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- PDB-7ppc: Ternary signalling complex of BMP10 bound to ALK1 and BMPRII -

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基本情報

登録情報
データベース: PDB / ID: 7ppc
タイトルTernary signalling complex of BMP10 bound to ALK1 and BMPRII
要素
  • Bone morphogenetic protein 10
  • Bone morphogenetic protein receptor type-2
  • Serine/threonine-protein kinase receptor R3
キーワードSIGNALING PROTEIN / BMPRII BMP10 ALK1 Signalling complex
機能・相同性
機能・相同性情報


semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of cardiac muscle hypertrophy in response to stress / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis ...semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of cardiac muscle hypertrophy in response to stress / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / dorsal aorta morphogenesis / chondrocyte development / tricuspid valve morphogenesis / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / blood vessel maturation / atrial cardiac muscle tissue morphogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / positive regulation of epithelial cell differentiation / aortic valve development / BMP binding / negative regulation of muscle cell differentiation / venous blood vessel development / atrial septum morphogenesis / proteoglycan biosynthetic process / ventricular cardiac muscle cell development / maternal placenta development / endochondral bone morphogenesis / telethonin binding / positive regulation of cartilage development / endocardial cushion development / transforming growth factor beta receptor activity / positive regulation of chondrocyte differentiation / lymphangiogenesis / mitral valve morphogenesis / BMP receptor complex / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / BMP receptor activity / endothelial tube morphogenesis / retina vasculature development in camera-type eye / negative regulation of cardiac muscle hypertrophy / positive regulation of axon extension involved in axon guidance / positive regulation of endothelial cell differentiation / lung vasculature development / transforming growth factor beta receptor activity, type I / negative regulation of focal adhesion assembly / regulation of blood vessel endothelial cell migration / activin receptor activity, type I / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of bicellular tight junction assembly / negative regulation of cell adhesion / positive regulation of BMP signaling pathway / adult heart development / endothelial cell apoptotic process / heart trabecula formation / receptor serine/threonine kinase binding / positive regulation of ossification / negative regulation of systemic arterial blood pressure / dorsal/ventral pattern formation / transforming growth factor beta binding / endothelial cell proliferation / limb development / negative regulation of endothelial cell migration / wound healing, spreading of epidermal cells / blood circulation / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / sarcomere organization / endocardial cushion morphogenesis / Molecules associated with elastic fibres / negative regulation of vasoconstriction / growth factor binding / lung alveolus development / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / positive regulation of cardiac muscle hypertrophy / positive regulation of Notch signaling pathway / blood vessel development / SMAD binding / negative regulation of endothelial cell proliferation / regulation of DNA replication / outflow tract morphogenesis / negative regulation of blood vessel endothelial cell migration / mesoderm formation / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / blood vessel remodeling / regulation of cardiac muscle contraction / cardiac muscle cell proliferation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / positive regulation of cardiac muscle cell proliferation / clathrin-coated pit
類似検索 - 分子機能
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Bone morphogenetic protein 10 / Activin receptor type-1-like / Bone morphogenetic protein receptor type-2
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: 3.6 Å
データ登録者Guo, J. / Yu, M. / Read, R.J. / Li, W.
資金援助 英国, 1件
組織認可番号国
British Heart FoundationPG/12/54/29734, PG/17/1/32532, FS/SBSRF/20/31005 英国
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10.
著者: Guo, J. / Liu, B. / Thorikay, M. / Yu, M. / Li, X. / Tong, Z. / Salmon, R.M. / Read, R.J. / Ten Dijke, P. / Morrell, N.W. / Li, W.
履歴
登録2021年9月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年5月11日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
C: Bone morphogenetic protein 10
D: Bone morphogenetic protein 10
E: Serine/threonine-protein kinase receptor R3
F: Serine/threonine-protein kinase receptor R3
G: Serine/threonine-protein kinase receptor R3
H: Serine/threonine-protein kinase receptor R3
I: Bone morphogenetic protein receptor type-2
J: Bone morphogenetic protein receptor type-2
K: Bone morphogenetic protein receptor type-2
L: Bone morphogenetic protein receptor type-2


分子量 (理論値)分子数
合計 (水以外)147,26612
ポリマ－147,26612
非ポリマー00
水905
1
A: Bone morphogenetic protein 10
B: Bone morphogenetic protein 10
E: Serine/threonine-protein kinase receptor R3
F: Serine/threonine-protein kinase receptor R3
I: Bone morphogenetic protein receptor type-2
J: Bone morphogenetic protein receptor type-2


分子量 (理論値)分子数
合計 (水以外)73,6336
ポリマ－73,6336
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Bone morphogenetic protein 10
D: Bone morphogenetic protein 10
G: Serine/threonine-protein kinase receptor R3
H: Serine/threonine-protein kinase receptor R3
K: Bone morphogenetic protein receptor type-2
L: Bone morphogenetic protein receptor type-2


分子量 (理論値)分子数
合計 (水以外)73,6336
ポリマ－73,6336
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)63.761, 130.387, 88.825
Angle α, β, γ (deg.)90.000, 103.383, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 321 through 323 or (resid 324...
d_2ens_1(chain "B" and (resid 321 through 323 or (resid 324...
d_3ens_1(chain "C" and (resid 321 through 332 or (resid 333...
d_4ens_1(chain "D" and (resid 321 through 323 or (resid 324...
d_1ens_2(chain "E" and (resid 30 through 74 or (resid 75...
d_2ens_2(chain "F" and (resid 30 through 60 or (resid 61...
d_3ens_2(chain "G" and (resid 30 through 64 or (resid 65...
d_4ens_2(chain "H" and (resid 30 through 60 or (resid 61...
d_1ens_3(chain "I" and (resid 33 through 36 or (resid 37...
d_2ens_3(chain "J" and (resid 33 through 38 or resid 53...
d_3ens_3(chain "K" and (resid 33 through 38 or resid 53...
d_4ens_3(chain "L" and (resid 33 through 36 or (resid 37...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNARGA1 - 104
d_21ens_1ASNARGB1 - 104
d_31ens_1ASNARGC1 - 104
d_41ens_1ASNARGD1 - 104
d_11ens_2PROASNE2 - 58
d_12ens_2TYRALAE60 - 77
d_21ens_2PROASNF1 - 57
d_22ens_2TYRALAF59 - 76
d_31ens_2PROASNG1 - 57
d_32ens_2TYRALAG59 - 76
d_41ens_2PROASNH1 - 57
d_42ens_2TYRALAH59 - 76
d_11ens_3LEUASPI4 - 9
d_12ens_3HISLYSI11 - 30
d_13ens_3ILEVALI32 - 80
d_21ens_3LEUASPJ1 - 6
d_22ens_3HISVALJ8 - 76
d_31ens_3LEUASPK3 - 8
d_32ens_3HISLYSK10 - 29
d_33ens_3ILEVALK31 - 79
d_41ens_3LEUASPL3 - 8
d_42ens_3HISLYSL10 - 29
d_43ens_3ILEVALL31 - 79

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.197051777367, 0.291199420604, -0.936148222493), (0.310069036136, -0.887345056615, -0.341285720961), (-0.930068701692, -0.357521534934, 0.0845609968737)38.255179729, 30.2788724478, 42.6797818577
2given(-0.809359007354, -0.0138820126491, -0.587150140033), (0.0214089048446, 0.998358859348, -0.0531154097752), (0.586923892859, -0.0555596768083, -0.807733536696)17.2974977075, -7.17936269421, 42.0272010593
3given(0.72485429914, -0.0066203070057, 0.688870391694), (0.32679549692, -0.876979787764, -0.352294131438), (0.606457705211, 0.480481657702, -0.633519082902)-37.7298965641, 20.7405403265, 29.9925427212
4given(-0.207326596948, 0.320251627604, -0.92436712253), (0.294129120158, -0.880772015647, -0.371118198326), (-0.933007900756, -0.348825961577, 0.0884121352346)37.9046353118, 31.6581584787, 42.3882387739
5given(-0.805972162219, 0.0293102074216, -0.591227355143), (0.00976921368398, 0.999295990968, 0.0362227124785), (0.591872820961, 0.0234186715295, -0.805691088216)18.4147502082, -11.3396830039, 42.4839650992
6given(0.704084979703, -0.044312205092, 0.708731803884), (0.36592707133, -0.832695484905, -0.415590673485), (0.60857351226, 0.551955304259, -0.570073348154)-39.1231573056, 24.0293353611, 27.6776532747
7given(-0.176349419599, 0.234648577094, -0.955950274583), (0.435759908717, -0.852209899907, -0.289571387493), (-0.882617801861, -0.467630550508, 0.0480362786902)40.6559560422, 29.8225116768, 47.062484609
8given(-0.793902935992, -0.0380314731994, -0.606853965357), (0.00558515467724, 0.997543787781, -0.0698226145749), (0.608018860128, -0.0588217519727, -0.791740530239)19.1280160951, -6.79227837723, 41.9741207846
9given(0.718297423604, 0.11610439151, 0.685980015391), (0.432218810347, -0.847099809196, -0.309206748377), (0.545193278779, 0.518595876895, -0.658652112455)-40.851104241, 20.2371811293, 29.5408232628

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要素

#1: タンパク質
Bone morphogenetic protein 10 / BMP-10


分子量: 12177.185 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BMP10 / 細胞株 (発現宿主): HEK EBNA / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O95393
#2: タンパク質
Serine/threonine-protein kinase receptor R3 / SKR3 / Activin receptor-like kinase 1 / ALK-1 / TGF-B superfamily receptor type I / TSR-I


分子量: 10731.074 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACVRL1, ACVRLK1, ALK1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P37023, receptor protein serine/threonine kinase
#3: タンパク質
Bone morphogenetic protein receptor type-2 / BMP type-2 receptor / BMPR-2 / Bone morphogenetic protein receptor type II / BMP type II receptor / BMPR-II


分子量: 13908.316 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BMPR2, PPH1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q13873, receptor protein serine/threonine kinase
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 5 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 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: 2.43 Å3/Da / 溶媒含有率: 49.36 % / 解説: Cluster of thin plates/blades
結晶化温度: 294.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 20% PEG 3350 0.2 M Calcium acetate hydrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.91188 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2019年11月26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: 0.91188 Å / 相対比: 1
反射解像度: 3.6→130.39 Å / Num. obs: 11220 / % possible obs: 99.9 % / 冗長度: 4.9 % / Biso Wilson estimate: 53 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.163 / Rrim(I) all: 0.371 / Net I/σ(I): 2.5
反射 シェル解像度: 3.6→3.94 Å / 冗長度: 4.9 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 789 / CC1/2: 0.673 / Rpim(I) all: 0.604 / Rrim(I) all: 1.369 / % possible all: 99.5

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解析

ソフトウェア
名称バージョン分類
DIALS1.14.13データ削減
Aimless0.7.4データスケーリング
PHASER2.8.3位相決定
PHENIX1.19.2_4158精密化
精密化構造決定の手法: 分子置換
開始モデル: 6SF3, 7PPA

6sf3

7ppa


解像度: 3.6→86.41 Å / SU ML: 0.4875 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 29.5195
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2825 541 4.83 %
Rwork0.2436 10658 -
obs0.2455 11199 68.2 %
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
原子変位パラメータBiso mean: 73.04 Å2
精密化ステップサイクル: LAST / 解像度: 3.6→86.41 Å
タンパク質核酸リガンド溶媒全体
原子数8126 0 0 5 8131
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00298342
X-RAY DIFFRACTIONf_angle_d0.621911332
X-RAY DIFFRACTIONf_chiral_restr0.04561243
X-RAY DIFFRACTIONf_plane_restr0.0051453
X-RAY DIFFRACTIONf_dihedral_angle_d3.86141126
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.822770441852
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.565951381743
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.04610925931
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS1.52149833826
ens_2d_3EX-RAY DIFFRACTIONTorsion NCS1.62288379081
ens_2d_4EX-RAY DIFFRACTIONTorsion NCS1.63291716889
ens_3d_2IX-RAY DIFFRACTIONTorsion NCS1.25982449558
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS1.24943427366
ens_3d_4IX-RAY DIFFRACTIONTorsion NCS1.4838210775
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.960.311090.26771918X-RAY DIFFRACTION49.49
3.96-4.540.31511080.23322276X-RAY DIFFRACTION58.13
4.54-5.710.26891380.23112707X-RAY DIFFRACTION69.36
5.72-86.410.26281860.24913757X-RAY DIFFRACTION94.69
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)
10.660038787282-0.1486313904580.2684348107850.7940100812030.06566699498120.9416940367640.2287990493910.0250396666148-0.1013403310170.0786465568939-0.0139265920505-0.06789809167560.204540577705-0.128535476139-0.001686084844470.487892963697-0.120345300049-0.04673274848160.352193823061-0.0930468674561-0.00640475772842-9.5489872949510.012581051142.2181877104
20.952783051634-0.200253323919-0.05137288394790.491278173256-0.1409469804670.5220655781820.101456185426-0.498370154805-0.1730780509190.0818562701314-0.0235914158309-0.2077106887180.151745591010.362077754206-0.1481279630130.555284394290.0331299043336-0.4135214111290.434130643442-0.08252129466260.2783443421223.70640145713.8646059038251.5983634304
31.247456492761.83316990686-0.8539589980054.04507624462-0.7806377094040.720716676478-0.1699103202390.00662263566358-0.0410872680364-0.05531147027040.1574198634530.0821004592761-0.3030201772790.09357613568310.0189746586060.830983883968-0.00311757372543-0.1548058533110.3238373587420.147969026930.277485928560.2905905439570.6469161654321.72768346973
41.521515476441.76576749594-0.7723061100793.43918938416-1.408833235910.5796635703570.07463128486020.2054706571780.1313322009710.1305323888610.1832733634050.514696632604-0.0964916794066-0.347907359614-0.3045387610330.9475045404310.09681350331070.05070670262910.3590851322520.1363068342060.274399481208-15.7559762784-6.151976849182.30460937379
51.50322044153-0.3260395832250.7144499292270.34148487544-0.8497061133884.7823946103-0.195989731516-0.1563863854350.07857543978850.4351895855360.0353814731160.129515025487-0.4898003208620.447845139225-0.1700068240430.803286884563-0.121890750860.2557431033070.232978208627-0.02220895947630.263216581372-2.33653392315-17.989999522243.1402769225
63.67431884738-0.4689501981180.8769331908622.009270826930.8170067046982.2609806950.0283364966993-0.373246037288-0.2477659100730.1967113165740.170464871929-0.331401939679-0.1382261494760.284849503157-0.1924183279540.490498844365-0.1830781552930.1441799881250.246828189539-0.08691862467090.213181539808-7.6846779284230.586631510154.763302065
72.824352210120.5210083739090.01587389423730.61961057892-0.1446241242931.415194689520.08985160982910.555844948260.0741807461335-0.3509696415170.03544229373510.106284194036-0.322777031697-0.0110279583120.0534637067081.275715852260.2183124863670.01458007259980.4248318955280.0190685854460.220090460962-5.64344685278-27.92377282215.52473036015
81.889013152290.731469878726-1.213585410620.81775961112-1.508844466583.64725578298-0.1289198367740.2885355198440.041048417728-0.2432463881880.109759579610.0004330962459890.0206977825906-0.252899145526-0.1841712650310.7201285033190.04643610667110.1663433357230.2686642563470.1475601730610.231590806826-9.2331598212920.0782139083-8.56369955051
98.70310856526-1.47268604149-2.256480427933.702238942380.2065225442259.579902436050.4500720312590.281303347541-0.3575261715060.0501824847902-0.4254448877830.3912452147690.200315423645-1.20206974139-0.001790337397290.870308576422-0.098548690078-0.02746378629490.64007807535-0.08360143359370.220471581256-19.695226922423.772245558821.7906782201
101.56859129794-3.774206774753.264279435799.09569176763-7.726977736557.606044276110.0201128684064-0.1506276730030.3681351896050.5621706354390.160115450707-1.09160688792-0.1872931925430.710972488054-0.1828633440520.821470059191-0.1119297557560.05140408088671.37294933226-0.2507982019820.92804967731428.631630576-5.7421074190453.9590664729
112.79935783970.279679109783-0.5347222200163.214603253871.913826572231.514688025040.102248859889-0.591782878322-0.553086434556-0.3030232522940.325689070353-0.153517078049-0.375019655567-0.122667924566-0.434811705061.7414563667-0.17058726336-0.7574120114551.355078104040.09942537920831.0137708363220.881328426615.656307220510.9302813611
126.86423483336-3.03716765474-1.64617151538.37072650527.913974771867.781320503070.1240646595670.382498984127-0.267240905902-0.632356490514-0.4947566436631.64921227499-0.708981096205-1.385279788040.343717798450.7654624402450.1378226343310.04776348330330.9940495383240.360952860641.10133107153-36.7531049026-15.22196202217.0566494711
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 321 through 424)AA321 - 4241 - 104
22(chain 'B' and resid 321 through 424)BB321 - 4241 - 104
33(chain 'C' and resid 321 through 424)CC321 - 4241 - 104
44(chain 'D' and resid 321 through 424)DD321 - 4241 - 104
55(chain 'E' and resid 29 through 105)EE29 - 1051 - 77
66(chain 'F' and resid 30 through 105)FF30 - 1051 - 76
77(chain 'G' and resid 30 through 105)GG30 - 1051 - 76
88(chain 'H' and resid 30 through 105)HH30 - 1051 - 76
99(chain 'I' and resid 30 through 130)II30 - 1301 - 85
1010(chain 'J' and resid 33 through 127)JJ33 - 1271 - 78
1111(chain 'K' and resid 31 through 132)KK31 - 1321 - 86
1212(chain 'L' and resid 31 through 125)LL31 - 1251 - 79

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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