112
93X-RAY DIFFRACTION93{BC|113 - 245}BC113 - 245
94X-RAY DIFFRACTION94{BD|5 - 30}BD5 - 30
95X-RAY DIFFRACTION95{BD|35 - 112}BD35 - 112
96X-RAY DIFFRACTION96{BD|113 - 245}BD113 - 245
97X-RAY DIFFRACTION97{BE|5 - 30}BE5 - 30
98X-RAY DIFFRACTION98{BE|35 - 112}BE35 - 112
99X-RAY DIFFRACTION99{BE|113 - 245}BE113 - 245
100X-RAY DIFFRACTION100{BF|5 - 30}BF5 - 30
101X-RAY DIFFRACTION101{BF|35 - 112}BF35 - 112
102X-RAY DIFFRACTION102{BF|113 - 245}BF113 - 245
103X-RAY DIFFRACTION103{BG|5 - 30}BG5 - 30
104X-RAY DIFFRACTION104{BG|35 - 112}BG35 - 112
105X-RAY DIFFRACTION105{BG|113 - 245}BG113 - 245
106X-RAY DIFFRACTION106{BH|5 - 30}BH5 - 30
107X-RAY DIFFRACTION107{BH|35 - 112}BH35 - 112
108X-RAY DIFFRACTION108{BH|113 - 245}BH113 - 245

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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