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基本情報

登録情報
データベース: PDB / ID: 4fao
タイトルSpecificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex
要素
  • Activin receptor type-2B
  • Growth/differentiation factor 2
  • Serine/threonine-protein kinase receptor R3
キーワードSIGNALING PROTEIN/SIGNALING PROTEIN / tgf-beta / CTK / cystine knot / extracellular domain / receptor / SIGNALING PROTEIN-SIGNALING PROTEIN complex
機能・相同性
機能・相同性情報


Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / activin receptor activity / dorsal aorta morphogenesis / blood vessel maturation / positive regulation of epithelial cell differentiation ...Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / regulation of endothelial cell proliferation / negative regulation of endothelial cell differentiation / activin receptor activity / dorsal aorta morphogenesis / blood vessel maturation / positive regulation of epithelial cell differentiation / venous blood vessel development / positive regulation of cartilage development / transforming growth factor beta receptor activity / lymphangiogenesis / positive regulation of chondrocyte differentiation / BMP receptor complex / retina vasculature development in camera-type eye / BMP receptor activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell differentiation / activin receptor activity, type I / activin receptor complex / transforming growth factor beta receptor activity, type I / embryonic foregut morphogenesis / endothelial tube morphogenesis / negative regulation of focal adhesion assembly / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / 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 / Signaling by Activin / positive regulation of BMP signaling pathway / kinase activator activity / negative regulation of cell adhesion / Signaling by NODAL / transforming growth factor beta binding / gastrulation with mouth forming second / dorsal/ventral pattern formation / pancreas development / skeletal system morphogenesis / determination of left/right symmetry / cartilage development / blood circulation / wound healing, spreading of epidermal cells / insulin secretion / blood vessel morphogenesis / negative regulation of cold-induced thermogenesis / negative regulation of endothelial cell migration / anterior/posterior pattern specification / organ growth / cell surface receptor protein serine/threonine kinase signaling pathway / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / roof of mouth development / odontogenesis of dentin-containing tooth / mesoderm development / negative regulation of endothelial cell proliferation / regulation of DNA replication / growth factor binding / SMAD binding / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / blood vessel remodeling / vasculogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / response to glucose / positive regulation of bone mineralization / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / protein serine/threonine/tyrosine kinase activity / post-embryonic development / ossification / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / kidney development / negative regulation of cell migration / cytokine activity / positive regulation of interleukin-8 production / lung development / growth factor activity / negative regulation of cell growth / cellular response to growth factor stimulus / regulation of blood pressure / osteoblast differentiation / positive regulation of angiogenesis / heart development / angiogenesis / in utero embryonic development / intracellular iron ion homeostasis / transcription by RNA polymerase II / receptor complex
類似検索 - 分子機能
TGF-beta, propeptide / TGF-beta propeptide / 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 / Transforming growth factor-beta-related / Activin types I and II receptor domain ...TGF-beta, propeptide / TGF-beta propeptide / 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 / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / 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 / Mainly Beta
類似検索 - ドメイン・相同性
Activin receptor type-1-like / Activin receptor type-2B / Growth/differentiation factor 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 3.357 Å
データ登録者Townson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. ...Townson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V.
引用ジャーナル: J.Biol.Chem. / 年: 2012
タイトル: Specificity and Structure of a High Affinity Activin Receptor-like Kinase 1 (ALK1) Signaling Complex.
著者: Townson, S.A. / Martinez-Hackert, E. / Greppi, C. / Lowden, P. / Sako, D. / Liu, J. / Ucran, J.A. / Liharska, K. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V.
履歴
登録2012年5月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年6月20日Provider: repository / タイプ: Initial release
改定 1.12012年7月25日Group: Database references
改定 1.22012年8月29日Group: Database references
改定 1.32020年7月29日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.42024年4月3日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Growth/differentiation factor 2
B: Growth/differentiation factor 2
C: Serine/threonine-protein kinase receptor R3
D: Serine/threonine-protein kinase receptor R3
E: Activin receptor type-2B
F: Activin receptor type-2B
G: Growth/differentiation factor 2
H: Growth/differentiation factor 2
I: Serine/threonine-protein kinase receptor R3
J: Serine/threonine-protein kinase receptor R3
K: Activin receptor type-2B
L: Activin receptor type-2B
M: Growth/differentiation factor 2
N: Growth/differentiation factor 2
O: Serine/threonine-protein kinase receptor R3
P: Serine/threonine-protein kinase receptor R3
Q: Activin receptor type-2B
R: Activin receptor type-2B
S: Growth/differentiation factor 2
T: Growth/differentiation factor 2
U: Serine/threonine-protein kinase receptor R3
V: Serine/threonine-protein kinase receptor R3
W: Activin receptor type-2B
X: Activin receptor type-2B
a: Growth/differentiation factor 2
b: Growth/differentiation factor 2
c: Serine/threonine-protein kinase receptor R3
d: Serine/threonine-protein kinase receptor R3
e: Activin receptor type-2B
f: Activin receptor type-2B
g: Growth/differentiation factor 2
h: Growth/differentiation factor 2
i: Serine/threonine-protein kinase receptor R3
j: Serine/threonine-protein kinase receptor R3
k: Activin receptor type-2B
l: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)459,21666
ポリマ－453,76936
非ポリマー5,44730
水00
1
A: Growth/differentiation factor 2
B: Growth/differentiation factor 2
C: Serine/threonine-protein kinase receptor R3
D: Serine/threonine-protein kinase receptor R3
E: Activin receptor type-2B
F: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-62 kcal/mol
Surface area26500 Å2
手法PISA
2
G: Growth/differentiation factor 2
H: Growth/differentiation factor 2
I: Serine/threonine-protein kinase receptor R3
J: Serine/threonine-protein kinase receptor R3
K: Activin receptor type-2B
L: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-64 kcal/mol
Surface area26330 Å2
手法PISA
3
M: Growth/differentiation factor 2
N: Growth/differentiation factor 2
O: Serine/threonine-protein kinase receptor R3
P: Serine/threonine-protein kinase receptor R3
Q: Activin receptor type-2B
R: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-65 kcal/mol
Surface area26390 Å2
手法PISA
4
S: Growth/differentiation factor 2
T: Growth/differentiation factor 2
U: Serine/threonine-protein kinase receptor R3
V: Serine/threonine-protein kinase receptor R3
W: Activin receptor type-2B
X: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-61 kcal/mol
Surface area26440 Å2
手法PISA
5
a: Growth/differentiation factor 2
b: Growth/differentiation factor 2
c: Serine/threonine-protein kinase receptor R3
d: Serine/threonine-protein kinase receptor R3
e: Activin receptor type-2B
f: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-63 kcal/mol
Surface area26390 Å2
手法PISA
6
g: Growth/differentiation factor 2
h: Growth/differentiation factor 2
i: Serine/threonine-protein kinase receptor R3
j: Serine/threonine-protein kinase receptor R3
k: Activin receptor type-2B
l: Activin receptor type-2B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,53611
ポリマ－75,6286
非ポリマー9085
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-64 kcal/mol
Surface area26190 Å2
手法PISA
単位格子
Length a, b, c (Å)216.453, 216.453, 216.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31G
41H
51M
61N
71S
81T
91a
101b
111g
121h
12E
22X
32e
42f
52k
62l
72W
82F
92K
102L
112Q
122R
13C
23U
33V
43c
53d
63i
73j
83P
93D
103I
113J
123O

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 8:110 )A8 - 110
211CHAIN B AND (RESSEQ 8:110 )B8 - 110
311CHAIN G AND (RESSEQ 8:110 )G8 - 110
411CHAIN H AND (RESSEQ 8:110 )H8 - 110
511CHAIN M AND (RESSEQ 8:110 )M8 - 110
611CHAIN N AND (RESSEQ 8:110 )N8 - 110
711CHAIN S AND (RESSEQ 8:110 )S8 - 110
811CHAIN T AND (RESSEQ 8:110 )T8 - 110
911CHAIN a AND (RESSEQ 8:110 )a8 - 110
1011CHAIN b AND (RESSEQ 8:110 )b8 - 110
1111CHAIN g AND (RESSEQ 8:110 )g8 - 110
1211CHAIN h AND (RESSEQ 8:110 )h8 - 110
112CHAIN E AND (RESSEQ 8:99 )E8 - 99
212CHAIN X AND (RESSEQ 8:99 )X8 - 99
312CHAIN e AND (RESSEQ 8:99 )e8 - 99
412CHAIN f AND (RESSEQ 8:99 )f8 - 99
512CHAIN k AND (RESSEQ 8:99 )k8 - 99
612CHAIN l AND (RESSEQ 8:99 )l8 - 99
712CHAIN W AND (RESSEQ 8:99 )W8 - 99
812CHAIN F AND (RESSEQ 8:99 )F8 - 99
912CHAIN K AND (RESSEQ 8:99 )K8 - 99
1012CHAIN L AND (RESSEQ 8:99 )L8 - 99
1112CHAIN Q AND (RESSEQ 8:99 )Q8 - 99
1212CHAIN R AND (RESSEQ 8:99 )R8 - 99
113CHAIN C AND (RESSEQ 30:56 OR RESSEQ 62:100 )C30 - 56
123CHAIN C AND (RESSEQ 30:56 OR RESSEQ 62:100 )C62 - 100
213CHAIN U AND (RESSEQ 30:56 OR RESSEQ 62:100 )U30 - 56
223CHAIN U AND (RESSEQ 30:56 OR RESSEQ 62:100 )U62 - 100
313CHAIN V AND (RESSEQ 30:56 OR RESSEQ 62:100 )V30 - 56
323CHAIN V AND (RESSEQ 30:56 OR RESSEQ 62:100 )V62 - 100
413CHAIN c AND (RESSEQ 30:56 OR RESSEQ 62:100 )c30 - 56
423CHAIN c AND (RESSEQ 30:56 OR RESSEQ 62:100 )c62 - 100
513CHAIN d AND (RESSEQ 30:56 OR RESSEQ 62:100 )d30 - 56
523CHAIN d AND (RESSEQ 30:56 OR RESSEQ 62:100 )d62 - 100
613CHAIN i AND (RESSEQ 30:56 OR RESSEQ 62:100 )i30 - 56
623CHAIN i AND (RESSEQ 30:56 OR RESSEQ 62:100 )i62 - 100
713CHAIN j AND (RESSEQ 30:56 OR RESSEQ 62:100 )j30 - 56
723CHAIN j AND (RESSEQ 30:56 OR RESSEQ 62:100 )j62 - 100
813CHAIN P AND (RESSEQ 30:56 OR RESSEQ 62:100 )P30 - 56
823CHAIN P AND (RESSEQ 30:56 OR RESSEQ 62:100 )P62 - 100
913CHAIN D AND (RESSEQ 30:56 OR RESSEQ 62:100 )D30 - 56
923CHAIN D AND (RESSEQ 30:56 OR RESSEQ 62:100 )D62 - 100
1013CHAIN I AND (RESSEQ 30:56 OR RESSEQ 62:100 )I30 - 56
1023CHAIN I AND (RESSEQ 30:56 OR RESSEQ 62:100 )I62 - 100
1113CHAIN J AND (RESSEQ 30:56 OR RESSEQ 62:100 )J30 - 56
1123CHAIN J AND (RESSEQ 30:56 OR RESSEQ 62:100 )J62 - 100
1213CHAIN O AND (RESSEQ 30:56 OR RESSEQ 62:100 )O30 - 56
1223CHAIN O AND (RESSEQ 30:56 OR RESSEQ 62:100 )O62 - 100

NCSアンサンブル:
ID
1
2
3

NCS oper:
IDCodeMatrixベクター
1given(0.282101, 0.063828, -0.957259), (0.081211, -0.995792, -0.042465), (-0.955941, -0.06576, -0.286097)64.132202, -45.986401, 82.197403
2given(-0.182977, 0.196952, -0.963187), (0.806922, 0.589752, -0.0327), (0.561601, -0.7832, -0.266836)67.609497, -99.916199, -37.686901
3given(-0.531447, 0.846433, -0.033397), (-0.846707, -0.531981, -0.009159), (-0.025519, 0.023409, 0.9994)111.679001, 61.540798, 33.497898
4given(-0.473919, 0.880124, -0.027977), (-0.87266, -0.473674, -0.118732), (-0.11775, -0.031855, 0.992532)108.794998, 68.126404, -55.629902
5given(-0.070637, 0.239238, -0.968388), (0.831485, 0.550416, 0.075328), (0.551038, -0.799879, -0.237803)152.283997, -102.438004, -11.7746
6given(-0.518628, -0.854305, -0.034469), (0.85356, -0.519672, 0.037097), (-0.049605, -0.010182, 0.998717)111.873001, -63.222698, -28.1033
7given(-0.032706, -0.259761, -0.965119), (-0.886549, 0.453397, -0.091988), (0.461477, 0.852616, -0.24512)117.972, 27.393299, -13.1889
8given(0.169977, -0.160202, 0.972339), (0.906411, 0.412594, -0.090474), (-0.386687, 0.896717, 0.21534)30.5408, -41.1408, 72.043503
9given(0.489412, -0.870145, 0.057652), (-0.867401, -0.478917, 0.13511), (-0.089955, -0.116131, -0.989152)0.77945, -5.99188, 35.135601
10given(0.049036, 0.270384, 0.961503), (-0.795192, 0.593074, -0.126224), (-0.604372, -0.75839, 0.244089)101.153, 27.396299, -13.4959
11given(0.524125, 0.85067, 0.04067), (0.836393, -0.523149, 0.163587), (0.160435, -0.051723, -0.98569)108.044998, -64.431198, -10.4809
12given(-0.076017, -0.261471, -0.962213), (-0.867695, 0.492781, -0.065358), (0.49125, 0.829939, -0.264337)118.972, 25.908701, -13.454
13given(0.222032, -0.156518, 0.962395), (0.883221, 0.45043, -0.130511), (-0.413064, 0.878985, 0.23825)26.872299, -35.633801, 72.0905
14given(0.484815, -0.872721, 0.057553), (-0.868925, -0.473121, 0.145345), (-0.099616, -0.120475, -0.987706)0.776625, -5.88748, 35.049198
15given(0.014145, 0.318598, 0.947784), (-0.811617, 0.557293, -0.175221), (-0.584018, -0.76676, 0.266462)102.684998, 26.528299, -13.9054
16given(0.5278, 0.847433, 0.057307), (0.829932, -0.528898, 0.177427), (0.180667, -0.046085, -0.982464)107.813004, -64.4459, -11.348
17given(-0.520215, -0.85396, -0.011317), (0.853411, -0.520296, 0.031352), (-0.032661, 0.006651, 0.999444)111.241997, -63.0261, -28.907101
18given(0.276987, 0.015839, -0.960743), (0.049891, -0.998752, -0.002082), (-0.959578, -0.047356, -0.277432)62.5481, -43.049198, 83.339996
19given(-0.124477, 0.241048, -0.962497), (0.824748, 0.564435, 0.034695), (0.55163, -0.789499, -0.269063)60.115299, -98.296402, -36.5644
20given(-0.533065, 0.844056, -0.058404), (-0.843237, -0.535659, -0.044962), (-0.069235, 0.025281, 0.99728)111.170998, 60.039398, 35.883099
21given(-0.471401, 0.881862, -0.010019), (-0.878311, -0.470469, -0.085025), (-0.079694, -0.031281, 0.996328)107.449997, 66.479202, -58.011799
22given(-0.050016, 0.267118, -0.962365), (0.851309, 0.515282, 0.09878), (0.522275, -0.814329, -0.253172)148.865997, -104.709, -7.48065
23given(-0.511139, -0.857758, -0.054671), (0.856785, -0.513543, 0.04682), (-0.068236, -0.022909, 0.997406)112.037003, -63.733501, -27.229099
24given(-0.051485, -0.268441, -0.961919), (-0.877591, 0.471866, -0.084711), (0.476637, 0.83981, -0.259875)118.695999, 26.705601, -13.4081
25given(0.493733, -0.869373, 0.020456), (-0.866866, -0.49017, 0.090974), (-0.069064, -0.062649, -0.995643)1.76353, -5.82206, 38.638901
26given(0.205103, -0.16771, 0.964264), (0.884691, 0.453169, -0.10936), (-0.418634, 0.875506, 0.241318)27.866301, -36.532299, 72.047302
27given(0.509165, 0.86056, 0.013697), (0.852252, -0.506342, 0.131471), (0.120074, -0.055268, -0.991225)108.859001, -65.020699, -8.74783
28given(0.059571, 0.319714, 0.94564), (-0.81683, 0.560147, -0.137925), (-0.573794, -0.764211, 0.294521)102.535004, 26.6448, -14.0081
29given(-0.054579, 0.270573, -0.961151), (0.851899, 0.514734, 0.096527), (0.520855, -0.813535, -0.258594)149.345001, -104.670998, -7.1911
30given(0.315427, 0.058642, -0.947136), (0.054205, -0.997573, -0.043713), (-0.947401, -0.037551, -0.31784)61.0574, -43.7589, 82.258202
31given(-0.531096, 0.846171, -0.043945), (-0.847006, -0.531583, 0.000717), (-0.022754, 0.037603, 0.999034)111.285004, 61.823399, 33.067001
32given(-0.19782, 0.235322, -0.951573), (0.827954, 0.559783, -0.033688), (0.524746, -0.794523, -0.305572)68.309998, -101.234001, -35.1936
33given(-0.464639, 0.885475, 0.006662), (-0.883345, -0.46297, -0.073219), (-0.061749, -0.039905, 0.997294)105.528, 64.954498, -59.2173

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要素

#1: タンパク質
Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


分子量: 12102.971 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BMP9, GDF2 / プラスミド: pAID4
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: Q9UK05
#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: 11592.863 Da / 分子数: 12 / Fragment: Extracellular domain / 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 / プラスミド: pAID4
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P37023
#3: タンパク質
Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


分子量: 14118.272 Da / 分子数: 12 / Fragment: Extracellular domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ActRIIB, ACVR2B / プラスミド: pAID4
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: Q13705
#4: 糖...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 24 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Na

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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: 3.23 Å3/Da / 溶媒含有率: 61.96 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 6.5
詳細: 20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, 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: 回転陽極 / タイプ: RIGAKU FR-E+ SUPERBRIGHT / 波長: 1.5418 Å
検出器タイプ: RIGAKU SATURN 944 / 検出器: CCD / 日付: 2010年8月5日 / 詳細: mirrors
放射モノクロメーター: Ni Filter / プロトコル: SINGLE WAVELENGTH / 散乱光タイプ: x-ray
放射波長波長: 1.5418 Å / 相対比: 1
反射解像度: 3.35→50 Å / Num. obs: 82408 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 5.8 % / Biso Wilson estimate: 64.18 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 20.91
反射 シェル解像度: 3.35→3.41 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4084 / Rsym value: 0.372 / % possible all: 99.4

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位相決定

位相決定手法: 分子置換
Phasing MRRfactor: 54.26 / Model details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation3.36 Å26.85 Å
Translation3.36 Å26.85 Å

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER2.1.4位相決定
PHENIX1.6.4_486精密化
PDB_EXTRACT3.11データ抽出
HKL-2000データ収集
精密化構造決定の手法: 分子置換
開始モデル: structures solved in-house, not deposited

解像度: 3.357→26.849 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8066 / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 3 / 位相誤差: 26.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2614 1685 2.42 %random
Rwork0.219 ---
all0.22 79681 --
obs0.22 69521 84.03 %-
溶媒の処理減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 30.918 Å2 / ksol: 0.289 e/Å3
原子変位パラメータBiso max: 251.72 Å2 / Biso mean: 80.4386 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1--21.5924 Å20 Å20 Å2
2---21.5924 Å20 Å2
3---17.9779 Å2
精密化ステップサイクル: LAST / 解像度: 3.357→26.849 Å
タンパク質核酸リガンド溶媒全体
原子数25069 0 342 0 25411
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01426917
X-RAY DIFFRACTIONf_angle_d1.24135486
X-RAY DIFFRACTIONf_chiral_restr0.0793834
X-RAY DIFFRACTIONf_plane_restr0.0044590
X-RAY DIFFRACTIONf_dihedral_angle_d16.1079304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A799X-RAY DIFFRACTIONPOSITIONAL0.064
12B799X-RAY DIFFRACTIONPOSITIONAL0.064
13G795X-RAY DIFFRACTIONPOSITIONAL0.065
14H806X-RAY DIFFRACTIONPOSITIONAL0.048
15M802X-RAY DIFFRACTIONPOSITIONAL0.054
16N796X-RAY DIFFRACTIONPOSITIONAL0.067
17S806X-RAY DIFFRACTIONPOSITIONAL0.044
18T798X-RAY DIFFRACTIONPOSITIONAL0.067
19a796X-RAY DIFFRACTIONPOSITIONAL0.066
110b806X-RAY DIFFRACTIONPOSITIONAL0.051
111g806X-RAY DIFFRACTIONPOSITIONAL0.064
112h806X-RAY DIFFRACTIONPOSITIONAL0.051
21E707X-RAY DIFFRACTIONPOSITIONAL0.049
22X707X-RAY DIFFRACTIONPOSITIONAL0.049
23e713X-RAY DIFFRACTIONPOSITIONAL0.052
24f717X-RAY DIFFRACTIONPOSITIONAL0.056
25k703X-RAY DIFFRACTIONPOSITIONAL0.056
26l709X-RAY DIFFRACTIONPOSITIONAL0.053
27W720X-RAY DIFFRACTIONPOSITIONAL0.037
28F711X-RAY DIFFRACTIONPOSITIONAL0.057
29K706X-RAY DIFFRACTIONPOSITIONAL0.06
210L719X-RAY DIFFRACTIONPOSITIONAL0.056
211Q729X-RAY DIFFRACTIONPOSITIONAL0.04
212R713X-RAY DIFFRACTIONPOSITIONAL0.061
31C495X-RAY DIFFRACTIONPOSITIONAL0.034
32U495X-RAY DIFFRACTIONPOSITIONAL0.034
33V491X-RAY DIFFRACTIONPOSITIONAL0.04
34c492X-RAY DIFFRACTIONPOSITIONAL0.039
35d487X-RAY DIFFRACTIONPOSITIONAL0.041
36i496X-RAY DIFFRACTIONPOSITIONAL0.039
37j497X-RAY DIFFRACTIONPOSITIONAL0.042
38P491X-RAY DIFFRACTIONPOSITIONAL0.043
39D497X-RAY DIFFRACTIONPOSITIONAL0.042
310I488X-RAY DIFFRACTIONPOSITIONAL0.034
311J481X-RAY DIFFRACTIONPOSITIONAL0.045
312O470X-RAY DIFFRACTIONPOSITIONAL0.04
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.357-3.47640.34361600.28636454661480
3.4764-3.61530.30191600.25686557671781
3.6153-3.77940.26321650.23466806697185
3.7794-3.97810.27311680.20756354652279
3.9781-4.22640.22911630.20326194635777
4.2264-4.55130.23311670.19176788695584
4.5513-5.00660.25241610.19436776693784
5.0066-5.7250.29851750.23237002717787
5.725-7.18980.24571760.22527215739189
7.1898-26.84950.23981900.21187690788093
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)
10.63440.6821-0.20611.2983-0.40250.0636-0.1729-0.0449-0.0036-0.30110.10380.13080.0548-0.10910.06240.11460.0327-0.02860.03360.01190.10786.573-10.5574-1.4267
20.92680.5044-0.11950.6094-0.52360.9982-0.23060.087-0.42550.12620.0131-0.3020.14-0.0880.22870.171-0.0760.09860.06870.02970.251389.2508-28.39281.0495
31.2190.30220.9960.8850.14130.9017-0.0241-0.5360.23040.5975-0.2996-0.2939-0.2045-0.14510.13230.3699-0.0293-0.2120.39640.08570.175897.2401-6.334519.9899
40.12780.0476-0.09710.05790.00850.1535-0.07090.1236-0.1016-0.1612-0.0574-0.06240.1748-0.13430.06760.3088-0.17380.10710.4126-0.12780.249472.5143-32.4906-16.3616
51.5728-0.1044-0.5290.35960.23540.4305-0.31250.36220.15950.1380.1072-0.05820.0509-0.18470.07970.3016-0.0094-0.01490.23190.11980.139195.886313.2469-9.587
61.9041-0.23871.2510.1464-0.56472.63350.4636-0.1871-0.8389-0.37890.3903-0.33240.94440.23210.1898-0.51260.38370.71230.1377-0.13310.8015100.828-51.5278-6.3886
70.668-0.52750.88091.9991-0.70741.119-0.06540.11230.23190.0548-0.2541-0.7068-0.10570.240.39070.0543-0.0281-0.0650.15520.09140.290789.019528.1053-30.7584
82.5761-0.67090.19050.40730.0890.1903-0.00720.4229-0.2370.0473-0.04550.05990.11460.06040.05140.14550.0024-0.04930.08550.03710.175875.279816.2975-33.4083
94.05870.0690.42290.71370.07170.2399-0.1106-1.39380.12130.2492-0.10810.1438-0.2611-0.21660.08510.2079-0.03890.05640.4876-0.16420.098665.498923.7254-12.6227
100.72370.1061-0.2180.9514-0.23751.4674-0.22750.61810.2121-0.492-0.2536-0.08740.34690.16910.32860.31480.18740.05420.58610.15950.1941101.304616.0772-48.1992
110.56880.06380.10390.14830.31391.29710.09330.12360.7380.11390.3709-0.2516-0.86040.3087-0.2550.6511-0.0883-0.16140.34610.42951.3493102.834350.0861-37.9929
121.3367-0.1307-0.30570.8236-1.33372.51260.02320.3349-0.4621-0.2102-0.3548-0.05070.6930.2653-0.07140.2543-0.0255-0.11010.189-0.05230.006550.608110.9915-42.1804
131.36140.19360.08410.5951-0.02080.0835-0.16940.071-0.43320.35850.012-0.3360.01170.1870.08430.12070.0596-0.0650.26620.00940.219372.691415.969463.6747
140.543-0.51260.95311.9966-1.24632.0714-0.2356-0.03470.22980.4357-0.3107-1.0019-0.24340.01990.45740.20540.0359-0.31670.26030.00360.569186.761826.563267.9193
152.48340.41720.2911.9275-1.42181.18670.0368-1.312-0.10391.1815-0.0768-0.0219-0.7789-0.01710.05560.86530.20710.02341.041-0.22240.468561.772622.483184.2479
160.7704-0.61120.15741.6474-1.02861.9835-0.16670.53330.4413-0.3688-0.533-0.6670.24450.18110.45560.10240.16830.04490.61670.21410.4671100.430114.484352.0847
170.05370.0669-0.05630.99480.01290.20520.0702-0.08450.00460.4262-0.2169-0.11890.04140.25110.01650.20540.0323-0.10910.3236-0.03810.099848.141113.037953.122
180.22470.19130.16090.34110.05321.12760.0765-0.20920.04220.70470.1202-0.7921-1.00510.22810.03090.9591-0.1336-0.62690.45690.42421.5529102.2448.21963.1248
190.0496-0.384-0.00472.01980.1460.07330.11550.1133-0.0062-0.155-0.2242-0.2406-0.0215-0.03790.07550.06450.0225-0.01330.0908-0.01180.074756.7666-6.030829.4579
200.42980.098-0.02090.53390.41060.5456-0.2773-0.21450.13620.0360.0270.3109-0.0084-0.06280.06670.11010.0703-0.06810.0995-0.07050.199640.15010.961430.9807
210.8792-0.2936-0.11741.1561-0.90751.2901-0.2952-0.3086-0.36290.6667-0.01010.12120.0224-0.10040.09550.37680.03150.17650.28040.11440.320953.722-17.765150.614
220.56070.0589-0.08770.6511-0.32590.68880.06790.32250.075-0.3744-0.32910.0423-0.13520.38460.18550.49990.0417-0.06690.2690.01610.091346.347117.813514.2813
231.08060.18110.35510.6173-0.38940.4931-0.2643-0.2615-0.14210.09790.004-0.0335-0.33480.02940.19410.30340.0460.00520.259-0.04830.08172.6807-26.526822.0839
240.57410.7748-0.53141.49290.07871.8390.2784-0.04110.563-0.0661-0.03821.03410.1264-0.9332-0.03190.3194-0.0918-0.27340.5142-0.22871.160914.58343.513622.0327
250.4215-0.21160.24050.8119-0.76110.7093-0.25780.23620.2864-0.0858-0.0838-0.3316-0.25370.14960.27120.4596-0.05280.06780.18320.16620.368565.832-62.163936.0266
260.2920.2355-0.16741.2484-0.35530.10940.16980.00560.3784-0.0873-0.23120.5994-0.2647-0.0046-0.0110.275-0.00770.05230.10620.0840.464749.2271-68.232540.5066
271.9228-0.39020.02342.87040.22120.0386-0.13940.7933-0.1192-1.67840.10040.12140.25540.02390.08350.83230.03190.09960.37270.05940.280348.8431-81.998820.4947
280.53770.13230.10190.65640.0350.1383-0.0914-0.27870.1110.6111-0.1855-0.0707-0.3419-0.03890.20720.72360.0044-0.03670.2670.11640.370362.5289-43.741851.2893
290.8653-0.9918-0.72651.37080.24831.93850.52020.04820.3663-0.2333-0.1479-0.97660.06510.78060.060.45130.1582-0.06530.63610.56451.239292.1079-60.37240.5932
301.75270.57521.27161.51370.4632.9854-0.10030.20760.56460.3951-0.11890.7603-0.5884-0.1545-0.18350.31710.04170.20550.24140.07570.431833.8255-86.781852.1163
310.80820.45480.58060.30130.42391.1267-0.14470.40160.30420.0057-0.04150.13480.0838-0.0708-0.15110.1563-0.0754-0.21540.2430.03160.287622.1834-35.5949-6.2959
322.48751.0640.22030.42620.03020.2202-0.03610.0445-0.5607-0.11440.079-0.14230.167-0.0204-0.29240.1218-0.0267-0.10410.07450.02030.201135.2617-46.9272-0.9818
332.15460.11920.14280.41390.37190.3816-0.5931.1734-0.2148-0.30520.19130.1034-0.05060.04260.28820.4956-0.1373-0.0780.79810.01280.268247.7631-41.0736-20.8787
341.54910.16020.29780.6597-0.32130.8433-0.2112-0.4767-0.26850.3019-0.2244-0.15440.05-0.20460.21270.3296-0.1901-0.06480.33010.02770.18887.4878-46.18789.9582
350.31690.25590.07950.7322-0.5630.9169-0.03530.00640.0784-0.30650.34310.5942-0.7061-0.1167-0.11820.7952-0.1302-0.40120.2684-0.09291.0937.6177-13.0152-2.797
362.53230.8029-0.79260.8111-0.23461.42340.1535-0.288-0.69150.0055-0.4297-0.07670.3995-0.18550.07160.2975-0.0352-0.14160.29090.07190.214558.8553-51.383311.0555
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:110)A6 - 110
2X-RAY DIFFRACTION2(CHAIN B AND RESID 6:110)B6 - 110
3X-RAY DIFFRACTION3(CHAIN C AND RESID 30:104)C30 - 104
4X-RAY DIFFRACTION4(CHAIN D AND RESID 30:101)D30 - 101
5X-RAY DIFFRACTION5(CHAIN E AND RESID 9:99)E9 - 99
6X-RAY DIFFRACTION6(CHAIN F AND RESID 9:99)F9 - 99
7X-RAY DIFFRACTION7(CHAIN G AND RESID 6:110)G6 - 110
8X-RAY DIFFRACTION8(CHAIN H AND RESID 6:110)H6 - 110
9X-RAY DIFFRACTION9(CHAIN I AND RESID 30:104)I30 - 104
10X-RAY DIFFRACTION10(CHAIN J AND RESID 30:101)J30 - 101
11X-RAY DIFFRACTION11(CHAIN K AND RESID 9:99)K9 - 99
12X-RAY DIFFRACTION12(CHAIN L AND RESID 9:99)L9 - 99
13X-RAY DIFFRACTION13(CHAIN M AND RESID 6:110)M6 - 110
14X-RAY DIFFRACTION14(CHAIN N AND RESID 7:110)N7 - 110
15X-RAY DIFFRACTION15(CHAIN O AND RESID 30:104)O30 - 104
16X-RAY DIFFRACTION16(CHAIN P AND RESID 30:101)P30 - 101
17X-RAY DIFFRACTION17(CHAIN Q AND RESID 9:99)Q9 - 99
18X-RAY DIFFRACTION18(CHAIN R AND RESID 9:99)R9 - 99
19X-RAY DIFFRACTION19(CHAIN S AND RESID 6:110)S6 - 110
20X-RAY DIFFRACTION20(CHAIN T AND RESID 6:110)T6 - 110
21X-RAY DIFFRACTION21(CHAIN U AND RESID 30:104)U30 - 104
22X-RAY DIFFRACTION22(CHAIN V AND RESID 30:101)V30 - 101
23X-RAY DIFFRACTION23(CHAIN W AND RESID 9:99)W9 - 99
24X-RAY DIFFRACTION24(CHAIN X AND RESID 9:99)X9 - 99
25X-RAY DIFFRACTION25(CHAIN a AND RESID 6:110)a6 - 110
26X-RAY DIFFRACTION26(CHAIN b AND RESID 6:110)b6 - 110
27X-RAY DIFFRACTION27(CHAIN c AND RESID 30:104)c30 - 104
28X-RAY DIFFRACTION28(CHAIN d AND RESID 30:101)d30 - 101
29X-RAY DIFFRACTION29(CHAIN e AND RESID 9:99)e9 - 99
30X-RAY DIFFRACTION30(CHAIN f AND RESID 9:99)f9 - 99
31X-RAY DIFFRACTION31(CHAIN g AND RESID 6:110)g6 - 110
32X-RAY DIFFRACTION32(CHAIN h AND RESID 6:110)h6 - 110
33X-RAY DIFFRACTION33(CHAIN i AND RESID 30:104)i30 - 104
34X-RAY DIFFRACTION34(CHAIN j AND RESID 30:101)j30 - 101
35X-RAY DIFFRACTION35(CHAIN k AND RESID 9:99)k9 - 99
36X-RAY DIFFRACTION36(CHAIN l AND RESID 9:99)l9 - 99

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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

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