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- PDB-7ol4: Mouse contactin-1 neurofascin-155 immunoglobulin domains adhesion... -

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基本情報

登録情報
データベース: PDB / ID: 7ol4
タイトルMouse contactin-1 neurofascin-155 immunoglobulin domains adhesion complex
要素
  • Contactin-1
  • Neurofascin
キーワードCELL ADHESION / Heterophilic complex / Immunoglobulin cell adhesion protein / Neural cell adhesion protein / Horseshoe
機能・相同性
機能・相同性情報


central nervous system myelin formation / positive regulation of sodium ion transport / side of membrane / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / positive regulation of neuron projection development / neuron projection development / myelin sheath ...central nervous system myelin formation / positive regulation of sodium ion transport / side of membrane / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / positive regulation of neuron projection development / neuron projection development / myelin sheath / presynaptic membrane / carbohydrate binding / gene expression / postsynaptic membrane / cell adhesion / synapse / positive regulation of gene expression / glutamatergic synapse / plasma membrane
類似検索 - 分子機能
Contactin-1 / : / : / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain ...Contactin-1 / : / : / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.8 Å
データ登録者Chataigner, L.M.P. / Janssen, B.J.C.
資金援助European Union, 1件
組織認可番号国
European Research Council (ERC)European Union
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structural insights into the contactin 1 - neurofascin 155 adhesion complex.
著者: Chataigner, L.M.P. / Gogou, C. / den Boer, M.A. / Frias, C.P. / Thies-Weesie, D.M.E. / Granneman, J.C.M. / Heck, A.J.R. / Meijer, D.H. / Janssen, B.J.C.
履歴
登録2021年5月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年12月14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9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Contactin-1
B: Contactin-1
C: Neurofascin
D: Neurofascin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)287,60622
ポリマ－273,0774
非ポリマー14,52918
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: surface plasmon resonance
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint206 kcal/mol
Surface area136910 Å2
手法PISA
単位格子
Length a, b, c (Å)146.773, 151.775, 162.340
Angle α, β, γ (deg.)90.000, 111.780, 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 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))
21(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))
12(chain C and (resid 24 through 623 or resid 624...
22(chain D and (resid 24 through 234 or resid 248...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A37 - 604
121(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A605 - 607
131(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A609
141(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A616 - 618
211(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B37 - 604
221(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B605 - 607
231(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B609
241(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B616 - 618
112(chain C and (resid 24 through 623 or resid 624...C24 - 623
122(chain C and (resid 24 through 623 or resid 624...C624 - 630
132(chain C and (resid 24 through 623 or resid 624...C636
142(chain C and (resid 24 through 623 or resid 624...C639
152(chain C and (resid 24 through 623 or resid 624...C641
162(chain C and (resid 24 through 623 or resid 624...C644
172(chain C and (resid 24 through 623 or resid 624...C646
212(chain D and (resid 24 through 234 or resid 248...D24 - 234
222(chain D and (resid 24 through 234 or resid 248...D248 - 623
232(chain D and (resid 24 through 234 or resid 248...D624 - 630
242(chain D and (resid 24 through 234 or resid 248...D632
252(chain D and (resid 24 through 234 or resid 248...D635
262(chain D and (resid 24 through 234 or resid 248...D637
272(chain D and (resid 24 through 234 or resid 248...D640
282(chain D and (resid 24 through 234 or resid 248...D642

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Contactin-1 / Neural cell surface protein F3


分子量: 66907.609 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Cntn1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P12960
#2: タンパク質 Neurofascin


分子量: 69630.703 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The promoter and 5' UTR for this variant have not ...詳細: Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The promoter and 5' UTR for this variant have not been determined. The resulting isoform (2) includes the third fibronectin type 3 (FNIII) repeat, lacks the mucin-like domain, and has several differences near the N-terminus, compared to isoform 1. Isoform 2 is also known as NF155, as described by Davis et al. (PMID: 8947556). https://www.ncbi.nlm.nih.gov/nuccore/NM_001160316.1
由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Nfasc / 発現宿主: Homo sapiens (ヒト)

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糖 , 12種, 18分子

#3: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1235.105 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1397.245 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a3-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#14: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
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

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詳細

研究の焦点であるリガンドがあるかY
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: 6.15 Å3/Da / 溶媒含有率: 80 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6
詳細: 2% v/v TacsimateTM pH 5.0, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 16% w/v PEG 3,350

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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: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2019年4月13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: 0.9762 Å / 相対比: 1
反射解像度: 4.795→76 Å / Num. obs: 15712 / % possible obs: 88.5 % / 冗長度: 7.1 % / Biso Wilson estimate: 109.76 Å2 / CC1/2: 0.993 / Net I/σ(I): 4.5
反射 シェル解像度: 4.795→5.352 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 786 / CC1/2: 0.399

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2精密化
XDSデータ削減
PHASER位相決定
PDB_EXTRACT3.27データ抽出
STARANISOデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 7OK5

7ok5


解像度: 4.8→75.38 Å / SU ML: 0.73 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 47.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.3258 791 5.05 %RANDOM
Rwork0.2884 14872 --
obs0.2901 15663 48 %-
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: 563.43 Å2 / Biso mean: 259.2276 Å2 / Biso min: 127.28 Å2
精密化ステップサイクル: final / 解像度: 4.8→75.38 Å
タンパク質核酸リガンド溶媒全体
原子数18329 0 971 0 19300
Biso mean--301.68 --
残基数----2315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5595X-RAY DIFFRACTION6.018TORSIONAL
12B5595X-RAY DIFFRACTION6.018TORSIONAL
21C6032X-RAY DIFFRACTION6.018TORSIONAL
22D6032X-RAY DIFFRACTION6.018TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.8-5.090.210290.35232602695
5.1-5.490.3101350.326182586016
5.49-6.040.3713760.3431423149928
6.04-6.910.341390.33142594273350
6.91-8.710.33662520.30724553480588
8.71-75.380.31672800.26465217549799
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)
110.0186-0.01524.90426.1588-7.53956.3114-0.69410.5863-0.89032.02230.48890.8184-1.93720.3721-02.5456-0.1005-0.06271.9815-0.42511.367131.7686-34.412860.8355
211.81790.3851-5.79318.83261.55348.2164-1.06311.01440.0547-0.94990.35570.86530.88010.0461-0.00062.90160.03490.09021.70690.11851.111841.19375.263446.4171
311.40453.5750.72934.5025-0.20373.33610.5759-0.4861.16060.0781-0.9236-1.47730.87822.296-0.00932.966-0.0661-0.78072.3179-0.28741.194356.01761.98965.162
41.2422-6.1358-0.10554.5678-1.84995.3339-1.9593-0.13960.4526-0.18071.37860.07580.50990.36690.00273.12690.181-0.15131.826-0.21351.986145.441-36.955880.8915
55.36771.09474.64812.7802-5.5045.8423-0.27050.8094-1.0031-0.2258-0.2165-1.05090.87831.68730.00033.4361-0.04920.45232.5982-0.05752.919465.5149-70.021588.9197
6-0.5390.94760.1419-1.2355-0.3142-2.071-0.5481-2.3213-0.5398-5.0263-1.3457-2.7009-3.3745-2.9862-0.01994.0149-1.0521-0.02397.13761.43145.920498.9861-62.647772.9801
77.34532.97782.3859.6155-1.12226.1051-0.1340.21230.4358-1.24740.0455-0.44911.0342-0.97180.00012.06060.30440.39771.6474-0.09012.05954.3878-37.81633.2159
85.9885-0.60142.96912.656210.95628.2002-0.0102-0.8006-0.1608-2.41230.31541.0529-1.5714-0.60730.00651.48690.18620.22011.8740.03651.572152.956-76.767420.6404
98.12121.73091.3274.7947-3.23873.4833-0.6634-1.48360.3726-0.8395-0.6736-1.7549-0.45190.2186-0.00191.36350.31060.39671.9912-0.12242.838776.3343-71.9617.1743
103.8796-1.21481.26597.5388-0.21862.1983-0.2722-0.0740.74661.66050.2594-0.67130.18090.37260.00012.58920.14630.72551.7903-0.07042.921678.1763-34.0269-2.7059
117.65374.81325.20215.6285-5.28183.19650.7064-1.49940.57171.1237-0.864-0.62241.08990.4610.00534.2185-0.01980.1192.34860.04582.28797.6252-1.65224.5034
12-1.1509-1.67890.2686-1.3905-0.2402-0.09620.4957-0.4652-7.64097.2308-4.32856.80380.08511.4957-1.09782.80450.5621-3.57177.07572.99163.4873112.1694-8.250939.3246
135.20312.2989-5.25075.70594.02023.3024-0.44051.3634-0.74638.2361-0.14194.5534.8463-7.5947-1.9675-19.12064.2463-6.63185.97272.52241.538.6586-1.658428.3213
148.73041.6501-1.906211.85525.10667.73390.0742-0.22450.41120.7016-0.51930.60640.52170.50440.00022.06370.0258-0.32551.5310.22571.412149.2951-16.829534.004
1510.953310.106-3.40167.3045-2.13677.48360.37862.32672.17960.22090.44191.1596-2.2754-1.13050.01232.55860.30540.69792.6444-0.30751.597847.752-11.032310.9999
165.62245.3301-0.67342.37470.68085.1958-1.14044.4275-1.56191.60831.78281.7757-1.49850.9701-0.0161-0.06080.13120.57236.3985-0.50794.93567.7293-5.83415.9907
170.2863-0.79712.22661.0014-1.43635.3797-2.38323.3976-1.40365.03145.1566-1.0497-7.4823-4.08081.1063.41732.0580.83937.31491.84614.591316.008429.03340.9727
180.07061.1001-1.26773.25870.29530.70272.4881-1.6641-0.27590.22710.30792.1987-3.4576-0.51061.18698.3198-0.96782.71473.75330.2034.747547.722140.236719.7372
192.898-5.50480.64755.24140.936410.5805-0.4579-0.6371-0.0995-1.3838-0.3411-0.30231.4952-2.3353-0.34211.2048-0.2384-0.49223.592-0.27152.594918.6833-74.576812.5206
205.0356-0.6195-7.474912.0736-2.45369.1241-0.51830.00130.344-1.68730.61940.1948-1.63711.90910.0032.1373-0.3280.13771.6479-0.09461.799550.5619-54.393635.5743
216.491-0.18123.86179.55470.41539.9331-0.935-0.5465-0.99350.37220.45120.96943.4018-0.6994-0.01363.2324-0.19350.49321.8432-0.17181.317833.5005-61.344850.934
223.21372.14132.0946-0.54180.822610.61620.0661-0.01510.8724-0.9796-0.5519-0.2780.5124-0.96230.00011.9259-0.03770.2023.4025-0.04953.73532.3496-74.730527.5264
234.1605-4.5721-4.24055.0212-3.23437.5108-1.5433-0.7399-0.88440.51110.392-0.2330.08890.27220.00033.5757-0.5139-0.12372.9373-0.09682.993514.3445-105.251739.5627
243.3248-1.78620.03071.5311-4.60355.07051.6762-0.0955-0.1870.7677-1.7858-1.74640.27270.85250.00014.4697-0.5717-0.15173.350.9173.110152.0643-105.781748.6126
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 133 )A35 - 133
2X-RAY DIFFRACTION2chain 'A' and ((resid 134 through 235 ) or (resid 605 through 607 ))A0
3X-RAY DIFFRACTION3chain 'A' and ((resid 236 through 328 ) or (resid 608 through 610 ))A0
4X-RAY DIFFRACTION4chain 'A' and ((resid 329 through 410 ) or (resid 611 through 611 ))A0
5X-RAY DIFFRACTION5chain 'A' and ((resid 411 through 503 ) or (resid 612 through 618 ))A0
6X-RAY DIFFRACTION6chain 'A' and (resid 504 through 604 )A504 - 604
7X-RAY DIFFRACTION7chain 'B' and (resid 37 through 133 )B37 - 133
8X-RAY DIFFRACTION8chain 'B' and ((resid 134 through 235 ) or (resid 605 through 608 ))B0
9X-RAY DIFFRACTION9chain 'B' and ((resid 236 through 328 ) or (resid 609 through 614 ))B0
10X-RAY DIFFRACTION10chain 'B' and ((resid 329 through 410 ) or (resid 615 through 615 ))B0
11X-RAY DIFFRACTION11chain 'B' and ((resid 411 through 503 ) or (resid 616 through 626 ))B0
12X-RAY DIFFRACTION12chain 'B' and (resid 504 through 604 )B504 - 604
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 131 )C24 - 131
14X-RAY DIFFRACTION14chain 'C' and (resid 132 through 234 )C132 - 234
15X-RAY DIFFRACTION15chain 'C' and ((resid 248 through 345 ) or (resid 635 through 639 ))C0
16X-RAY DIFFRACTION16chain 'C' and ((resid 346 through 438 ) or (resid 624 through 630 ))C0
17X-RAY DIFFRACTION17chain 'C' and ((resid 439 through 530 ) or (resid 640 through 648 ))C0
18X-RAY DIFFRACTION18chain 'C' and (resid 531 through 623 )C531 - 623
19X-RAY DIFFRACTION19chain 'D' and (resid 24 through 131 )D24 - 131
20X-RAY DIFFRACTION20chain 'D' and (resid 132 through 237 )D132 - 237
21X-RAY DIFFRACTION21chain 'D' and ((resid 248 through 345 ) or (resid 632 through 636 ))D0
22X-RAY DIFFRACTION22chain 'D' and ((resid 346 through 438 ) or (resid 624 through 631 ))D0
23X-RAY DIFFRACTION23chain 'D' and ((resid 439 through 530 ) or (resid 637 through 645 ))D0
24X-RAY DIFFRACTION24chain 'D' and (resid 531 through 623 )D531 - 623

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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