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- PDB-4kzz: Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA... -

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基本情報

登録情報
データベース: PDB / ID: 4kzz
タイトルRabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A
要素
  • (40S Ribosomal Protein ...) x 33
  • 18S Ribosomal RNA
  • human initiation factor eIF1A
  • initiator Met-RNA-i
  • mRNA
キーワードRIBOSOME / translation initiation
機能・相同性
機能・相同性情報


multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / phagocytic cup / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / laminin binding / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / small-subunit processome / translational initiation / spindle / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / synapse / dendrite / centrosome / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S6e
類似検索 - ドメイン・相同性
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS10 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 1A, X-chromosomal
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Oryctolagus cuniculus (ウサギ)
Synthetic (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 7.0305 Å
データ登録者Lomakin, I.B. / Steitz, T.A.
引用ジャーナル: Nature / 年: 2013
タイトル: The initiation of mammalian protein synthesis and mRNA scanning mechanism.
著者: Lomakin, I.B. / Steitz, T.A.
履歴
登録2013年5月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年7月24日Provider: repository / タイプ: Initial release
改定 1.12013年8月7日Group: Database references
改定 1.22013年9月4日Group: Database references
改定 1.32023年9月20日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年11月20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: 40S Ribosomal Protein SA
B: 40S Ribosomal Protein S3A
C: 40S Ribosomal Protein S2
D: 40S Ribosomal Protein S3
E: 40S Ribosomal Protein S4X
F: 40S Ribosomal Protein S5
G: 40S Ribosomal Protein S6
H: 40S Ribosomal Protein S7
I: 40S Ribosomal Protein S8
J: 40S Ribosomal Protein S9
K: 40S Ribosomal Protein S10
L: 40S Ribosomal Protein S11
M: 40S Ribosomal Protein S12
N: 40S Ribosomal Protein S13
O: 40S Ribosomal Protein S14
P: 40S Ribosomal Protein S15
Q: 40S Ribosomal Protein S16
R: 40S Ribosomal Protein S17
S: 40S Ribosomal Protein S18
T: 40S Ribosomal Protein S19
U: 40S Ribosomal Protein S20
V: 40S Ribosomal Protein S21
W: 40S Ribosomal Protein S15A
X: 40S Ribosomal Protein S23
Y: 40S Ribosomal Protein S24
Z: 40S Ribosomal Protein S25
a: 40S Ribosomal Protein S26
b: 40S Ribosomal Protein S27
c: 40S Ribosomal Protein S28
d: 40S Ribosomal Protein S29
e: 40S Ribosomal Protein S30
f: 40S Ribosomal Protein S27A
g: 40S Ribosomal Protein RACK1
i: 18S Ribosomal RNA
j: initiator Met-RNA-i
k: mRNA
n: human initiation factor eIF1A


分子量 (理論値)分子数
合計 (水以外)1,274,24937
ポリマ－1,274,24937
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)297.750, 297.750, 485.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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要素

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40S Ribosomal Protein ... , 33種, 33分子 ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: タンパク質 40S Ribosomal Protein SA


分子量: 32927.988 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TGI6*PLUS
#2: タンパク質 40S Ribosomal Protein S3A


分子量: 29928.967 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TN72
#3: タンパク質 40S Ribosomal Protein S2


分子量: 29575.578 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1U2Z9
#4: タンパク質 40S Ribosomal Protein S3


分子量: 26715.344 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TNM3
#5: タンパク質 40S Ribosomal Protein S4X


分子量: 29658.920 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TK17
#6: タンパク質 40S Ribosomal Protein S5


分子量: 22913.453 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TFM5
#7: タンパク質 40S Ribosomal Protein S6


分子量: 28751.906 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TM55
#8: タンパク質 40S Ribosomal Protein S7


分子量: 22168.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SVB0
#9: タンパク質 40S Ribosomal Protein S8


分子量: 24163.244 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TJW1
#10: タンパク質 40S Ribosomal Protein S9


分子量: 22641.564 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: B7NZS8
#11: タンパク質 40S Ribosomal Protein S10


分子量: 18933.846 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1T168
#12: タンパク質 40S Ribosomal Protein S11


分子量: 18468.826 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TRM4
#13: タンパク質 40S Ribosomal Protein S12


分子量: 14538.987 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SFR8
#14: タンパク質 40S Ribosomal Protein S13


分子量: 17259.389 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SP51
#15: タンパク質 40S Ribosomal Protein S14


分子量: 16302.772 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1U472
#16: タンパク質 40S Ribosomal Protein S15


分子量: 17049.182 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1U0Q2
#17: タンパク質 40S Ribosomal Protein S16


分子量: 16477.377 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SGX4
#18: タンパク質 40S Ribosomal Protein S17


分子量: 15552.119 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TU13
#19: タンパク質 40S Ribosomal Protein S18


分子量: 17759.777 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TPG3
#20: タンパク質 40S Ribosomal Protein S19


分子量: 16235.796 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TN62
#21: タンパク質 40S Ribosomal Protein S20


分子量: 13398.763 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SIZ2
#22: タンパク質 40S Ribosomal Protein S21


分子量: 9043.276 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TM82
#23: タンパク質 40S Ribosomal Protein S15A


分子量: 14865.555 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TG89
#24: タンパク質 40S Ribosomal Protein S23


分子量: 15844.666 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SZ47
#25: タンパク質 40S Ribosomal Protein S24


分子量: 15434.267 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TS40
#26: タンパク質 40S Ribosomal Protein S25


分子量: 13776.224 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TDB3
#27: タンパク質 40S Ribosomal Protein S26


分子量: 12961.455 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TFE8
#28: タンパク質 40S Ribosomal Protein S27


分子量: 9480.186 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TZ76
#29: タンパク質 40S Ribosomal Protein S28


分子量: 7855.052 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TIB4
#30: タンパク質 40S Ribosomal Protein S29


分子量: 6690.821 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1U7M4
#31: タンパク質 40S Ribosomal Protein S30


分子量: 14498.884 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1T8A2
#32: タンパク質 40S Ribosomal Protein S27A


分子量: 18004.041 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SK22
#33: タンパク質 40S Ribosomal Protein RACK1


分子量: 35115.652 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1SJB4

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RNA鎖 , 3種, 3分子 ijk

#34: RNA鎖 18S Ribosomal RNA


分子量: 600900.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: GenBank: 283837872
#35: RNA鎖 initiator Met-RNA-i


分子量: 24231.510 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: GenBank: 174924
#36: RNA鎖 mRNA


分子量: 7635.679 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: mRNA / 由来: (合成) Synthetic (人工物)

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タンパク質 , 1種, 1分子 n

#37: タンパク質 human initiation factor eIF1A


分子量: 16488.449 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: N-terminal His6/TEV / 由来: (組換発現) Homo sapiens (ヒト) / 株: K12 / 遺伝子: EIF1AX / プラスミド: pET28a-heIF1Atev / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21*DE3 / 参照: UniProt: P47813

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詳細

Has protein modificationY
配列の詳細The reference for chain A is XP_002712810.1 at NCBI. For chain X, the first residue should be the ...The reference for chain A is XP_002712810.1 at NCBI. For chain X, the first residue should be the initiating M.

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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: 4.87 Å3/Da / 溶媒含有率: 74.75 %
結晶化温度: 292 K / 手法: 蒸気拡散法 / pH: 8.5
詳細: 0.1M Ammonium acetate, 0.05M Tris-HCl pH 8.5, 2.5% PEG-20K, 4-6% MPD, 5.0mM Mg acetate, 2.0mM TCEP, vapor diffusion, temperature 292K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.97949 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2011年7月9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: 0.97949 Å / 相対比: 1
反射解像度: 7.03→80 Å / Num. all: 39353 / Num. obs: 38696 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / 冗長度: 9.6 % / Biso Wilson estimate: 551.17 Å2

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解析

ソフトウェア
名称バージョン分類NB
PHENIX1.7.3_928精密化
PDB_EXTRACT3.11データ抽出
ADSCQuantumデータ収集
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3J3A AND 3J3D

3j3a
PDB 未公開エントリ

3j3d
PDB 未公開エントリ


解像度: 7.0305→77.529 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6057 / SU ML: 1.62 / σ(F): 1.34 / 位相誤差: 43.5 / 立体化学のターゲット値: ML
詳細: AUTHORS PERFORMED RIGID BODY REFINEMENT USING THE HUMAN PROTEINS WITH SIDECHAINS FROM PDB ENTRIES 3J3A AND 3J3D. THIS RESULTS IN CLOSE CONTACTS BETWEEN SIDECHAINS
Rfactor反射数%反射Selection details
Rfree0.3592 1941 5.02 %RANDOM
Rwork0.345 ---
obs0.3454 38696 98.33 %-
all-39353 --
溶媒の処理減衰半径: 1.2 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 100 Å2 / ksol: 0.334 e/Å3
原子変位パラメータBiso max: 529.05 Å2 / Biso mean: 179.8919 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-583.8464 Å20 Å20 Å2
2--583.8464 Å20 Å2
3---498.2526 Å2
精密化ステップサイクル: LAST / 解像度: 7.0305→77.529 Å
タンパク質核酸リガンド溶媒全体
原子数39654 39394 0 0 79048
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.02684421
X-RAY DIFFRACTIONf_angle_d2.743122711
X-RAY DIFFRACTIONf_chiral_restr0.23815186
X-RAY DIFFRACTIONf_plane_restr0.0228713
X-RAY DIFFRACTIONf_dihedral_angle_d20.56738025
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.0305-7.20620.40191230.41632183230683
7.2062-7.40090.38091540.40082598275299
7.4009-7.61850.43651320.397926422774100
7.6185-7.86420.44341490.388926092758100
7.8642-8.1450.41181350.40826332768100
8.145-8.47070.49061270.385726502777100
8.4707-8.85570.40461370.38326552792100
8.8557-9.32190.43791230.380626852808100
9.3219-9.90480.35921360.382926522788100
9.9048-10.66780.31281300.365526762806100
10.6678-11.7380.36561530.351826502803100
11.738-13.42890.35851430.342226902833100
13.4289-16.89020.39381620.366627072869100
16.8902-77.53350.3181370.30232725286295
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)
11.5945-0.15230.11482.23851.0992.2404-0.42351.93050.375-0.49350.62660.26580.10210.54030.8230.0933-0.874-0.49184.6297-0.58930.922964.1164108.3827-127.376
20.0348-0.01760.03520.0071-0.01670.01770.35110.0258-0.09520.43840.0659-0.53160.29980.1201-0.1354.11262.0749-0.77934.4016-1.14233.33312.1581148.927855.0803
30.16480.1315-0.04890.158-0.17280.3335-0.2285-0.1874-0.01740.47780.45311.5361-0.0671-0.0147-0.07444.92650.9141.36454.8736-0.23014.12060.4331190.687717.0872
40.0592-0.14890.09010.2337-0.15730.08210.11240.50330.0499-0.2070.24710.2327-0.1904-0.3825-0.09865.49410.01510.73796.4557-0.55616.2162-20.1938123.8437-41.7898
50.96930.5795-0.31160.7386-0.81540.95560.12570.78940.15460.12260.05710.4024-1.5746-0.2997-0.12691.444-0.2491-1.0422.48321.23272.40257.6459155.1786-5.4449
61.9399-0.7401-0.18962.7569-0.33092.0472-0.48520.8479-0.31181.4319-0.15450.95091.1509-1.3696-0.706-1.5449-0.5912-0.28721.2541-0.36210.250129.7284123.2812-32.5802
70.08940.1199-0.05981.02240.20410.179-0.6952-0.21690.20290.9574-0.098-0.97640.47580.78170.23362.9461-1.12930.38846.6561-0.24486.0556107.1339108.0298-79.9485
80.2017-0.05520.11620.1847-0.07090.083-0.05050.1734-0.08630.00710.17010.2503-0.21160.51720.04462.8869-0.85281.34773.56770.00512.528879.2053140.4342-79.2595
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)D1 - 227
2X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)F14 - 204
3X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)K1 - 98
4X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)M9 - 132
5X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)P4 - 130
6X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)Q6 - 146
7X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)R1 - 126
8X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)S6 - 142
9X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)T4 - 144
10X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)U16 - 119
11X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)Z41 - 115
12X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)c5 - 68
13X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)d4 - 56
14X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)f82 - 152
15X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)g2 - 314
16X-RAY DIFFRACTION1chain D or chain F or chain K or chain M or chain P or chain Q or chain R or chain S or chain T or chain U or chain Z or chain c or chain d or chain f or chain g or (chain i and resid 1207:1683)i1207 - 1683
17X-RAY DIFFRACTION2chain i and resid 184:209i184 - 209
18X-RAY DIFFRACTION3chain i and resid 305:326i305 - 326
19X-RAY DIFFRACTION4chain i and resid 681:737i681 - 737
20X-RAY DIFFRACTION5chain i and resid 1699:1826i1699 - 1826
21X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)A2 - 209
22X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)B19 - 233
23X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)C38 - 263
24X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)E1 - 263
25X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)G1 - 237
26X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)H5 - 194
27X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)I2 - 207
28X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)J7 - 188
29X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)L1 - 158
30X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)N2 - 151
31X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)O16 - 151
32X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)V1 - 82
33X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)W2 - 130
34X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)X1 - 142
35X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)Y3 - 128
36X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)a2 - 108
37X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)b1 - 84
38X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)e75 - 133
39X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1 - 183
40X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i210 - 304
41X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i327 - 680
42X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i738 - 1206
43X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1684 - 1698
44X-RAY DIFFRACTION6chain A or chain B or chain C or chain E or chain G or chain H or chain I or chain J or chain L or chain N or chain O or chain V or chain W or chain X or chain Y or chain a or chain b or chain e or (chain i and not resid 184:209 and not resid 305:326 and not resid 681:737 and not resid 1207:1683 and not resid 1699:1826)i1827 - 1863
45X-RAY DIFFRACTION7chain j or chain kj1 - 75
46X-RAY DIFFRACTION7chain j or chain kk10 - 22
47X-RAY DIFFRACTION8chain nn32 - 113

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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