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- PDB-7m5c: Crystal Structure of human BAK in complex with WT BAK BH3 peptide -

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基本情報

登録情報
データベース: PDB / ID: 7m5c
タイトルCrystal Structure of human BAK in complex with WT BAK BH3 peptide
要素(Bcl-2 homologous antagonist/killer) x 2
キーワードAPOPTOSIS / protein-peptide complex
機能・相同性
機能・相同性情報


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
類似検索 - 分子機能
Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
類似検索 - ドメイン・相同性
COPPER (II) ION / Bcl-2 homologous antagonist/killer
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: 3.06 Å
データ登録者Singh, G. / Aggarwal, A. / Moldoveanu, T.
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structural basis of BAK activation in mitochondrial apoptosis initiation.
著者: Singh, G. / Guibao, C.D. / Seetharaman, J. / Aggarwal, A. / Grace, C.R. / McNamara, D.E. / Vaithiyalingam, S. / Waddell, M.B. / Moldoveanu, T.
履歴
登録2021年3月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月12日Provider: repository / タイプ: Initial release
改定 1.12022年8月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer
M: Bcl-2 homologous antagonist/killer
N: Bcl-2 homologous antagonist/killer
O: Bcl-2 homologous antagonist/killer
P: Bcl-2 homologous antagonist/killer
Q: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
S: Bcl-2 homologous antagonist/killer
T: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)215,04037
ポリマ－213,69920
非ポリマー1,34017
水00
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,5304
ポリマ－21,3702
非ポリマー1602
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-35 kcal/mol
Surface area8330 Å2
手法PISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,4333
ポリマ－21,3702
非ポリマー641
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-22 kcal/mol
Surface area7860 Å2
手法PISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,4333
ポリマ－21,3702
非ポリマー641
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-28 kcal/mol
Surface area8650 Å2
手法PISA
4
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,7226
ポリマ－21,3702
非ポリマー3524
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-45 kcal/mol
Surface area7920 Å2
手法PISA
5
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,4333
ポリマ－21,3702
非ポリマー641
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-21 kcal/mol
Surface area8430 Å2
手法PISA
6
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer


分子量 (理論値)分子数
合計 (水以外)21,3702
ポリマ－21,3702
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-25 kcal/mol
Surface area8150 Å2
手法PISA
7
M: Bcl-2 homologous antagonist/killer
N: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,6265
ポリマ－21,3702
非ポリマー2563
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-47 kcal/mol
Surface area8100 Å2
手法PISA
8
O: Bcl-2 homologous antagonist/killer
P: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,5304
ポリマ－21,3702
非ポリマー1602
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-34 kcal/mol
Surface area8240 Å2
手法PISA
9
Q: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,4333
ポリマ－21,3702
非ポリマー641
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-22 kcal/mol
Surface area8160 Å2
手法PISA
10
S: Bcl-2 homologous antagonist/killer
T: Bcl-2 homologous antagonist/killer
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,5304
ポリマ－21,3702
非ポリマー1602
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-33 kcal/mol
Surface area8360 Å2
手法PISA
単位格子
Length a, b, c (Å)89.385, 132.215, 89.379
Angle α, β, γ (deg.)90.000, 119.200, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 24 or (resid 25 and (name...
21(chain C and (resid 24 or (resid 25 and (name...
31(chain E and (resid 24 or (resid 25 and (name...
41(chain G and (resid 24 through 26 or (resid 27...
51(chain I and (resid 24 or (resid 25 and (name...
61(chain K and (resid 24 or (resid 25 and (name...
71(chain M and (resid 24 or (resid 25 and (name...
81(chain O and (resid 24 or (resid 25 and (name...
91(chain Q and (resid 24 or (resid 25 and (name...
101(chain S and (resid 24 or (resid 25 and (name...
12(chain B and (resid 83 or (resid 84 and (name...
22(chain F and (resid 83 through 84 or (resid 87...
32(chain H and (resid 83 or (resid 84 and (name...
42(chain J and (resid 83 or (resid 84 and (name...
52(chain L and (resid 83 or (resid 84 and (name...
62(chain N and (resid 83 or (resid 84 and (name...
72(chain P and (resid 83 or (resid 84 and (name...
82(chain R and (resid 83 or (resid 84 and (name...
92(chain T and (resid 83 or (resid 84 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLUGLU(chain A and (resid 24 or (resid 25 and (name...AA244
121GLUGLUGLUGLU(chain A and (resid 24 or (resid 25 and (name...AA255
131SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
141SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
151SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
161SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
171SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
181SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
191SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
211GLUGLUGLUGLU(chain C and (resid 24 or (resid 25 and (name...CC244
221GLUGLUGLUGLU(chain C and (resid 24 or (resid 25 and (name...CC255
231SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
241SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
251SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
261SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
271SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
281SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
291SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
311GLUGLUGLUGLU(chain E and (resid 24 or (resid 25 and (name...EE244
321GLUGLUGLUGLU(chain E and (resid 24 or (resid 25 and (name...EE255
331ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
341ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
351ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
361ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
371ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
381ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
391ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
411GLUGLUGLNGLN(chain G and (resid 24 through 26 or (resid 27...GG24 - 264 - 6
421VALVALVALVAL(chain G and (resid 24 through 26 or (resid 27...GG277
431SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
441SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
451SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
461SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
471SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
481SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
491SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
4101SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
511GLUGLUGLUGLU(chain I and (resid 24 or (resid 25 and (name...II244
521GLUGLUGLUGLU(chain I and (resid 24 or (resid 25 and (name...II255
531SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
541SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
551SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
561SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
571SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
581SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
591SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
611GLUGLUGLUGLU(chain K and (resid 24 or (resid 25 and (name...KK244
621GLUGLUGLUGLU(chain K and (resid 24 or (resid 25 and (name...KK255
631SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
641SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
651SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
661SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
671SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
681SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
691SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
711GLUGLUGLUGLU(chain M and (resid 24 or (resid 25 and (name...MM244
721GLUGLUGLUGLU(chain M and (resid 24 or (resid 25 and (name...MM255
731SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
741SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
751SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
761SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
771SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
781SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
791SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
811GLUGLUGLUGLU(chain O and (resid 24 or (resid 25 and (name...OO244
821GLUGLUGLUGLU(chain O and (resid 24 or (resid 25 and (name...OO255
831GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
841GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
851GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
861GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
871GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
881GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
891GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
911GLUGLUGLUGLU(chain Q and (resid 24 or (resid 25 and (name...QQ244
921GLUGLUGLUGLU(chain Q and (resid 24 or (resid 25 and (name...QQ255
931SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
941SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
951SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
961SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
971SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
981SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
991SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
1011GLUGLUGLUGLU(chain S and (resid 24 or (resid 25 and (name...SS244
1021GLUGLUGLUGLU(chain S and (resid 24 or (resid 25 and (name...SS255
1031GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1041GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1051GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1061GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1071GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1081GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1091GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
112ASPASPASPASP(chain B and (resid 83 or (resid 84 and (name...BB8316
122ASPASPASPASP(chain B and (resid 83 or (resid 84 and (name...BB8417
132SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
142SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
152SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
162SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
172SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
182SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
212ASPASPASPASP(chain F and (resid 83 through 84 or (resid 87...FF83 - 8416 - 17
222ARGARGARGARG(chain F and (resid 83 through 84 or (resid 87...FF8720
232SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
242SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
252SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
262SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
312ASPASPASPASP(chain H and (resid 83 or (resid 84 and (name...HH8316
322ASPASPASPASP(chain H and (resid 83 or (resid 84 and (name...HH8417
332SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
342SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
352SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
362SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
372SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
382SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
412ASPASPASPASP(chain J and (resid 83 or (resid 84 and (name...JJ8316
422ASPASPASPASP(chain J and (resid 83 or (resid 84 and (name...JJ8417
432SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
442SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
452SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
462SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
472SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
482SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
512ASPASPASPASP(chain L and (resid 83 or (resid 84 and (name...LL8316
522ASPASPASPASP(chain L and (resid 83 or (resid 84 and (name...LL8417
532SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
542SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
552SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
562SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
572SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
582SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
612ASPASPASPASP(chain N and (resid 83 or (resid 84 and (name...NN8316
622ASPASPASPASP(chain N and (resid 83 or (resid 84 and (name...NN8417
632METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
642METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
652METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
662METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
672METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
682METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
712ASPASPASPASP(chain P and (resid 83 or (resid 84 and (name...PP8316
722ASPASPASPASP(chain P and (resid 83 or (resid 84 and (name...PP8417
732SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
742SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
752SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
762SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
772SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
782SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
812ASPASPASPASP(chain R and (resid 83 or (resid 84 and (name...RR8316
822ASPASPASPASP(chain R and (resid 83 or (resid 84 and (name...RR8417
832METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
842METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
852METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
862METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
872METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
882METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
912ASPASPASPASP(chain T and (resid 83 or (resid 84 and (name...TT8316
922ASPASPASPASP(chain T and (resid 83 or (resid 84 and (name...TT8417
932SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
942SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
952SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
962SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
972SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
982SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22

NCSアンサンブル:
ID
1
2

-
要素

#1: タンパク質
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


分子量: 18698.918 Da / 分子数: 10 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BAK1, BAK, BCL2L7, CDN1 / プラスミド: pNIC28Bsa4 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): T7 placI/Y / 参照: UniProt: Q16611
#2: タンパク質・ペプチド
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


分子量: 2671.003 Da / 分子数: 10 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q16611
#3: 化合物
ChemComp-CU / COPPER (II) ION


分子量: 63.546 Da / 分子数: 9 / 由来タイプ: 合成 / 式: Cu
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.23 Å3/Da / 溶媒含有率: 44.84 % / Mosaicity: 0.11 °
結晶化温度: 293 K / 手法: 蒸発脱水法 / pH: 6.5 / 詳細: 0.1 M MES (pH 6.5), 0.5 M Ammonium Sulfate

-
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: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.9793 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月1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: 0.9793 Å / 相対比: 1
反射解像度: 3.06→29.59 Å / Num. obs: 30995 / % possible obs: 91.1 % / 冗長度: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.083 / Rrim(I) all: 0.148 / Net I/σ(I): 7 / Num. measured all: 86262
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.06-3.142.10.596302914580.6040.4870.7741.358.7
13.69-29.5930.04310243410.9950.0290.05222.285.1

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
Aimless0.5.21データスケーリング
PDB_EXTRACT3.25データ抽出
PHASER位相決定
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 5vwz

5vwz


解像度: 3.06→29.34 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 27.05 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2494 2028 6.55 %RANDOM
Rwork0.2133 28923 --
obs0.2157 30951 90.78 %-
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 max: 143.79 Å2 / Biso mean: 60.6415 Å2 / Biso min: 26.94 Å2
精密化ステップサイクル: final / 解像度: 3.06→29.34 Å
タンパク質核酸リガンド溶媒全体
原子数13470 0 49 0 13519
Biso mean--79.13 --
残基数----1688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3180X-RAY DIFFRACTION9.581TORSIONAL
12C3180X-RAY DIFFRACTION9.581TORSIONAL
13E3180X-RAY DIFFRACTION9.581TORSIONAL
14G3180X-RAY DIFFRACTION9.581TORSIONAL
15I3180X-RAY DIFFRACTION9.581TORSIONAL
16K3180X-RAY DIFFRACTION9.581TORSIONAL
17M3180X-RAY DIFFRACTION9.581TORSIONAL
18O3180X-RAY DIFFRACTION9.581TORSIONAL
19Q3180X-RAY DIFFRACTION9.581TORSIONAL
110S3180X-RAY DIFFRACTION9.581TORSIONAL
21B63X-RAY DIFFRACTION9.581TORSIONAL
22F63X-RAY DIFFRACTION9.581TORSIONAL
23H63X-RAY DIFFRACTION9.581TORSIONAL
24J63X-RAY DIFFRACTION9.581TORSIONAL
25L63X-RAY DIFFRACTION9.581TORSIONAL
26N63X-RAY DIFFRACTION9.581TORSIONAL
27P63X-RAY DIFFRACTION9.581TORSIONAL
28R63X-RAY DIFFRACTION9.581TORSIONAL
29T63X-RAY DIFFRACTION9.581TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.06-3.140.3445830.31841358144160
3.14-3.230.35491120.29351638175072
3.23-3.320.30881360.27251955209185
3.32-3.430.29361480.25172165231396
3.43-3.550.2621530.22692214236798
3.55-3.690.25221500.22282161231196
3.69-3.860.27541430.23192177232095
3.86-4.060.26291490.21772036218589
4.06-4.320.23221650.18362193235897
4.32-4.650.22751560.1762212236898
4.65-5.110.22121650.18492220238597
5.11-5.850.27131450.2072222236797
5.85-7.350.25961600.22822194235496
7.35-29.340.20361630.19342178234194
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)
15.0475-0.2354-1.5064.55170.32473.9294-0.19950.3878-0.353-0.32490.02910.1275-0.03160.0338-0.00020.36260.0043-0.06240.42460.00020.4891-36.03663.2481-43.399
20.10560.0636-0.07350.3439-0.19330.46670.19260.11591.30010.4310.4897-0.302-0.4375-0.05360.00180.82880.02010.07470.70350.1130.7879-36.52616.9188-46.6526
34.8783-0.6692-2.25384.9590.47573.88210.45250.17160.3932-0.2028-0.1367-0.0076-0.5648-0.11530.02090.4980.03590.07780.29890.04120.4171-20.3019-28.9723-61.1583
40.74060.64540.31741.0436-0.03150.31840.0479-0.1555-0.8842-0.2928-0.4851-0.0192-0.74440.7401-0.00070.43570.00480.10010.50080.02890.4973-23.3309-42.7526-61.58
54.1467-0.1654-0.12084.5718-0.06384.3750.17120.46850.1031-0.3092-0.25840.2608-0.0544-0.1695-0.00020.51210.1138-0.06750.57040.03070.4667-8.2806-31.342917.6934
60.20980.052-0.11110.2221-0.15620.5068-0.0401-0.0194-0.192-0.51780.58480.38451.12090.07870.00430.86760.0324-0.1550.8683-0.06670.7308-10.0731-45.043820.6752
73.63420.71690.39024.84730.93292.96690.0280.3583-0.1586-0.14220.0401-0.17330.2035-0.40210.00030.611-0.0213-0.04650.71260.05510.503326.97692.23275.1143
80.9237-0.45460.81790.2695-0.44340.9105-1.45420.350.4633-0.5770.3452-1.5341-1.3780.1934-0.11980.9572-0.1249-0.08560.63250.11670.802231.082114.99132.991
92.82930.50231.40935.46430.70053.1528-0.0815-0.3983-0.01060.38090.132-0.00230.0407-0.2336-0.00020.36480.02110.05610.3731-0.00570.3374-13.40421.3226-18.2518
100.7027-0.56130.14471.1494-0.41810.1659-0.6692-0.38720.06670.1449-0.36830.1896-0.87680.2666-0.0010.51240.03680.02790.4046-0.07540.5222-16.508814.8593-19.5057
113.5260.03510.94564.2796-0.2182.9073-0.0081-0.0118-0.2597-0.17360.0896-0.12410.06790.1966-0.00020.3599-0.01010.0560.3434-0.01110.4216-9.455-25.0644-28.4847
122.52631.614-0.87662.1185-1.67141.4285-0.01920.1865-2.1306-0.6101-0.5516-0.34661.08080.194-0.43440.66960.17120.01050.6258-0.09040.7462-9.1893-38.7618-32.7561
136.22940.3928-1.45843.8266-0.92872.3941-0.0362-0.2032-0.11980.1128-0.2037-0.1066-0.06190.035900.36360.0101-0.06930.3233-0.01120.366518.62090.9591-31.9797
140.4731-0.0631-0.520.79470.2070.58250.27240.09511.73250.731-0.7440.22710.2309-0.2348-0.00670.60170.0529-0.12620.5852-0.01470.680217.200314.8656-29.0539
153.76680.4487-0.00694.2452-0.26383.2815-0.06280.00360.4362-0.03630.08560.1425-0.222-0.5902-0.00010.37620.0246-0.01350.47150.00230.44825.8554-30.2608-28.296
160.239-0.57260.17891.28-0.31540.2719-0.1374-1.3411-0.26220.3281-0.02790.1976-0.11790.2691-0.00020.4451-0.0805-0.06380.52440.05460.416328.1916-42.7874-23.4151
173.09940.2263-1.3544.99070.46385.22780.2154-0.3657-0.00640.0761-0.1655-0.1417-0.44830.4773-0.00010.4609-0.06530.00620.42280.00460.3793-37.1504-27.1933-7.7613
180.4969-0.3456-0.22460.7008-0.13290.1948-0.4708-0.0133-0.5024-0.3376-0.1072-0.70651.38590.9851-0.0050.60510.0420.04330.86420.08630.8257-31.7683-40.3141-8.2273
191.9961-0.71-0.27723.50630.45433.8754-0.04910.126-0.1122-0.119-0.12940.13890.26480.111-0.00010.49460.0306-0.01760.4340.03380.3687-28.97992.188112.3241
200.43330.31310.41580.57640.66610.80810.64040.28130.2257-0.0718-0.2275-0.8605-1.58690.62770.00770.5759-0.01180.03860.62950.00410.5807-26.883415.424516.3579
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 23 through 185)M23 - 185
2X-RAY DIFFRACTION2(chain 'N' and resid 71 through 89)N71 - 89
3X-RAY DIFFRACTION3(chain 'O' and resid 24 through 184)O24 - 184
4X-RAY DIFFRACTION4(chain 'P' and resid 68 through 89)P68 - 89
5X-RAY DIFFRACTION5(chain 'Q' and resid 23 through 182)Q23 - 182
6X-RAY DIFFRACTION6(chain 'R' and resid 71 through 89)R71 - 89
7X-RAY DIFFRACTION7(chain 'S' and resid 24 through 179)S24 - 179
8X-RAY DIFFRACTION8(chain 'T' and resid 69 through 89)T69 - 89
9X-RAY DIFFRACTION9(chain 'A' and resid 23 through 182)A23 - 182
10X-RAY DIFFRACTION10(chain 'B' and resid 68 through 89)B68 - 89
11X-RAY DIFFRACTION11(chain 'C' and resid 23 through 181)C23 - 181
12X-RAY DIFFRACTION12(chain 'D' and resid 70 through 86)D70 - 86
13X-RAY DIFFRACTION13(chain 'E' and resid 22 through 185)E22 - 185
14X-RAY DIFFRACTION14(chain 'F' and resid 69 through 92)F69 - 92
15X-RAY DIFFRACTION15(chain 'G' and resid 23 through 181)G23 - 181
16X-RAY DIFFRACTION16(chain 'H' and resid 68 through 89)H68 - 89
17X-RAY DIFFRACTION17(chain 'I' and resid 21 through 183)I21 - 183
18X-RAY DIFFRACTION18(chain 'J' and resid 69 through 88)J69 - 88
19X-RAY DIFFRACTION19(chain 'K' and resid 23 through 181)K23 - 181
20X-RAY DIFFRACTION20(chain 'L' and resid 68 through 89)L68 - 89

+
万見について

-
お知らせ

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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

+
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

+
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

+
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。

-
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。
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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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