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- PDB-7f7i: Stapled Peptide Inhibitor in complex with PSD95 GK domain -

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基本情報

登録情報
データベース: PDB / ID: 7f7i
タイトルStapled Peptide Inhibitor in complex with PSD95 GK domain
要素
  • ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
  • Disks large homolog 4
キーワードPEPTIDE BINDING PROTEIN / MAGUK Stapled peptide entropy GK domain
機能・相同性
機能・相同性情報


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / protein localization to synapse / positive regulation of dendrite morphogenesis / proximal dendrite / Trafficking of AMPA receptors / dendritic branch / LGI-ADAM interactions / Activation of Ca-permeable Kainate Receptor / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / regulation of NMDA receptor activity / dendritic spine organization / cellular response to potassium ion / RAF/MAP kinase cascade / positive regulation of synapse assembly / beta-2 adrenergic receptor binding / NMDA selective glutamate receptor signaling pathway / Synaptic adhesion-like molecules / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / AMPA glutamate receptor complex / excitatory synapse / kinesin binding / social behavior / regulation of neuronal synaptic plasticity / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / neuromuscular junction / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / postsynaptic density membrane / cerebral cortex development / kinase binding / synaptic vesicle / cell-cell junction / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Disks large homolog 4
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.595 Å
データ登録者Shang, Y. / Huang, X. / Li, X. / Zhang, M.
資金援助 香港, 4件
組織認可番号国
The University Grants Committee, Research Grants Council (RGC)17309616 香港
The University Grants Committee, Research Grants Council (RGC)T13-605/18-W 香港
The University Grants Committee, Research Grants Council (RGC)AoE/M-09/12 香港
The University Grants Committee, Research Grants Council (RGC)AoE/P-705/16 香港
引用ジャーナル: Rsc Chem Biol / 年: 2021
タイトル: Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain.
著者: Unarta, I.C. / Xu, J. / Shang, Y. / Cheung, C.H.P. / Zhu, R. / Chen, X. / Cao, S. / Cheung, P.P. / Bierer, D. / Zhang, M. / Huang, X. / Li, X.
履歴
登録2021年6月29日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年4月6日Provider: repository / タイプ: Initial release
改定 1.12023年11月29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
改定 1.22024年10月23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: Disks large homolog 4
B: Disks large homolog 4
C: Disks large homolog 4
D: Disks large homolog 4
E: Disks large homolog 4
F: Disks large homolog 4
G: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
H: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
I: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
J: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
K: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
L: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)151,29312
ポリマ－151,29312
非ポリマー00
水6,846380
1
A: Disks large homolog 4
G: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-1 kcal/mol
Surface area10650 Å2
手法PISA
2
B: Disks large homolog 4
H: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area11430 Å2
手法PISA
3
C: Disks large homolog 4
I: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area10470 Å2
手法PISA
4
D: Disks large homolog 4
J: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-3 kcal/mol
Surface area10550 Å2
手法PISA
5
E: Disks large homolog 4
K: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-4 kcal/mol
Surface area10400 Å2
手法PISA
6
F: Disks large homolog 4
L: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量 (理論値)分子数
合計 (水以外)25,2152
ポリマ－25,2152
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-3 kcal/mol
Surface area10350 Å2
手法PISA
単位格子
Length a, b, c (Å)51.029, 51.954, 144.500
Angle α, β, γ (deg.)91.780, 91.430, 120.970
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 533:551 or resseq 553:557 or (resid...
21(chain B and (resseq 533:551 or resseq 553:557 or (resid...
31(chain C and (resseq 533:551 or resseq 553:557 or (resid...
41(chain D and (resseq 533:551 or resseq 553:557 or (resid...
51(chain E and (resseq 533:551 or resseq 553:571 or resseq...
61(chain F and (resseq 533:551 or resseq 553:571 or resseq...
12(chain L and (resseq -6 or resseq -4 or (resid...
22(chain H and (resseq -6 or resseq -4 or (resid...
32(chain I and (resseq -6 or resseq -4 or (resid...
42(chain J and (resseq -6 or resseq -4 or (resid...
52(chain K and (resseq -6 or resseq -4 or (resid...

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
111TYRTYRLEULEU(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA533 - 55125 - 43
121SERSERASPASP(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA553 - 55745 - 49
131LYSLYSLYSLYS(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA55850
141HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
151HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
161HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
171HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
181HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
211TYRTYRLEULEU(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB533 - 55125 - 43
221SERSERASPASP(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB553 - 55745 - 49
231PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
241PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
251PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
261PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
271PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
281PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
291PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
311TYRTYRLEULEU(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC533 - 55125 - 43
321SERSERASPASP(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC553 - 55745 - 49
331LYSLYSLYSLYS(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC55850
341HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
351HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
361HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
371HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
381HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
411TYRTYRLEULEU(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD533 - 55125 - 43
421SERSERASPASP(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD553 - 55745 - 49
431HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
441HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
451HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
461HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
471HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
481HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
511TYRTYRLEULEU(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE533 - 55125 - 43
521SERSERARGARG(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE553 - 57145 - 63
531TYRTYRGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE573 - 57765 - 69
541LYSLYSGLUGLU(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE588 - 59080 - 82
551ALAALAILEILE(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE595 - 59387 - 85
561PHEPHESERSER(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE598 - 69690 - 188
571HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
581ASNASNASNASN(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE60597
591HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5101HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5111HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5121HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5131HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5141HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
611TYRTYRLEULEU(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF533 - 55125 - 43
621SERSERARGARG(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF553 - 57145 - 63
631TYRTYRGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF573 - 57765 - 69
641ASPASPARGARG(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF579 - 58671 - 78
651ALAALAILEILE(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF595 - 59387 - 85
661PHEPHESERSER(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF598 - 60690 - 98
671HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
681ASNASNASNASN(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF60597
691HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6101HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6111HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6121HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6131HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
112ACEACEACEACE(chain L and (resseq -6 or resseq -4 or (resid...LL-61
122ILEILEILEILE(chain L and (resseq -6 or resseq -4 or (resid...LL-43
132ARGARGARGARG(chain L and (resseq -6 or resseq -4 or (resid...LL-34
142ACEACENH2NH2(chain L and (resseq -6 or resseq -4 or (resid...LL-6 - 71 - 14
212ACEACEACEACE(chain H and (resseq -6 or resseq -4 or (resid...HH-61
222ILEILEILEILE(chain H and (resseq -6 or resseq -4 or (resid...HH-43
232ARGARGARGARG(chain H and (resseq -6 or resseq -4 or (resid...HH-34
242ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
252ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
262ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
312ACEACEACEACE(chain I and (resseq -6 or resseq -4 or (resid...II-61
322ILEILEILEILE(chain I and (resseq -6 or resseq -4 or (resid...II-43
332ARGARGARGARG(chain I and (resseq -6 or resseq -4 or (resid...II-34
342ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
352ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
362ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
412ACEACEACEACE(chain J and (resseq -6 or resseq -4 or (resid...JJ-61
422ILEILEILEILE(chain J and (resseq -6 or resseq -4 or (resid...JJ-43
432ARGARGARGARG(chain J and (resseq -6 or resseq -4 or (resid...JJ-34
442ACEACENH2NH2(chain J and (resseq -6 or resseq -4 or (resid...JJ-6 - 71 - 14
512ACEACEACEACE(chain K and (resseq -6 or resseq -4 or (resid...KK-61
522ILEILEILEILE(chain K and (resseq -6 or resseq -4 or (resid...KK-43
532ARGARGARGARG(chain K and (resseq -6 or resseq -4 or (resid...KK-34
542ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14
552ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14
562ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Disks large homolog 4


分子量: 23611.574 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Dlg4, Dlgh4 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P31016
#2: タンパク質・ペプチド
ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


分子量: 1603.869 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 380 / 由来タイプ: 天然 / 式: H2O
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: 2.17 Å3/Da / 溶媒含有率: 43.26 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 35 % w/v PEP 629, 100 mM HEPES (pH7.5)

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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: SSRF / ビームライン: BL19U1 / 波長: 0.97799 Å
検出器タイプ: DECTRIS PILATUS 300K / 検出器: PIXEL / 日付: 2016年1月17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: 0.97799 Å / 相対比: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.07
反射解像度: 2.595→50 Å / Num. obs: 37969 / % possible obs: 97.2 % / 冗長度: 3.8 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.087 / Rrim(I) all: 0.171 / Χ2: 1.195 / Net I/σ(I): 5
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.70.69418930.6320.4170.8111.0997.1
2.64-2.693.70.60419370.710.3630.7061.13197
2.69-2.743.60.57618680.7390.3450.6721.02397.2
2.74-2.83.70.50519090.7670.3020.5891.10197
2.8-2.863.60.46218990.7670.2780.541.0996.9
2.86-2.933.70.4218410.8390.2520.491.13196.7
2.93-33.70.31819500.9060.1910.3721.20996.8
3-3.083.70.28818540.9110.1720.3361.12996.6
3.08-3.173.70.25419270.9260.1520.2961.24696.7
3.17-3.283.70.21718350.9430.1290.2531.1996
3.28-3.393.70.17919070.9550.1070.2081.23396.4
3.39-3.533.70.15618360.9690.0930.1811.22695.7
3.53-3.693.70.1419010.9710.0840.1631.29395.1
3.69-3.883.70.1117990.980.0660.1281.30392.7
3.88-4.133.90.09418990.9890.0550.1091.25899.2
4.13-4.453.90.08219410.990.0480.0961.29399.2
4.45-4.893.90.07819390.9890.0460.091.17899.3
4.89-5.640.08519730.990.0490.0981.20299.4
5.6-7.0540.08719180.9920.0510.1011.2199.6
7.05-503.90.05519430.9950.0320.0641.32998.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10_2155精密化
PDB_EXTRACT3.27データ抽出
HKL-3000データ削減
HKL-3000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3UAT

3uat


解像度: 2.595→33.523 Å / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 30.32 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2624 1987 5.23 %
Rwork0.2142 36038 -
obs0.2167 37969 96.65 %
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: 145 Å2 / Biso mean: 48.8892 Å2 / Biso min: 7 Å2
精密化ステップサイクル: final / 解像度: 2.595→33.523 Å
タンパク質核酸リガンド溶媒全体
原子数9422 0 0 380 9802
Biso mean---37.22 -
残基数----1185
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0089605
X-RAY DIFFRACTIONf_angle_d1.22512958
X-RAY DIFFRACTIONf_chiral_restr0.0641412
X-RAY DIFFRACTIONf_plane_restr0.011718
X-RAY DIFFRACTIONf_dihedral_angle_d28.1643600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4000X-RAY DIFFRACTION16.388TORSIONAL
12B4000X-RAY DIFFRACTION16.388TORSIONAL
13C4000X-RAY DIFFRACTION16.388TORSIONAL
14D4000X-RAY DIFFRACTION16.388TORSIONAL
15E4000X-RAY DIFFRACTION16.388TORSIONAL
16F4000X-RAY DIFFRACTION16.388TORSIONAL
21L173X-RAY DIFFRACTION16.388TORSIONAL
22H173X-RAY DIFFRACTION16.388TORSIONAL
23I173X-RAY DIFFRACTION16.388TORSIONAL
24J173X-RAY DIFFRACTION16.388TORSIONAL
25K173X-RAY DIFFRACTION16.388TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5988-2.66380.35021450.2784249689
2.6638-2.73570.3461670.2775254591
2.7357-2.81620.28961310.2562258392
2.8162-2.90710.3361340.2628255292
2.9071-3.01090.25331230.2484260192
3.0109-3.13140.30741360.2397254792
3.1314-3.27380.29171280.2261254792
3.2738-3.44620.25361230.206260592
3.4462-3.66190.25131320.2006252791
3.6619-3.94420.26571150.1904250490
3.9442-4.34040.22511370.1795264394
4.3404-4.96670.22721360.1764262194
4.9667-6.25090.22741580.2199263094
6.2509-33.5230.241420.2057263795
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)
13.7458-1.26171.30813.3918-0.35179.0675-0.0048-0.1511-1.06470.57460.35290.5730.0769-0.455-0.31650.19380.00160.03670.28310.01430.491618.602719.4869-10.9583
23.37170.9566-2.17212.11390.84955.59330.1482-0.37290.01780.1539-0.027-0.2725-0.44980.5565-0.1620.2882-0.0407-0.05630.3169-0.02040.257821.277832.93870.6848
35.6194-1.74371.92566.0398-2.36684.9514-0.0205-0.0206-0.1607-0.31330.06620.1157-0.3860.3035-0.04520.2989-0.06090.07570.1641-0.0410.200920.053524.7211-24.2238
40.9647-0.22961.08150.92370.370.93970.0346-0.0446-0.1358-0.0285-0.0316-0.0019-0.2345-0.02740.00240.4142-0.0480.01390.17610.0330.34937.443536.4721-53.3749
53.8299-0.6398-1.37750.23870.39683.76290.1691-0.3364-0.45530.1108-0.203-0.35160.53260.17880.04910.3965-0.0352-0.05740.18550.09040.328820.371428.1284-43.8018
68.3015-0.96051.49040.1574-0.39930.36830.3037-0.26470.0928-0.2682-0.18270.0330.2747-0.1013-0.06150.4412-0.03770.01760.2140.07070.239210.194731.831-50.5687
74.35381.8639-2.87453.5252-2.63684.2152-0.03570.0901-0.02590.19350.16730.14340.30960.2646-0.19160.3324-0.0257-0.02230.1784-0.09290.26588.59527.0242-64.3904
85.5531-0.6367-1.28711.1992-0.73484.10830.09110.38020.0458-0.2064-0.1033-0.16770.14630.39920.01660.5088-0.04610.02440.2604-0.02340.25412.042634.8827-73.5273
92.57780.12991.40060.2297-0.91135.09610.1840.1095-0.07120.0309-0.1388-0.18090.21560.59570.00510.33080.019-0.02450.17550.01740.427-0.087413.8834-48.4683
107.15086.0289-5.74348.8973-5.19995.3486-0.21510.70020.1929-0.54510.37720.57780.1467-0.311-0.12290.43410.0111-0.07560.2791-0.02530.1663-13.65322.6704-66.8113
112.33530.34880.17272.0214-1.17543.0337-0.0024-0.3414-0.1259-0.5123-0.04360.56040.159-0.21330.05250.2727-0.078-0.07680.2421-0.01760.3726-14.198516.6166-58.9397
122.20471.37230.9222.12642.19036.45660.016-0.18970.1393-0.0325-0.20230.1485-0.0565-0.490.17070.2345-0.01310.02150.15810.04020.3471-6.39814.1822-37.9009
132.7249-1.69381.4912.92841.64675.0852-0.3450.34770.4230.18130.0940.14240.0427-0.59420.22670.1768-0.04430.03510.3275-0.00880.4326-6.980525.37670.5817
142.960.72572.86963.510.94424.22110.17060.1887-0.3762-0.06030.0107-0.20260.30430.1526-0.17170.2493-0.01890.07080.2165-0.05050.3074-5.107410.7704-15.4885
154.58672.1871-2.93244.222-1.01548.907-0.1958-0.2758-0.4470.37940.2765-0.23860.6924-0.0041-0.0630.46880.0069-0.09330.20240.01350.2808-3.374915.67559.2191
168.7521-0.3623-2.37646.9239-3.05274.8180.17690.02410.04150.65590.33420.3118-0.3060.1107-0.5060.2868-0.0713-0.03650.2644-0.03950.2721-3.409627.720211.8179
177.47051.3596-2.7612.2943-0.32595.72620.010.0219-0.8443-0.2167-0.018-0.63560.58090.34580.0370.47370.0580.02870.299-0.00030.532-16.69154.16347.8976
182.4435-2.2972-1.88676.9265.79644.8005-0.0463-0.32050.3774-1.6828-0.2025-0.29950.53060.59610.14720.94070.19630.16910.38460.19030.26960.18675.722127.8623
199.07750.27881.93480.1806-0.94245.9090.15170.54910.1090.3512-0.0209-0.0086-0.32620.1355-0.13920.5995-0.10930.02270.2602-0.00540.3771-3.362815.711532.8888
206.48692.7114-4.81431.5203-1.43054.3324-0.00820.73280.518-0.37270.13310.1913-0.1248-0.2203-0.07750.63180.0127-0.03720.28320.05190.2759-11.872113.818135.8973
214.84180.8143-0.57372.8061-1.50138.15750.1421-0.45350.16920.760.0532-0.1445-0.904-0.1226-0.22310.7668-0.05570.04210.33860.08550.3775-15.607614.029550.1282
224.97892.4887-3.48443.3151-2.8332.86720.2439-1.298-0.2670.7004-0.7764-0.5673-0.84261.16540.4881.3337-0.043-0.15460.90220.00870.5049-8.130210.055863.3297
231.9987-3.8141-2.77418.8976.30294.6030.1511-0.4793-0.5439-0.65430.1109-0.14270.8692-0.4756-0.27870.59370.01950.04890.38970.16870.4491-22.78634.303757.8166
241.60281.1089-2.63243.8587-4.27977.9282-0.313-0.1345-0.1629-0.1615-0.0907-0.11150.54620.21780.40040.54540.03790.0630.25230.01940.392524.220726.319142.46
258.2027-1.95680.53595.66111.68354.68680.3956-0.5881-0.17550.3004-0.63580.54360.3769-0.13570.23470.6339-0.02370.12690.28360.03010.30911.504623.785954.8931
265.80276.2744-3.26228.8083-4.72015.46510.0324-0.4510.103-0.11320.0344-0.0074-0.3871-0.2369-0.09050.27840.10070.04080.3403-0.04960.303413.067627.484147.9415
274.24971.8170.90181.12221.68037.99730.0317-0.32550.22210.067-0.24120.6146-0.4402-0.46460.19060.64510.06650.06080.2460.05210.52216.629334.290237.0028
283.9061-3.5185-1.63137.71031.39722.06820.29110.9317-0.9937-1.002-0.98520.76340.7102-1.35990.63071.304-0.1049-0.10611.0218-0.39520.764116.570723.219820.7014
297.3389-4.7705-4.10313.96912.62822.6070.06080.3058-0.1496-1.2454-0.1939-0.4545-0.32120.47310.18951.0807-0.01050.15620.42760.01530.370127.270334.499725.5335
303.64533.83894.83824.06875.12316.4071-0.1328-0.5849-0.4589-0.1876-1.15140.9227-0.50030.27360.99580.4301-0.03910.00840.39520.08630.43910.383331.2313-4.69
311.9601-0.1862-0.69412.6242-4.02846.74920.29870.23570.0359-2.1360.1407-0.54820.1666-0.8024-0.40760.583-0.01510.13560.26110.01690.391813.546338.0188-6.6402
322.01151.3855-1.70762.1012-0.49851.8021-0.58840.82121.2287-0.98180.24870.3386-0.1467-0.9058-0.05360.9131-0.041-0.18020.55930.33720.586420.30839.5016-51.5567
338.6277-1.86624.68111.4361.60589.36120.30241.10330.8286-0.8513-0.0740.324-0.340.8462-0.11290.4514-0.02230.06890.12360.02880.42524.736433.4973-54.5165
346.6116-3.77550.19965.27231.95341.3549-0.508-0.3269-0.73930.4241.7886-0.0076-0.2361-0.6061-0.54660.7732-0.06520.12330.30.19270.5475-6.687126.7007-54.9061
359.84844.4001-3.74274.2161-4.38766.91960.1784-0.8353-0.58110.6142-0.10730.0452-0.78390.8293-0.09140.3933-0.18040.09410.41850.0350.275-14.194527.3589-52.6848
365.92964.4193.66278.35176.55158.107-0.4996-0.54811.8123-0.649-0.95130.5577-2.4649-0.1431.35230.70450.0032-0.13980.4118-0.05440.8392-13.868914.5038-6.3282
375.20016.15491.65167.29982.04322.0477-0.3808-0.938-0.35522.1512-0.1779-0.07280.4564-0.34810.03711.0250.05760.1729-0.7669-0.39880.3468-10.79567.0318-5.0332
381.25480.98430.92584.834-3.0414.0681-0.25430.0059-0.62681.7807-0.03521.5243-0.3191-0.06850.18831.12070.27820.14030.54250.10131.0108-2.9893.880340.9497
398.2655-5.5429-3.30043.77882.84332.01140.9707-0.94390.51240.7550.677-0.4311-0.6105-0.3921-1.25860.9473-0.12240.0280.38710.02450.43451.313910.119643.246
400.7879-0.53511.25110.323-0.83962.0515-0.43420.55110.4389-0.1767-0.53660.4258-0.98132.1005-0.21540.8241-0.13220.52861.0814-0.15220.875220.330418.11243.45
414.58124.49832.83244.45212.26437.3004-0.47421.4986-0.1263-0.57090.2737-0.08070.93080.75540.28190.36260.02960.02510.4079-0.06910.612.902416.955241.4892
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 532 through 564 )A532 - 564
2X-RAY DIFFRACTION2chain 'A' and (resid 565 through 640 )A565 - 640
3X-RAY DIFFRACTION3chain 'A' and (resid 641 through 713 )A641 - 713
4X-RAY DIFFRACTION4chain 'B' and (resid 523 through 573 )B523 - 573
5X-RAY DIFFRACTION5chain 'B' and (resid 574 through 606 )B574 - 606
6X-RAY DIFFRACTION6chain 'B' and (resid 607 through 631 )B607 - 631
7X-RAY DIFFRACTION7chain 'B' and (resid 632 through 654 )B632 - 654
8X-RAY DIFFRACTION8chain 'B' and (resid 655 through 713 )B655 - 713
9X-RAY DIFFRACTION9chain 'C' and (resid 532 through 564 )C532 - 564
10X-RAY DIFFRACTION10chain 'C' and (resid 565 through 594 )C565 - 594
11X-RAY DIFFRACTION11chain 'C' and (resid 595 through 622 )C595 - 622
12X-RAY DIFFRACTION12chain 'C' and (resid 623 through 713 )C623 - 713
13X-RAY DIFFRACTION13chain 'D' and (resid 532 through 563 )D532 - 563
14X-RAY DIFFRACTION14chain 'D' and (resid 564 through 621 )D564 - 621
15X-RAY DIFFRACTION15chain 'D' and (resid 622 through 687 )D622 - 687
16X-RAY DIFFRACTION16chain 'D' and (resid 688 through 713 )D688 - 713
17X-RAY DIFFRACTION17chain 'E' and (resid 532 through 564 )E532 - 564
18X-RAY DIFFRACTION18chain 'E' and (resid 565 through 574 )E565 - 574
19X-RAY DIFFRACTION19chain 'E' and (resid 575 through 606 )E575 - 606
20X-RAY DIFFRACTION20chain 'E' and (resid 607 through 621 )E607 - 621
21X-RAY DIFFRACTION21chain 'E' and (resid 622 through 654 )E622 - 654
22X-RAY DIFFRACTION22chain 'E' and (resid 655 through 696 )E655 - 696
23X-RAY DIFFRACTION23chain 'E' and (resid 697 through 713 )E697 - 713
24X-RAY DIFFRACTION24chain 'F' and (resid 532 through 574 )F532 - 574
25X-RAY DIFFRACTION25chain 'F' and (resid 575 through 594 )F575 - 594
26X-RAY DIFFRACTION26chain 'F' and (resid 595 through 622 )F595 - 622
27X-RAY DIFFRACTION27chain 'F' and (resid 623 through 650 )F623 - 650
28X-RAY DIFFRACTION28chain 'F' and (resid 651 through 687 )F651 - 687
29X-RAY DIFFRACTION29chain 'F' and (resid 688 through 713 )F688 - 713
30X-RAY DIFFRACTION30chain 'G' and (resid -6 through 0 )G-6 - 0
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 7 )G1 - 7
32X-RAY DIFFRACTION32chain 'H' and (resid -6 through 0 )H-6 - 0
33X-RAY DIFFRACTION33chain 'H' and (resid 1 through 7 )H1 - 7
34X-RAY DIFFRACTION34chain 'I' and (resid -6 through 0 )I-6 - 0
35X-RAY DIFFRACTION35chain 'I' and (resid 1 through 7 )I1 - 7
36X-RAY DIFFRACTION36chain 'J' and (resid -6 through 0 )J-6 - 0
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 7 )J1 - 7
38X-RAY DIFFRACTION38chain 'K' and (resid -6 through 0 )K-6 - 0
39X-RAY DIFFRACTION39chain 'K' and (resid 1 through 7 )K1 - 7
40X-RAY DIFFRACTION40chain 'L' and (resid -6 through 0 )L-6 - 0
41X-RAY DIFFRACTION41chain 'L' and (resid 1 through 7 )L1 - 7

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る