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- PDB-6axg: Structure of RasGRP4 in complex with HRas -

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基本情報

登録情報
データベース: PDB / ID: 6axg
タイトルStructure of RasGRP4 in complex with HRas
要素
  • GTPase HRas
  • RAS guanyl-releasing protein 4
キーワードSIGNALING PROTEIN
機能・相同性
機能・相同性情報


positive regulation of natural killer cell mediated immunity / diacylglycerol binding / antibacterial innate immune response / myeloid cell differentiation / phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process ...positive regulation of natural killer cell mediated immunity / diacylglycerol binding / antibacterial innate immune response / myeloid cell differentiation / phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / EPHB-mediated forward signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / positive regulation of epithelial cell proliferation / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / guanyl-nucleotide exchange factor activity / regulation of actin cytoskeleton organization / animal organ morphogenesis / FCERI mediated MAPK activation / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / positive regulation of MAP kinase activity / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / G protein activity / FCERI mediated NF-kB activation / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / positive regulation of type II interferon production / endocytosis / RAS processing / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis
類似検索 - 分子機能
Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases ...Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
GTPase HRas / RAS guanyl-releasing protein 4
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.302 Å
データ登録者Kondo, Y. / Iwig, J.S. / Kuriyan, J.
引用ジャーナル: Elife / 年: 2017
タイトル: A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1.
著者: Vercoulen, Y. / Kondo, Y. / Iwig, J.S. / Janssen, A. / White, K.A. / Amini, M. / Barber, D.L. / Kuriyan, J. / Roose, J.P.
履歴
登録2017年9月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年10月11日Provider: repository / タイプ: Initial release
改定 1.12023年10月4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
A: RAS guanyl-releasing protein 4
B: GTPase HRas
C: RAS guanyl-releasing protein 4
D: GTPase HRas
E: RAS guanyl-releasing protein 4
F: GTPase HRas
G: RAS guanyl-releasing protein 4
H: GTPase HRas
I: RAS guanyl-releasing protein 4
J: GTPase HRas
K: RAS guanyl-releasing protein 4
L: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)395,19512
ポリマ－395,19512
非ポリマー00
水00
1
A: RAS guanyl-releasing protein 4
B: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-9 kcal/mol
Surface area23630 Å2
手法PISA
2
C: RAS guanyl-releasing protein 4
D: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-9 kcal/mol
Surface area23670 Å2
手法PISA
3
E: RAS guanyl-releasing protein 4
F: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-8 kcal/mol
Surface area24150 Å2
手法PISA
4
G: RAS guanyl-releasing protein 4
H: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-6 kcal/mol
Surface area23720 Å2
手法PISA
5
I: RAS guanyl-releasing protein 4
J: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-7 kcal/mol
Surface area23560 Å2
手法PISA
6
K: RAS guanyl-releasing protein 4
L: GTPase HRas


分子量 (理論値)分子数
合計 (水以外)65,8662
ポリマ－65,8662
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-7 kcal/mol
Surface area23510 Å2
手法PISA
単位格子
Length a, b, c (Å)114.105, 114.105, 680.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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要素

#1: タンパク質
RAS guanyl-releasing protein 4


分子量: 46660.285 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RASGRP4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8TDF6
#2: タンパク質
GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


分子量: 19205.596 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HRAS, HRAS1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01112

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.24 Å3/Da / 溶媒含有率: 62.01 %
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: 20% PEG3350 and 300 mM sodium thiocyanate

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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: ALS / ビームライン: 8.2.1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年2月11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: 3.3→49.21 Å / Num. obs: 76133 / % possible obs: 98.7 % / 冗長度: 9.2 % / CC1/2: 0.968 / Rmerge(I) obs: 0.224 / Net I/σ(I): 8.3
反射 シェル解像度: 3.3→3.37 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.521

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)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: 4l9m

4l9m


解像度: 3.302→49.21 Å / 交差検証法: FREE R-VALUE / σ(F): 105.97 / 位相誤差: 37.99
Rfactor反射数%反射
Rfree0.2602 3814 5.06 %
Rwork0.2273 --
obs0.2295 76133 98.65 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.302→49.21 Å
タンパク質核酸リガンド溶媒全体
原子数23168 0 0 0 23168
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00323601
X-RAY DIFFRACTIONf_angle_d0.77631966
X-RAY DIFFRACTIONf_dihedral_angle_d6.94114207
X-RAY DIFFRACTIONf_chiral_restr0.0453631
X-RAY DIFFRACTIONf_plane_restr0.0054130
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3025-3.35940.30492120.2843467X-RAY DIFFRACTION89
3.3594-3.42050.35811490.29863383X-RAY DIFFRACTION91
3.4205-3.48620.30731870.28843481X-RAY DIFFRACTION91
3.4862-3.55740.28652040.27263495X-RAY DIFFRACTION91
3.5574-3.63470.35591940.33485X-RAY DIFFRACTION92
3.6347-3.71920.37231890.34093527X-RAY DIFFRACTION93
3.7192-3.81210.31941880.24353656X-RAY DIFFRACTION94
3.8121-3.91510.35521350.28773634X-RAY DIFFRACTION96
3.9151-4.03030.26611980.23223612X-RAY DIFFRACTION95
4.0303-4.16030.23161860.22513603X-RAY DIFFRACTION95
4.1603-4.30880.24962010.21623644X-RAY DIFFRACTION95
4.3088-4.48120.22781820.20923672X-RAY DIFFRACTION95
4.4812-4.68490.21491610.19923683X-RAY DIFFRACTION96
4.6849-4.93160.23332120.19583662X-RAY DIFFRACTION95
4.9316-5.24010.25512040.20413644X-RAY DIFFRACTION95
5.2401-5.6440.25142010.2233673X-RAY DIFFRACTION95
5.644-6.21050.27671910.24393676X-RAY DIFFRACTION95
6.2105-7.1060.24792260.22793703X-RAY DIFFRACTION94
7.106-8.94050.2071900.17693732X-RAY DIFFRACTION95
8.9405-44.05520.21912030.19033861X-RAY DIFFRACTION95
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)
16.5943-0.06382.41.17880.48633.8783-0.2221-0.5892-0.31240.21720.25420.05230.0221-0.43190.05110.6920.5843-0.07261.1958-0.1790.1747326.9722479.7312745.8503
26.72081.60691.86548.16456.32536.7460.05870.75690.0677-1.56490.5085-0.0644-1.0271.3922-0.62281.34610.13310.14230.7334-0.07040.3709330.111481.9374740.7828
31.53661.65671.08542.20880.95320.8735-0.34540.5791-0.1776-0.2810.4071-0.2124-0.2294-0.1135-0.0571.35570.27720.05420.934-0.14230.3689318.3532489.7252742.9973
41.0585-1.56022.51813.4537-3.48526.61490.3045-0.1498-0.1057-0.01660.34040.6541-0.75420.7104-0.72080.75150.05460.15790.9299-0.15490.6074298.1701412.8235705.3308
52.7544-0.57180.85822.75881.27951.897-0.85111.4170.5776-0.2784-0.28120.47220.23680.41870.67090.58470.2126-0.23921.1964-0.15310.7275294.0131402.8103701.4444
61.0790.67480.89888.5366-2.06464.4222-0.8420.5293-0.0671-0.44380.20020.2743-0.08110.46210.44860.4897-0.18670.04240.674-0.28070.561302.4939396.3129700.2178
71.72050.3931-0.08540.6309-0.11110.19850.09970.0635-0.11280.05310.0069-0.0653-0.4358-0.2272-0.01771.18010.0071-0.03710.6293-0.29760.0188331.5218425.1972699.7701
81.5992-0.2332-0.01953.1816-1.26225.2909-0.21440.71810.2534-0.31790.25980.45720.7027-0.02220.09270.46540.0919-0.16071.0245-0.30440.5702310.7554421.1719708.2363
92.73830.53442.68432.5314-0.27442.8395-0.1580.0315-0.37440.23220.2209-0.4993-0.2468-0.03510.02210.57980.1430.04570.3602-0.14250.5928340.0187419.5365697.0105
103.82040.6493-0.3636.83631.07440.22690.04610.6902-0.0923-0.0264-0.15040.60470.8315-0.57760.02520.9999-0.1893-0.27570.6719-0.02780.2679320.0462429.6841723.9259
118.2947-2.6989-2.78957.0936-2.33782.6330.0738-0.57990.56871.25931.6022-0.85150.39910.5512-1.56280.6819-0.2459-0.26010.7854-0.04670.5264325.3421427.9748719.5603
120.48230.48590.12460.69220.25380.2569-0.01690.0904-0.19760.13860.2195-0.12610.04130.47540.24311.29820.3469-0.10311.052-0.2558-0.6656333.4364417.2589725.6876
131.3523-0.29471.57570.538-0.65272.0354-0.0915-0.44530.14230.48650.42110.27810.1614-0.1281-0.13591.0458-0.29690.53820.6462-0.25070.9494325.2135424.259733.8363
140.4506-0.1028-0.56440.28580.10052.73430.15260.4908-0.1799-0.25920.12060.7149-0.0486-1.17680.04770.35030.1534-0.62250.70640.13861.0604298.8553439.7875774.5754
151.1882-0.634-2.0775.6461-0.01974.8194-0.0286-1.0881-0.0760.369-0.3121-0.1381-0.59430.30790.28180.4964-0.28-0.11271.0437-0.03170.5376299.4717452.5396777.7166
162.6604-0.7965-0.06171.2112-0.59630.4985-0.108-0.14960.4445-0.26870.06620.23160.09810.02940.08550.9647-0.1455-0.00920.292-0.15250.4691327.2444438.3569781.0799
171.7888-0.46730.46321.19180.75151.9069-0.0374-0.1412-0.1087-0.23540.12430.1050.4369-0.1481-0.04570.7794-0.25950.02770.3786-0.01460.24331.5656425.9333775.7462
182.03031.2459-0.9693.4874-0.06340.64540.1694-0.2997-0.103-0.0529-0.75690.21530.502-0.54940.53630.8784-0.145-0.01870.67320.02040.473322.0858421.4099754.7116
190.104-0.09590.11620.1035-0.21471.5787-0.1775-0.10980.0873-0.04320.0326-0.014-0.11110.05550.01351.1903-0.24570.13051.0706-0.1869-0.3774333.1814433.9615755.7559
204.4664-3.68950.30284.91810.93895.83330.24570.94370.3747-0.6268-0.5251-0.3467-0.30860.49850.10291.0142-0.2624-0.23121.18710.04450.1811328.6802430.8666744.1674
210.56260.53360.32340.5442-0.04183.29690.3567-0.3456-0.41350.0161-0.0742-0.230.8164-0.1114-0.29360.7609-0.0644-0.12180.90440.37940.4502291.1643444.1315699.6749
224.2894-1.31361.10832.8445-0.46682.16210.52630.3190.4747-0.4225-0.4799-0.6457-0.01190.398-0.06370.40520.0850.06331.0788-0.01030.4066301.9865450.5741696.5054
233.5224-2.75190.72612.7329-0.10530.4420.5164-0.06260.4726-0.2958-0.298-0.3579-0.0306-0.1787-0.1330.6442-0.0770.18510.61110.08430.2851276.462465.8548692.8131
241.3057-0.3285-0.40462.2003-0.26041.02560.0199-0.02180.238-0.2170.10260.2798-0.0166-0.08160.11020.1155-0.29760.02330.37080.21350.6928256.9648474.6658696.7815
250.74840.488-0.74740.393-0.26082.18410.1231-0.3365-0.03030.2129-0.25740.07010.0531-0.05570.15390.55630.20310.28710.9630.1980.1038253.3616465.0091702.91
261.14110.28040.33740.8675-0.3310.5851-0.15640.0373-0.10230.1063-0.0080.18770.3361-0.18330.01360.5665-0.16890.16180.69150.0630.0176270.818462.905700.5656
271.62390.3125-1.32133.0607-0.79672.6234-0.14580.4819-0.0827-0.38620.1701-0.24540.18320.5690.01740.61460.23780.04090.77320.05450.1443266.5816458.3404720.9992
281.3576-0.2467-0.65593.8551-1.17261.28470.24870.32220.7349-0.47540.48990.845-0.1516-0.6547-0.71490.6797-0.02790.47270.90130.59131.5254267.3833447.5908714.7226
291.83640.43850.42284.876-1.00830.5348-0.09160.0864-0.3769-0.04550.33130.47170.6553-0.5258-0.14910.8382-0.42340.05150.966-0.08560.3613259.9911452.1792723.5433
301.9124-0.5268-3.08221.6481.19985.89180.2065-0.01310.237-0.2130.0244-0.3122-0.20550.7868-0.05130.5454-0.19520.02050.60370.1845-0.0119264.1634467.666710.5042
310.74640.04441.92272.85550.53665.0134-0.41540.59240.1637-0.12430.1758-0.1663-0.23120.43310.11470.54-0.16330.18760.75010.08550.2182271.3171466.7545723.6026
324.835-1.491.51371.4232-0.57430.4871-0.40090.2110.17420.1470.18360.2477-0.81770.790.15380.6314-0.17580.04870.6260.03410.2868268.8385475.6344720.438
336.3854-1.0794-0.57820.81960.1750.7393-0.0764-0.42830.94170.37330.017-0.03650.0061-0.16420.34940.69-0.54170.08341.1033-0.39370.3169271.3202472.1345730.2057
342.4985-2.1938-4.07495.16364.83937.1406-0.4464-0.2908-0.24250.73520.54990.26961.23890.7510.01491.1589-0.11220.1340.68050.10080.0978274.7774460.8638730.8655
351.37510.7673-0.21098.3366-2.24936.0170.1737-0.67040.50240.04350.14790.02150.46390.7124-0.38190.532-0.1917-0.05921.53210.03070.578261.4805460.1335730.7906
362.1415-0.10571.57920.3856-0.31511.84780.07140.3828-1.1152-0.23290.4354-1.395-0.54950.3351-0.53050.6284-0.04130.12150.5354-0.22650.9562266.1162426.9013773.7832
374.45660.4494-0.27980.6980.83261.16330.211-0.5990.04420.0140.104-0.8845-0.22390.1246-0.25030.34980.12570.4451.19470.07861.5279256.6657426.1779.4327
380.1877-0.49540.40983.20350.32871.2784-0.0947-0.06490.08860.24130.19080.0699-0.05510.7774-0.0540.3292-0.07030.10781.035-0.05850.3256258.0142463.3031778.8705
390.3411-0.22730.00360.7724-0.00260.7721-0.10070.0692-0.12950.18290.0553-0.0749-0.32940.35070.14680.7741-0.3530.2211.19480.0922-0.1209269.0009460.2986769.4946
401.50030.82660.69822.3831-0.91175.3001-0.13250.421-0.0319-0.1860.00850.42110.28330.3850.07010.2381-0.03880.08930.4826-0.15510.1144252.6787470.9716778.3116
411.2212-0.94641.15692.2960.06361.6764-0.0974-0.2051-0.09530.3739-0.233-0.20590.0453-0.14760.2260.908-0.06370.15680.72770.35050.1731267.293458.4699752.1708
420.6040.28020.03763.77891.0461.29320.10040.1241-0.3303-0.1031-0.0441-0.83340.07890.4893-0.03260.5705-0.05040.09851.16110.27310.2298270.4924460.4178756.6123
431.17031.0457-1.22621.6942-1.50731.5155-0.11830.1103-0.0267-0.30620.1950.0417-0.0540.00780.17020.754-0.2913-0.12820.74880.02-0.2446257.7302458.5719749.7631
440.60890.2485-0.1491.88961.37031.17190.1169-0.04890.00890.5047-0.21820.3745-0.1865-0.2843-0.01750.54190.09160.18760.8210.10490.116251.1404464.9318753.4758
450.0425-0.0441-0.15010.1640.62722.3802-0.0162-0.0386-0.0163-0.05190.09140.039-0.6373-0.32690.09410.5849-0.2739-0.10211.11510.1344-0.0504257.9381467.2058747.1104
460.431-0.56940.73811.8074-0.57351.41610.12160.5371-0.336-0.72570.18751.67380.3993-0.6308-0.23720.4435-0.2226-0.28521.2074-0.14360.8484253.8281455.7196741.584
478.6992-6.6984-1.71075.97481.99682.6616-0.21120.42720.4782-0.85570.1724-1.4013-0.41170.7992-0.07420.4796-0.41570.04211.15750.09590.5104268.088463.5389742.3916
483.14111.6288-1.74871.3122-1.18722.19760.1-0.48480.64380.22220.2091-0.1959-0.24910.7625-0.03320.9935-0.1588-0.66640.8231-0.25541.169323.2637521.0046704.4687
491.12460.88880.19572.7217-0.04380.3651-0.28970.4335-0.0716-0.61850.3825-0.3950.2822-0.157-0.0660.6121-0.8766-0.07470.89-0.09621.0019312.1532528.5805699.7564
500.78180.0455-0.6162.23580.19380.66970.0937-0.00770.3532-0.1125-0.05660.0938-0.174-0.04180.17380.423-0.1295-0.26241.1980.30070.2383311.0481495.5149695.1993
511.38490.31190.78920.98720.74761.823-0.1839-0.06440.13230.3487-0.071-0.21480.00470.70380.25620.3248-0.1427-0.0411.3771-0.04070.4737322.1429477.0424699.1493
522.0672-0.16710.25541.2788-1.10771.0826-0.1197-0.00990.00790.30250.3184-0.4097-0.60930.57880.0110.4351-0.12670.00341.3770.14870.5113324.4463505.7691706.11
530.3458-0.46990.00621.8847-1.19584.18810.0292-0.33790.033-0.038-0.22450.3057-0.4110.26170.1490.366-0.05990.09181.1293-0.25670.0964307.4706481.3313694.8657
542.3510.21071.65830.6345-0.08951.27-0.70590.57360.6477-0.5790.1254-0.05980.12380.23850.34980.936-0.3071-0.0821.03540.12190.5004328.3615494.2913720.0225
550.14620.2735-0.07260.92540.9182.57560.08890.070.0504-0.1360.2105-0.0722-0.12170.1602-0.00040.7347-0.18950.04861.41770.083-0.0528321.6867486.5389715.5913
560.6722-0.11550.39260.38570.28520.6215-0.07320.1133-0.24730.0873-0.0069-0.0041-0.2634-0.1243-0.04650.7623-0.2356-0.08771.33870.08610.1166310.8191486.5526722.8466
573.45410.6568-2.9031.4112-0.09263.32320.1218-0.2518-0.8660.0141-0.16270.10660.0677-0.06490.03130.38020.07480.31490.98440.04561.4295305.9222492.529733.1074
580.49880.95730.01293.5614-1.37141.1256-0.1478-0.39060.20720.8383-0.1791.0396-0.3668-0.98070.1441.0280.14340.14551.4883-0.45480.5524317.0775497.1645731.5887
590.9097-1.6070.91459.8801-2.87571.1445-0.185-0.9039-0.15831.13080.25480.0242-0.29310.1363-0.03490.77890.46210.161.4964-0.15210.5686324.5026486.1665730.7863
602.79432.0040.67762.32880.52580.218-0.3950.15250.56160.16320.50220.66050.21830.3961-0.12921.0815-0.0121-0.00730.81440.1080.3524355.2019506.0983772.0097
612.3236-3.92510.04148.9555-2.22718.0495-0.022-0.0642-0.09920.1427-0.4757-0.44240.44560.47030.27990.8123-0.1543-0.06010.52480.47160.575361.0067494.4384774.62
621.96831.1842-0.28532.2097-0.37271.33110.37620.3534-0.22730.1174-0.3808-0.4471-0.1532-0.185-0.04941.07170.3689-0.1750.83540.03960.2395331.0568484.3324779.0593
631.31810.07421.40731.93850.04572.08250.3375-0.05840.3629-0.25690.01390.6471-0.1029-1.0815-0.29180.67330.2463-0.08161.26960.08380.5742314.1889478.1815776.0911
643.29812.193-3.20993.1386-2.50323.20110.208-0.07140.04930.14940.080.5134-0.4296-0.1502-0.34350.72540.45780.04650.9110.09240.2826312.6755493.0302770.5808
652.24860.01770.86752.53390.66390.506-0.27180.08270.13760.4511-0.0264-0.0575-0.05880.10840.16880.88260.0677-0.68321.0025-0.23960.7883328.6758495.3323770.318
662.6283-1.56991.71831.9513-0.23671.740.70080.45860.2425-0.0848-0.11620.179-0.2652-0.6149-0.57851.07470.1555-0.46920.8712-0.18891.5735339.2087503.0393765.9146
673.2203-0.72192.11971.45322.07676.60310.16460.4978-0.5357-0.86010.0313-0.0358-0.64860.4588-0.45020.6786-0.0350.00720.9342-0.03920.1975322.2091473.6673779.219
680.0842-0.3469-0.0933.13390.0490.1711-0.2457-0.431-0.13330.8120.0177-0.2688-0.1606-0.48620.18110.7034-0.2133-0.02330.9115-0.06060.3438324.0455491.9458752.2517
691.1402-0.0215-0.06256.8867-4.80223.3525-0.07640.52240.25160.21160.36070.68360.0717-0.9265-0.23610.9180.0096-0.02681.04420.03120.3853326.138504.9621757.8087
703.7551-4.2783.55195.5455-5.18995.3067-0.3729-1.09140.6210.53660.5283-0.26260.1330.3196-0.0440.82740.3393-0.0331.0287-0.11630.4663318.2482500.4442751.3243
716.67370.14871.76935.04811.09772.0002-0.29370.38040.3534-0.4242-0.03780.6715-0.7502-0.83390.28781.2411-0.034-0.36661.3322-0.0530.3333316.0051495.7823748.9233
725.3583-1.79024.05986.6106-0.57895.8873-0.2672-0.36320.2870.37110.2974-0.69950.63291.7183-0.10760.74660.1474-0.13170.90450.10650.4374322.2871483.1892763.4192
730.8668-0.22970.01050.1850.02750.9499-0.1043-0.07940.050.12550.1013-0.02460.07880.17390.16750.7257-0.0204-0.08370.6681-0.0982-0.0418328.4821483.5146749.7956
743.3734-0.5698-0.3670.3255-0.25190.46420.0501-0.9395-0.33140.050.0576-0.01440.1518-0.08760.00481.1918-0.0809-0.14670.70910.1250.2438326.4181474.8564753.4373
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 105 through 126 )
2X-RAY DIFFRACTION2chain 'H' and (resid 127 through 151 )
3X-RAY DIFFRACTION3chain 'H' and (resid 152 through 166 )
4X-RAY DIFFRACTION4chain 'I' and (resid 61 through 92 )
5X-RAY DIFFRACTION5chain 'I' and (resid 93 through 131 )
6X-RAY DIFFRACTION6chain 'I' and (resid 132 through 155 )
7X-RAY DIFFRACTION7chain 'I' and (resid 156 through 342 )
8X-RAY DIFFRACTION8chain 'I' and (resid 343 through 393 )
9X-RAY DIFFRACTION9chain 'I' and (resid 394 through 430 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 48 )
11X-RAY DIFFRACTION11chain 'J' and (resid 49 through 64 )
12X-RAY DIFFRACTION12chain 'J' and (resid 65 through 137 )
13X-RAY DIFFRACTION13chain 'J' and (resid 138 through 166 )
14X-RAY DIFFRACTION14chain 'K' and (resid 60 through 92 )
15X-RAY DIFFRACTION15chain 'K' and (resid 93 through 154 )
16X-RAY DIFFRACTION16chain 'K' and (resid 155 through 260 )
17X-RAY DIFFRACTION17chain 'K' and (resid 261 through 430 )
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 57 )
19X-RAY DIFFRACTION19chain 'L' and (resid 58 through 126 )
20X-RAY DIFFRACTION20chain 'L' and (resid 127 through 166 )
21X-RAY DIFFRACTION21chain 'A' and (resid 61 through 92 )
22X-RAY DIFFRACTION22chain 'A' and (resid 93 through 156 )
23X-RAY DIFFRACTION23chain 'A' and (resid 157 through 237 )
24X-RAY DIFFRACTION24chain 'A' and (resid 238 through 284 )
25X-RAY DIFFRACTION25chain 'A' and (resid 285 through 342 )
26X-RAY DIFFRACTION26chain 'A' and (resid 343 through 430 )
27X-RAY DIFFRACTION27chain 'B' and (resid 1 through 23 )
28X-RAY DIFFRACTION28chain 'B' and (resid 24 through 37 )
29X-RAY DIFFRACTION29chain 'B' and (resid 38 through 57 )
30X-RAY DIFFRACTION30chain 'B' and (resid 58 through 74 )
31X-RAY DIFFRACTION31chain 'B' and (resid 75 through 86 )
32X-RAY DIFFRACTION32chain 'B' and (resid 87 through 104 )
33X-RAY DIFFRACTION33chain 'B' and (resid 105 through 137 )
34X-RAY DIFFRACTION34chain 'B' and (resid 138 through 151 )
35X-RAY DIFFRACTION35chain 'B' and (resid 152 through 166 )
36X-RAY DIFFRACTION36chain 'C' and (resid 62 through 115 )
37X-RAY DIFFRACTION37chain 'C' and (resid 116 through 155 )
38X-RAY DIFFRACTION38chain 'C' and (resid 156 through 284 )
39X-RAY DIFFRACTION39chain 'C' and (resid 285 through 393 )
40X-RAY DIFFRACTION40chain 'C' and (resid 394 through 430 )
41X-RAY DIFFRACTION41chain 'D' and (resid 1 through 23 )
42X-RAY DIFFRACTION42chain 'D' and (resid 24 through 74 )
43X-RAY DIFFRACTION43chain 'D' and (resid 75 through 86 )
44X-RAY DIFFRACTION44chain 'D' and (resid 87 through 104 )
45X-RAY DIFFRACTION45chain 'D' and (resid 105 through 116 )
46X-RAY DIFFRACTION46chain 'D' and (resid 117 through 151 )
47X-RAY DIFFRACTION47chain 'D' and (resid 152 through 166 )
48X-RAY DIFFRACTION48chain 'E' and (resid 62 through 94 )
49X-RAY DIFFRACTION49chain 'E' and (resid 95 through 156 )
50X-RAY DIFFRACTION50chain 'E' and (resid 157 through 259 )
51X-RAY DIFFRACTION51chain 'E' and (resid 260 through 342 )
52X-RAY DIFFRACTION52chain 'E' and (resid 343 through 394 )
53X-RAY DIFFRACTION53chain 'E' and (resid 395 through 430 )
54X-RAY DIFFRACTION54chain 'F' and (resid 1 through 46 )
55X-RAY DIFFRACTION55chain 'F' and (resid 47 through 74 )
56X-RAY DIFFRACTION56chain 'F' and (resid 75 through 116 )
57X-RAY DIFFRACTION57chain 'F' and (resid 117 through 137 )
58X-RAY DIFFRACTION58chain 'F' and (resid 138 through 151 )
59X-RAY DIFFRACTION59chain 'F' and (resid 152 through 166 )
60X-RAY DIFFRACTION60chain 'G' and (resid 61 through 131 )
61X-RAY DIFFRACTION61chain 'G' and (resid 132 through 155 )
62X-RAY DIFFRACTION62chain 'G' and (resid 156 through 237 )
63X-RAY DIFFRACTION63chain 'G' and (resid 238 through 313 )
64X-RAY DIFFRACTION64chain 'G' and (resid 314 through 342 )
65X-RAY DIFFRACTION65chain 'G' and (resid 343 through 364 )
66X-RAY DIFFRACTION66chain 'G' and (resid 365 through 393 )
67X-RAY DIFFRACTION67chain 'G' and (resid 394 through 430 )
68X-RAY DIFFRACTION68chain 'H' and (resid 1 through 23 )
69X-RAY DIFFRACTION69chain 'H' and (resid 24 through 37 )
70X-RAY DIFFRACTION70chain 'H' and (resid 38 through 46 )
71X-RAY DIFFRACTION71chain 'H' and (resid 47 through 57 )
72X-RAY DIFFRACTION72chain 'H' and (resid 58 through 74 )
73X-RAY DIFFRACTION73chain 'H' and (resid 75 through 86 )
74X-RAY DIFFRACTION74chain 'H' and (resid 87 through 104 )

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万見について

-
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