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- PDB-8p2l: A CHIMERA construct containing human SARM1 ARM and SAM domains an... -

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基本情報

登録情報
データベース: PDB / ID: 8p2l
タイトルA CHIMERA construct containing human SARM1 ARM and SAM domains and C. elegans TIR domain.
要素NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
キーワードHYDROLASE / SARM1 / TIR-1 / C. elegans / neurodegeneration / cryo-EM / structural biology / NAD+ metabolism / axon Wallerian degeneration
機能・相同性
機能・相同性情報


serotonin biosynthetic process / negative regulation of MyD88-independent toll-like receptor signaling pathway / extrinsic component of synaptic membrane / MyD88-independent TLR4 cascade / NADP+ nucleosidase activity / Toll Like Receptor 3 (TLR3) Cascade / NAD+ nucleosidase activity / antibacterial innate immune response / regulation of synapse pruning / modification of postsynaptic structure ...serotonin biosynthetic process / negative regulation of MyD88-independent toll-like receptor signaling pathway / extrinsic component of synaptic membrane / MyD88-independent TLR4 cascade / NADP+ nucleosidase activity / Toll Like Receptor 3 (TLR3) Cascade / NAD+ nucleosidase activity / antibacterial innate immune response / regulation of synapse pruning / modification of postsynaptic structure / NAD+ catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / protein localization to mitochondrion / cell fate specification / nervous system process / 加水分解酵素; 糖加水分解酵素; N-グリコシル化合物加水分解酵素 / regulation of dendrite morphogenesis / defense response to fungus / response to axon injury / response to glucose / axon cytoplasm / signaling adaptor activity / regulation of neuron apoptotic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / neuromuscular junction / small GTPase binding / intracellular protein localization / cell-cell signaling / nervous system development / cell body / defense response to Gram-negative bacterium / microtubule / cell differentiation / mitochondrial outer membrane / defense response to bacterium / negative regulation of gene expression / innate immune response / axon / positive regulation of gene expression / synapse / dendrite / protein kinase binding / glutamatergic synapse / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / identical protein binding / cytoplasm / cytosol
類似検索 - 分子機能
Sterile alpha and TIR motif-containing protein 1 / TIR domain / SAM domain (Sterile alpha motif) / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...Sterile alpha and TIR motif-containing protein 1 / TIR domain / SAM domain (Sterile alpha motif) / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Armadillo-like helical / Armadillo-type fold
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(+) hydrolase SARM1 / NAD(+) hydrolase tir-1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.68 Å
データ登録者Isupov, M.N. / Opatowsky, Y.
資金援助 イスラエル, 米国, 3件
組織認可番号国
Israel Science Foundation1425/15 イスラエル
Israel Science Foundation909/19 イスラエル
United States - Israel Binational Science Foundation (BSF)2019150 米国
引用ジャーナル: Cell Rep / 年: 2023
タイトル: Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans.
著者: Tami Khazma / Atira Grossman / Julia Guez-Haddad / Chengye Feng / Hadas Dabas / Radhika Sain / Michal Weitman / Ran Zalk / Michail N Isupov / Marc Hammarlund / Michael Hons / Yarden Opatowsky /
要旨: Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed ...Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed in C. elegans (ceSARM/ceTIR-1). We hypothesized that differences in SARM between species might exist and account for the divergence in WD. We first show that expression of the human (h)SARM1, but not ceTIR-1, in C. elegans neurons is sufficient to confer axon degeneration after nerve injury. Next, we determined the cryoelectron microscopy structure of ceTIR-1 and found that, unlike hSARM1, which exists as an auto-inhibited ring octamer, ceTIR-1 forms a readily active 9-mer. Enzymatically, the NADase activity of ceTIR-1 is substantially weaker (10-fold higher Km) than that of hSARM1, and even when fully active, it falls short of consuming all cellular NAD. Our experiments provide insight into the molecular mechanisms and evolution of SARM orthologs and WD across species.
履歴
登録2023年5月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年9月6日Provider: repository / タイプ: Initial release

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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: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
B: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
C: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
D: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
E: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
F: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
G: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
H: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
J: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
I: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
K: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
L: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
M: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
N: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
O: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
P: NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,302,43824
ポリマ－1,297,13016
非ポリマー5,3078
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_5551
Buried area46510 Å2
ΔGint-89 kcal/mol
Surface area211150 Å2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158B
168C
179B
189D
1910B
2010E
2111B
2211F
2312B
2412G
2513B
2613H
2714C
2814D
2915C
3015E
3116C
3216F
3317C
3417G
3518C
3618H
3719D
3819E
3920D
4020F
4121D
4221G
4322D
4422H
4523E
4623F
4724E
4824G
4925E
5025H
5126F
5226G
5327F
5427H
5528G
5628H
5729J
5829I
5930J
6030K
6131J
6231L
6332J
6432M
6533J
6633N
6734J
6834O
6935J
7035P
7136I
7236K
7337I
7437L
7538I
7638M
7739I
7839N
7940I
8040O
8141I
8241P
8342K
8442L
8543K
8643M
8744K
8844N
8945K
9045O
9146K
9246P
9347L
9447M
9548L
9648N
9749L
9849O
9950L
10050P
10151M
10251N
10352M
10452O
10553M
10653P
10754N
10854O
10955N
11055P
11156O
11256P

NCSドメイン領域:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROAA56 - 55158 - 553
211PROPROBB56 - 55158 - 553
322PROPROAA56 - 55158 - 553
422PROPROCC56 - 55158 - 553
533PROPROAA56 - 55158 - 553
633PROPRODD56 - 55158 - 553
744PROPROAA56 - 55158 - 553
844PROPROEE56 - 55158 - 553
955PROPROAA56 - 55158 - 553
1055PROPROFF56 - 55158 - 553
1166PROPROAA56 - 55158 - 553
1266PROPROGG56 - 55158 - 553
1377PROPROAA56 - 55158 - 553
1477PROPROHH56 - 55158 - 553
1588PROPROBB56 - 55158 - 553
1688PROPROCC56 - 55158 - 553
1799PROPROBB56 - 55158 - 553
1899PROPRODD56 - 55158 - 553
191010PROPROBB56 - 55158 - 553
201010PROPROEE56 - 55158 - 553
211111PROPROBB56 - 55158 - 553
221111PROPROFF56 - 55158 - 553
231212PROPROBB56 - 55158 - 553
241212PROPROGG56 - 55158 - 553
251313PROPROBB56 - 55158 - 553
261313PROPROHH56 - 55158 - 553
271414PROPROCC56 - 55158 - 553
281414PROPRODD56 - 55158 - 553
291515PROPROCC56 - 55158 - 553
301515PROPROEE56 - 55158 - 553
311616PROPROCC56 - 55158 - 553
321616PROPROFF56 - 55158 - 553
331717PROPROCC56 - 55158 - 553
341717PROPROGG56 - 55158 - 553
351818PROPROCC56 - 55158 - 553
361818PROPROHH56 - 55158 - 553
371919PROPRODD56 - 55158 - 553
381919PROPROEE56 - 55158 - 553
392020PROPRODD56 - 55158 - 553
402020PROPROFF56 - 55158 - 553
412121PROPRODD56 - 55158 - 553
422121PROPROGG56 - 55158 - 553
432222PROPRODD56 - 55158 - 553
442222PROPROHH56 - 55158 - 553
452323PROPROEE56 - 55158 - 553
462323PROPROFF56 - 55158 - 553
472424PROPROEE56 - 55158 - 553
482424PROPROGG56 - 55158 - 553
492525PROPROEE56 - 55158 - 553
502525PROPROHH56 - 55158 - 553
512626PROPROFF56 - 55158 - 553
522626PROPROGG56 - 55158 - 553
532727PROPROFF56 - 55158 - 553
542727PROPROHH56 - 55158 - 553
552828PROPROGG56 - 55158 - 553
562828PROPROHH56 - 55158 - 553
572929ASNASNJI705 - 852561 - 708
582929ASNASNIJ705 - 852561 - 708
593030ASNASNJI705 - 852561 - 708
603030ASNASNKK705 - 852561 - 708
613131ASNASNJI705 - 852561 - 708
623131ASNASNLL705 - 852561 - 708
633232ASNASNJI705 - 852561 - 708
643232ASNASNMM705 - 852561 - 708
653333ASNASNJI705 - 852561 - 708
663333ASNASNNN705 - 852561 - 708
673434ASNASNJI705 - 852561 - 708
683434ASNASNOO705 - 852561 - 708
693535ASNASNJI705 - 852561 - 708
703535ASNASNPP705 - 852561 - 708
713636ASNASNIJ705 - 852561 - 708
723636ASNASNKK705 - 852561 - 708
733737ASNASNIJ705 - 852561 - 708
743737ASNASNLL705 - 852561 - 708
753838ASNASNIJ705 - 852561 - 708
763838ASNASNMM705 - 852561 - 708
773939ASNASNIJ705 - 852561 - 708
783939ASNASNNN705 - 852561 - 708
794040ASNASNIJ705 - 852561 - 708
804040ASNASNOO705 - 852561 - 708
814141ASNASNIJ705 - 852561 - 708
824141ASNASNPP705 - 852561 - 708
834242ASNASNKK705 - 852561 - 708
844242ASNASNLL705 - 852561 - 708
854343ASNASNKK705 - 852561 - 708
864343ASNASNMM705 - 852561 - 708
874444ASNASNKK705 - 852561 - 708
884444ASNASNNN705 - 852561 - 708
894545ASNASNKK705 - 852561 - 708
904545ASNASNOO705 - 852561 - 708
914646ASNASNKK705 - 852561 - 708
924646ASNASNPP705 - 852561 - 708
934747ASNASNLL705 - 852561 - 708
944747ASNASNMM705 - 852561 - 708
954848ASNASNLL705 - 852561 - 708
964848ASNASNNN705 - 852561 - 708
974949ASNASNLL705 - 852561 - 708
984949ASNASNOO705 - 852561 - 708
995050ASNASNLL705 - 852561 - 708
1005050ASNASNPP705 - 852561 - 708
1015151ASNASNMM705 - 852561 - 708
1025151ASNASNNN705 - 852561 - 708
1035252ASNASNMM705 - 852561 - 708
1045252ASNASNOO705 - 852561 - 708
1055353ASNASNMM705 - 852561 - 708
1065353ASNASNPP705 - 852561 - 708
1075454ASNASNNN705 - 852561 - 708
1085454ASNASNOO705 - 852561 - 708
1095555ASNASNNN705 - 852561 - 708
1105555ASNASNPP705 - 852561 - 708
1115656ASNASNOO705 - 852561 - 708
1125656ASNASNPP705 - 852561 - 708

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66
34Local NCS retraints between domains: 67 68
35Local NCS retraints between domains: 69 70
36Local NCS retraints between domains: 71 72
37Local NCS retraints between domains: 73 74
38Local NCS retraints between domains: 75 76
39Local NCS retraints between domains: 77 78
40Local NCS retraints between domains: 79 80
41Local NCS retraints between domains: 81 82
42Local NCS retraints between domains: 83 84
43Local NCS retraints between domains: 85 86
44Local NCS retraints between domains: 87 88
45Local NCS retraints between domains: 89 90
46Local NCS retraints between domains: 91 92
47Local NCS retraints between domains: 93 94
48Local NCS retraints between domains: 95 96
49Local NCS retraints between domains: 97 98
50Local NCS retraints between domains: 99 100
51Local NCS retraints between domains: 101 102
52Local NCS retraints between domains: 103 104
53Local NCS retraints between domains: 105 106
54Local NCS retraints between domains: 107 108
55Local NCS retraints between domains: 109 110
56Local NCS retraints between domains: 111 112

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要素

#1: タンパク質
NAD(+) hydrolase SARM1,NAD(+) hydrolase tir-1 / NADase SARM1 / hSARM1 / NADP(+) hydrolase SARM1 / Sterile alpha and Armadillo repeat protein / ...NADase SARM1 / hSARM1 / NADP(+) hydrolase SARM1 / Sterile alpha and Armadillo repeat protein / Sterile alpha and TIR motif-containing protein 1 / Sterile alpha motif domain-containing protein 2 / MyD88-5 / SAM domain-containing protein 2 / Tir-1 homolog / HsTIR / NADase tir-1 / Neuronal symmetry protein 2 / SARM1 homolog / Sterile alpha and TIR motif-containing protein tir-1


分子量: 81070.656 Da / 分子数: 16 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
遺伝子: SARM1, KIAA0524, SAMD2, SARM, tir-1, nsy-2, F13B10.1
細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q6SZW1, UniProt: Q86DA5, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 加水分解酵素; 糖加水分解酵素; N-グリコシル化合物加水分解酵素
#2: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: NAD*YM
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: A CHIMERA construct containing human SARM1 ARM and SAM domains and C. elegans TIR domain.
タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Homo sapiens (ヒト) / 細胞: HEK293F
緩衝液pH: 8.5
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドのタイプ: Quantifoil R1.2/1.3
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 2800 nm / 最小 デフォーカス（公称値）: 800 nm
撮影電子線照射量: 41.4 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)
電子光学装置エネルギーフィルター名称: GIF Quantum LS

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0267 / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
2EPU画像取得
7Coot9.6モデルフィッティング
9REFMAC5モデル精密化
10UCSF ChimeraXモデル精密化
11ISOLDEモデル精密化
12cryoSPARC初期オイラー角割当
13cryoSPARC最終オイラー角割当
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 298564
3次元再構成解像度: 2.68 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 136346 / 対称性のタイプ: POINT
原子モデル構築プロトコル: FLEXIBLE FIT / 空間: RECIPROCAL
原子モデル構築
ID 3D fitting-IDAccession codeChain residue range詳細Source nameタイプ
117ANW26-560The initial octameric model containing human ARM and SAM domainsOtherexperimental model
21561-708AlphaFoldin silico model
精密化解像度: 2.68→252 Å / Cor.coef. Fo:Fc: 0.82 / WRfactor Rwork: 0.456 / Average fsc overall: 0.4533 / Average fsc work: 0.4533 / ESU R: 0.196 / 詳細: Hydrogens have not been used
Rfactor反射数%反射
Rwork0.456 1740894 -
all0.456 --
Rfree--0 %
obs--100 %
溶媒の処理溶媒モデル: BABINET MODEL
原子変位パラメータBiso mean: 39.983 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.005 Å20 Å2
2---1.025 Å20.004 Å2
3---2.045 Å2
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01241472
ELECTRON MICROSCOPYr_angle_refined_deg1.6491.63256144
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.47155136
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.38521.12328
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.132157360
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.98115408
ELECTRON MICROSCOPYr_chiral_restr0.1280.25312
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0231072
ELECTRON MICROSCOPYr_nbd_refined0.2050.236706
ELECTRON MICROSCOPYr_nbtor_refined0.2930.257962
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.070.22314
ELECTRON MICROSCOPYr_mcbond_it0420592
ELECTRON MICROSCOPYr_mcangle_it0625712
ELECTRON MICROSCOPYr_scbond_it0420880
ELECTRON MICROSCOPYr_scangle_it0630432
ELECTRON MICROSCOPYr_lrange_it075.943171628
ELECTRON MICROSCOPYr_ncsr_local_group_10.0120.0532888
ELECTRON MICROSCOPYr_ncsr_local_group_20.0030.0532920
ELECTRON MICROSCOPYr_ncsr_local_group_30.0130.0532882
ELECTRON MICROSCOPYr_ncsr_local_group_40.0010.0532920
ELECTRON MICROSCOPYr_ncsr_local_group_50.0120.0532874
ELECTRON MICROSCOPYr_ncsr_local_group_60.0030.0532916
ELECTRON MICROSCOPYr_ncsr_local_group_70.0130.0532864
ELECTRON MICROSCOPYr_ncsr_local_group_80.0120.0532882
ELECTRON MICROSCOPYr_ncsr_local_group_90.0050.0532922
ELECTRON MICROSCOPYr_ncsr_local_group_100.0120.0532886
ELECTRON MICROSCOPYr_ncsr_local_group_110.0040.0532926
ELECTRON MICROSCOPYr_ncsr_local_group_120.0120.0532876
ELECTRON MICROSCOPYr_ncsr_local_group_130.0050.0532904
ELECTRON MICROSCOPYr_ncsr_local_group_140.0130.0532876
ELECTRON MICROSCOPYr_ncsr_local_group_150.0030.0532914
ELECTRON MICROSCOPYr_ncsr_local_group_160.0130.0532882
ELECTRON MICROSCOPYr_ncsr_local_group_170.0040.0532922
ELECTRON MICROSCOPYr_ncsr_local_group_180.0130.0532860
ELECTRON MICROSCOPYr_ncsr_local_group_190.0120.0532882
ELECTRON MICROSCOPYr_ncsr_local_group_200.0060.0532914
ELECTRON MICROSCOPYr_ncsr_local_group_210.0130.0532878
ELECTRON MICROSCOPYr_ncsr_local_group_220.0090.0532912
ELECTRON MICROSCOPYr_ncsr_local_group_230.0120.0532872
ELECTRON MICROSCOPYr_ncsr_local_group_240.0030.0532906
ELECTRON MICROSCOPYr_ncsr_local_group_250.0130.0532858
ELECTRON MICROSCOPYr_ncsr_local_group_260.0130.0532876
ELECTRON MICROSCOPYr_ncsr_local_group_270.0060.0532904
ELECTRON MICROSCOPYr_ncsr_local_group_280.0130.0532868
ELECTRON MICROSCOPYr_ncsr_local_group_290.0020.059878
ELECTRON MICROSCOPYr_ncsr_local_group_300.0180.059856
ELECTRON MICROSCOPYr_ncsr_local_group_310.0030.059870
ELECTRON MICROSCOPYr_ncsr_local_group_320.0030.059898
ELECTRON MICROSCOPYr_ncsr_local_group_330.0030.059876
ELECTRON MICROSCOPYr_ncsr_local_group_340.0170.059858
ELECTRON MICROSCOPYr_ncsr_local_group_350.0030.059876
ELECTRON MICROSCOPYr_ncsr_local_group_360.0170.059838
ELECTRON MICROSCOPYr_ncsr_local_group_370.0030.059896
ELECTRON MICROSCOPYr_ncsr_local_group_380.0030.059882
ELECTRON MICROSCOPYr_ncsr_local_group_390.0020.059898
ELECTRON MICROSCOPYr_ncsr_local_group_400.0170.059840
ELECTRON MICROSCOPYr_ncsr_local_group_410.0030.059906
ELECTRON MICROSCOPYr_ncsr_local_group_420.0170.059838
ELECTRON MICROSCOPYr_ncsr_local_group_430.0180.059868
ELECTRON MICROSCOPYr_ncsr_local_group_440.0170.059838
ELECTRON MICROSCOPYr_ncsr_local_group_450.0050.059912
ELECTRON MICROSCOPYr_ncsr_local_group_460.0170.059840
ELECTRON MICROSCOPYr_ncsr_local_group_470.0010.059878
ELECTRON MICROSCOPYr_ncsr_local_group_480.0030.059898
ELECTRON MICROSCOPYr_ncsr_local_group_490.0180.059838
ELECTRON MICROSCOPYr_ncsr_local_group_500.0030.059902
ELECTRON MICROSCOPYr_ncsr_local_group_510.0030.059876
ELECTRON MICROSCOPYr_ncsr_local_group_520.0170.059872
ELECTRON MICROSCOPYr_ncsr_local_group_530.0030.059882
ELECTRON MICROSCOPYr_ncsr_local_group_540.0170.059840
ELECTRON MICROSCOPYr_ncsr_local_group_550.0020.059906
ELECTRON MICROSCOPYr_ncsr_local_group_560.0170.059842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.011770.05013
12BELECTRON MICROSCOPYLocal ncs0.011770.05013
23AELECTRON MICROSCOPYLocal ncs0.002930.05013
24CELECTRON MICROSCOPYLocal ncs0.002930.05013
35AELECTRON MICROSCOPYLocal ncs0.012580.05013
36DELECTRON MICROSCOPYLocal ncs0.012580.05013
47AELECTRON MICROSCOPYLocal ncs0.001260.05013
48EELECTRON MICROSCOPYLocal ncs0.001260.05013
59AELECTRON MICROSCOPYLocal ncs0.012210.05013
510FELECTRON MICROSCOPYLocal ncs0.012210.05013
611AELECTRON MICROSCOPYLocal ncs0.002850.05013
612GELECTRON MICROSCOPYLocal ncs0.002850.05013
713AELECTRON MICROSCOPYLocal ncs0.012780.05013
714HELECTRON MICROSCOPYLocal ncs0.012780.05013
815BELECTRON MICROSCOPYLocal ncs0.012150.05013
816CELECTRON MICROSCOPYLocal ncs0.012150.05013
917BELECTRON MICROSCOPYLocal ncs0.005250.05013
918DELECTRON MICROSCOPYLocal ncs0.005250.05013
1019BELECTRON MICROSCOPYLocal ncs0.01190.05013
1020EELECTRON MICROSCOPYLocal ncs0.01190.05013
1121BELECTRON MICROSCOPYLocal ncs0.004090.05013
1122FELECTRON MICROSCOPYLocal ncs0.004090.05013
1223BELECTRON MICROSCOPYLocal ncs0.012050.05013
1224GELECTRON MICROSCOPYLocal ncs0.012050.05013
1325BELECTRON MICROSCOPYLocal ncs0.005090.05013
1326HELECTRON MICROSCOPYLocal ncs0.005090.05013
1427CELECTRON MICROSCOPYLocal ncs0.012540.05013
1428DELECTRON MICROSCOPYLocal ncs0.012540.05013
1529CELECTRON MICROSCOPYLocal ncs0.003240.05013
1530EELECTRON MICROSCOPYLocal ncs0.003240.05013
1631CELECTRON MICROSCOPYLocal ncs0.012540.05013
1632FELECTRON MICROSCOPYLocal ncs0.012540.05013
1733CELECTRON MICROSCOPYLocal ncs0.00390.05013
1734GELECTRON MICROSCOPYLocal ncs0.00390.05013
1835CELECTRON MICROSCOPYLocal ncs0.013010.05013
1836HELECTRON MICROSCOPYLocal ncs0.013010.05013
1937DELECTRON MICROSCOPYLocal ncs0.012430.05013
1938EELECTRON MICROSCOPYLocal ncs0.012430.05013
2039DELECTRON MICROSCOPYLocal ncs0.006310.05013
2040FELECTRON MICROSCOPYLocal ncs0.006310.05013
2141DELECTRON MICROSCOPYLocal ncs0.013070.05013
2142GELECTRON MICROSCOPYLocal ncs0.013070.05013
2243DELECTRON MICROSCOPYLocal ncs0.008580.05013
2244HELECTRON MICROSCOPYLocal ncs0.008580.05013
2345EELECTRON MICROSCOPYLocal ncs0.012270.05013
2346FELECTRON MICROSCOPYLocal ncs0.012270.05013
2447EELECTRON MICROSCOPYLocal ncs0.003080.05013
2448GELECTRON MICROSCOPYLocal ncs0.003080.05013
2549EELECTRON MICROSCOPYLocal ncs0.0130.05013
2550HELECTRON MICROSCOPYLocal ncs0.0130.05013
2651FELECTRON MICROSCOPYLocal ncs0.01250.05013
2652GELECTRON MICROSCOPYLocal ncs0.01250.05013
2753FELECTRON MICROSCOPYLocal ncs0.006280.05013
2754HELECTRON MICROSCOPYLocal ncs0.006280.05013
2855GELECTRON MICROSCOPYLocal ncs0.012660.05013
2856HELECTRON MICROSCOPYLocal ncs0.012660.05013
2957JELECTRON MICROSCOPYLocal ncs0.002350.05011
2958IELECTRON MICROSCOPYLocal ncs0.002350.05011
3059JELECTRON MICROSCOPYLocal ncs0.017890.05011
3060KELECTRON MICROSCOPYLocal ncs0.017890.05011
3161JELECTRON MICROSCOPYLocal ncs0.003450.05011
3162LELECTRON MICROSCOPYLocal ncs0.003450.05011
3263JELECTRON MICROSCOPYLocal ncs0.003140.05011
3264MELECTRON MICROSCOPYLocal ncs0.003140.05011
3365JELECTRON MICROSCOPYLocal ncs0.003110.05011
3366NELECTRON MICROSCOPYLocal ncs0.003110.05011
3467JELECTRON MICROSCOPYLocal ncs0.017460.05011
3468OELECTRON MICROSCOPYLocal ncs0.017460.05011
3569JELECTRON MICROSCOPYLocal ncs0.003250.05011
3570PELECTRON MICROSCOPYLocal ncs0.003250.05011
3671IELECTRON MICROSCOPYLocal ncs0.017230.05011
3672KELECTRON MICROSCOPYLocal ncs0.017230.05011
3773IELECTRON MICROSCOPYLocal ncs0.002960.05011
3774LELECTRON MICROSCOPYLocal ncs0.002960.05011
3875IELECTRON MICROSCOPYLocal ncs0.002740.05011
3876MELECTRON MICROSCOPYLocal ncs0.002740.05011
3977IELECTRON MICROSCOPYLocal ncs0.002490.05011
3978NELECTRON MICROSCOPYLocal ncs0.002490.05011
4079IELECTRON MICROSCOPYLocal ncs0.017380.05011
4080OELECTRON MICROSCOPYLocal ncs0.017380.05011
4181IELECTRON MICROSCOPYLocal ncs0.00280.05011
4182PELECTRON MICROSCOPYLocal ncs0.00280.05011
4283KELECTRON MICROSCOPYLocal ncs0.017450.05011
4284LELECTRON MICROSCOPYLocal ncs0.017450.05011
4385KELECTRON MICROSCOPYLocal ncs0.0180.05011
4386MELECTRON MICROSCOPYLocal ncs0.0180.05011
4487KELECTRON MICROSCOPYLocal ncs0.017340.05011
4488NELECTRON MICROSCOPYLocal ncs0.017340.05011
4589KELECTRON MICROSCOPYLocal ncs0.005240.05011
4590OELECTRON MICROSCOPYLocal ncs0.005240.05011
4691KELECTRON MICROSCOPYLocal ncs0.017380.05011
4692PELECTRON MICROSCOPYLocal ncs0.017380.05011
4793LELECTRON MICROSCOPYLocal ncs0.001370.05011
4794MELECTRON MICROSCOPYLocal ncs0.001370.05011
4895LELECTRON MICROSCOPYLocal ncs0.002880.05011
4896NELECTRON MICROSCOPYLocal ncs0.002880.05011
4997LELECTRON MICROSCOPYLocal ncs0.01750.05011
4998OELECTRON MICROSCOPYLocal ncs0.01750.05011
5099LELECTRON MICROSCOPYLocal ncs0.003150.05011
50100PELECTRON MICROSCOPYLocal ncs0.003150.05011
51101MELECTRON MICROSCOPYLocal ncs0.002840.05011
51102NELECTRON MICROSCOPYLocal ncs0.002840.05011
52103MELECTRON MICROSCOPYLocal ncs0.017430.05011
52104OELECTRON MICROSCOPYLocal ncs0.017430.05011
53105MELECTRON MICROSCOPYLocal ncs0.003160.05011
53106PELECTRON MICROSCOPYLocal ncs0.003160.05011
54107NELECTRON MICROSCOPYLocal ncs0.017390.05011
54108OELECTRON MICROSCOPYLocal ncs0.017390.05011
55109NELECTRON MICROSCOPYLocal ncs0.001560.05011
55110PELECTRON MICROSCOPYLocal ncs0.001560.05011
56111OELECTRON MICROSCOPYLocal ncs0.017440.05011
56112PELECTRON MICROSCOPYLocal ncs0.017440.05011
LS精密化 シェル

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

解像度 (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.68-2.751.1391288131.1391288130.0981.139
2.75-2.8250.9841254520.9841254520.1150.984
2.825-2.9070.6841222090.6841222090.190.684
2.907-2.9960.6351192220.6351192220.2060.635
2.996-3.0950.5991141810.5991141810.2720.599
3.095-3.2030.5511113650.5511113650.3230.551
3.203-3.3240.5151071410.5151071410.4130.515
3.324-3.460.4841035010.4841035010.5240.484
3.46-3.6140.471986710.471986710.5730.471
3.614-3.790.468950210.468950210.6180.468
3.79-3.9950.464898440.464898440.6650.464
3.995-4.2370.462853370.462853370.6820.462
4.237-4.530.451796940.451796940.6980.451
4.53-4.8930.444745120.444745120.6890.444
4.893-5.3590.439687050.439687050.7040.439
5.359-5.9920.429622170.429622170.6780.429
5.992-6.9180.44544080.44544080.6910.44
6.918-8.4710.428462520.428462520.7310.428
8.471-11.9730.375357200.375357200.8320.375
11.973-2520.406195540.406195540.8940.406

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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